CMPO subset
Term not to be used for direct annotation
Term not to be used for direct manual annotation
Catalytic activity terms in need of attention
Terms created by TermGenie that do not follow a template and require additional vetting by editors
Relational slim: types of quality that require an additional entity in order to exist
Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2.
We use the has_part relation to relate complex qualities to more primitive ones. A complex quality is a collection of qualities. The complex quality cannot exist without the sub-qualities. For example, the quality 'swollen' necessarily comes with the qualities of 'protruding' and 'increased size'.
This relation will be used after 2013-05-21.
This relation is currently used to connect two regulation processes p1 and p2, such that if r1 regulates p1 and r2 regulates p2, and r1 results_in r2 then the regulation of p1 is required for the regulation of p2. For an example of use, see GO:0035958 'regulation of glyoxylate cycle by regulation of transcription from RNA polymerase II promoter'. Note that a precise definition of this relation is under discussion. After it has been formalized it will be added to RO, where it will have a RO ID. Note that the existing identifier and label are subject to change.
This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'.
q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
Example: 'Lewy bodies increased number related to dystrophic neurite increased number' (from annotation of PMID:8740227 in http://ccdb.ucsd.edu/1.0/NDPO.owl#ndpo_404). Here the increase in the number of lewy bodies is directly_associated_with the increase in the number of dystrophic neurites. Association is weaker than correlation or proportionality. These relations may be later added to PATO.
q1 directly_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 increases if the magnitude of q2 is increased, or the magnitude of q1 decreases if the magnitude of q2 is decreased. The relationship is not necessarily linear.
Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round.
s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2.
This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'.
q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
Association is weaker than correlation or proportionality. These relations may be later added to PATO.
q1 inversely_associated_with q2 iff q1 is dependent on q2, and the magnitude of q1 decreases if the magnitude of q2 is increased, or the magnitude of q1 increases if the magnitude of q2 is decreased. The relationship is not necessarily linear.
There are frequently two ways to state the same thing: we can say 'spermatocyte lacks asters' or 'asters absent from spermatocyte'. In this case the quality is 'lacking all parts of type' - it is a (relational) quality of the spermatocyte, and it is with respect to instances of 'aster'. One of the popular requirements of PATO is that it continue to support 'absent', so we need to relate statements which use this quality to the 'lacking all parts of type' quality.
q1 reciprocal_of q2 if and only if : q1 and q2 are relational qualities and a phenotype e q1 e2 mutually implies a phenotype e2 q2 e.
q1 similar_in_magnitude_relative_to q2 if and only if magnitude(q1) =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale.
Relation binding a relational quality or disposition to the relevant type of entity.
A cell that is maintained or propagated in a controlled artificial environment for use in an investigation.
The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
mitotic sister-chromatid adhesion release
Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct process is 'regulation of x/y phase transition'.
The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis.
The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle.
The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis.
The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
G2/M Transition, Saccharomyces cerevisiae
G2/M Transition, Dictyostelium discoideum
G2/M Transition, Schizosaccharomyces pombe
G2/M Transition, Drosophila melanogaster
A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle.
The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell.
Mitotic Prophase, Schizosaccharomyces pombe
Mitotic Prophase, Drosophila melanogaster
Mitotic Prophase, Dictyostelium discoideum
Mitotic Prophase, Caenorhabditis elegans
Mitotic Prophase, Saccharomyces cerevisiae
The cell cycle phase, following prophase, during which chromosomes become aligned on the equatorial plate of the cell as part of a mitotic cell cycle.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
microtubule cytoskeleton organization and biogenesis
The cell cycle phase in higher eukaryotes which follows mitotic prophase and during which the nuclear envelope is disrupted and breaks into membrane vesicles, and the spindle microtubules enter the nuclear region. Kinetochores mature on each centromere and attach to some of the spindle microtubules. Kinetochore microtubules begin the process of aligning chromosomes in one plane halfway between the poles.
Mitotic Prometaphase, Saccharomyces cerevisiae
Mitotic Prometaphase, Drosophila melanogaster
Mitotic Prometaphase, Xenopus tropicalis
Mitotic Prometaphase, Schizosaccharomyces pombe
Mitotic Prometaphase, Caenorhabditis elegans
Mitotic Prometaphase, Dictyostelium discoideum
Mitotic Prometaphase, Taeniopygia guttata
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
Cell Cycle, Mitotic, Mycobacterium tuberculosis
Cell Cycle, Mitotic, Schizosaccharomyces pombe
Cell Cycle, Mitotic, Caenorhabditis elegans
Cell Cycle, Mitotic, Saccharomyces cerevisiae
Cell Cycle, Mitotic, Arabidopsis thaliana
Cell Cycle, Mitotic, Drosophila melanogaster
Cell Cycle, Mitotic, Dictyostelium discoideum
Cell Cycle, Mitotic, Plasmodium falciparum
Cell Cycle, Mitotic, Taeniopygia guttata
A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase.
The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.
The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.
The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets.
The developmental process in which the size or shape of a cell is generated and organized.
cell morphogenesis involved in differentiation
The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
The division of the cytoplasm and the plasma membrane of a cell and its separation into two daughter cells.
Mitotic Telophase /Cytokinesis, Taeniopygia guttata
Mitotic Telophase /Cytokinesis, Caenorhabditis elegans
Mitotic Telophase /Cytokinesis, Drosophila melanogaster
Mitotic Telophase /Cytokinesis, Rattus norvegicus
Mitotic Telophase /Cytokinesis, Gallus gallus
Mitotic Telophase /Cytokinesis, Dictyostelium discoideum
Mitotic Telophase /Cytokinesis, Xenopus tropicalis
Mitotic Telophase /Cytokinesis, Schizosaccharomyces pombe
Mitotic Telophase /Cytokinesis, Bos taurus
Mitotic Telophase /Cytokinesis, Homo sapiens
Mitotic Telophase /Cytokinesis, Danio rerio
Mitotic Telophase /Cytokinesis, Mus musculus
Mitotic Telophase /Cytokinesis, Canis familiaris
Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair.
transcription regulatory region sequence-specific DNA binding
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding".
Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair.
nucleic acid binding transcription factor activity
Interacting selectively and non-covalently with a DNA or RNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
Note that this term is in the subset of terms that should not be used for direct gene product annotation. This term does not provide specificity with respect to the type of nucleic acid binding, e.g. RNA or DNA. Please use a child term that provides that specificity or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.
An actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell, contain an F-actin-rich core surrounded by a ring structure containing proteins such as vinculin and talin, and have a diameter of 0.5 mm.
Note that podosomes can be distinguished from other F-actin-rich structures or from other matrix contacts. For example, focal adhesions and focal contacts do not display a core structure of F-actin. Unlike focal adhesions, podosome assembly does not require de novo protein synthesis. However, most of the podosome ring components are found in focal adhesions and other cell-matrix contacts. Podosomes are typically found in cells that cross tissue boundaries, recruited to the leading edge of migrating cells, and are often sites of extracellular matrix degradation.
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. Note that when this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
Interacting selectively and non-covalently with any nucleic acid.
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
sequence-specific DNA binding transcription factor activity
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence.
Elongation of Extended Telomeric Chromosome End, Saccharomyces cerevisiae
Elongation of Extended Telomeric Chromosome End, Schizosaccharomyces pombe
Elongation of Extended Telomeric Chromosome End, Arabidopsis thaliana
Elongation of Extended Telomeric Chromosome End, Gallus gallus
Elongation Of The Telomeric Chromosome End, Schizosaccharomyces pombe
Elongation of Extended Telomeric Chromosome End, Oryza sativa
Elongation Of The Telomeric Chromosome End, Homo sapiens
Elongation of Extended Telomeric Chromosome End, Taeniopygia guttata
Elongation of Extended Telomeric Chromosome End, Xenopus tropicalis
Elongation Of The Telomeric Chromosome End, Bos taurus
Elongation Of The Telomeric Chromosome End, Oryza sativa
Elongation and translocation of the telomeric chromosome end, Gallus gallus
Elongation of Extended Telomeric Chromosome End, Danio rerio
Elongation of Extended Telomeric Chromosome End, Homo sapiens
Elongation Of The Telomeric Chromosome End, Gallus gallus
Elongation Of The Telomeric Chromosome End, Saccharomyces cerevisiae
Elongation Of The Telomeric Chromosome End, Arabidopsis thaliana
Elongation of Extended Telomeric Chromosome End, Sus scrofa
Elongation Of The Telomeric Chromosome End, Xenopus tropicalis
Elongation Of The Telomeric Chromosome End, Mus musculus
Elongation of Extended Telomeric Chromosome End, Mus musculus
Elongation and translocation of the extended telomeric chromosome end, Gallus gallus
Elongation Of The Telomeric Chromosome End, Sus scrofa
Elongation Of The Telomeric Chromosome End, Canis familiaris
Elongation Of The Telomeric Chromosome End, Taeniopygia guttata
Elongation Of The Telomeric Chromosome End, Danio rerio
Elongation of Extended Telomeric Chromosome End, Canis familiaris
Elongation of Extended Telomeric Chromosome End, Bos taurus
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
DNA nucleotidyltransferase (RNA-directed) activity
RNA-dependent deoxyribonucleate nucleotidyltransferase activity
RNA-directed DNA polymerase, group II intron encoded
RNA-directed DNA polymerase, transposon encoded
deoxynucleoside-triphosphate:DNA deoxynucleotidyltransferase (RNA-directed) activity
Minus strand DNA synthesis resumes, Homo sapiens
Synthesis of minus strand strong stop DNA (-sssDNA), Homo sapiens
For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children.
The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule.
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. Note that when this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
That part of the nuclear content other than the chromosomes or the nucleolus.
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
An adherens junction which connects a cell to the extracellular matrix.
Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
Note that we deem cilium and microtubule-based flagellum to be equivalent.
The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
nucleobase-containing compound metabolic process
Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism
nucleobase, nucleoside and nucleotide metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
nucleobase, nucleoside, nucleotide and nucleic acid metabolism
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
The process in which the number of copies of a gene is increased in certain cells as extra copies of DNA are made in response to certain signals of cell development or of stress from the environment.
The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
DNA fragmentation involved in apoptotic nuclear change
The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
endonucleolytic DNA catabolic process involved in apoptosis
Apoptosis induced DNA fragmentation, Taeniopygia guttata
Apoptosis induced DNA fragmentation, Drosophila melanogaster
Apoptosis induced DNA fragmentation, Plasmodium falciparum
Apoptosis induced DNA fragmentation, Canis familiaris
Apoptosis induced DNA fragmentation, Bos taurus
Apoptosis induced DNA fragmentation, Sus scrofa
Apoptosis induced DNA fragmentation, Gallus gallus
Apoptosis induced DNA fragmentation, Mus musculus
Apoptosis induced DNA fragmentation, Rattus norvegicus
Apoptosis induced DNA fragmentation, Xenopus tropicalis
Apoptosis induced DNA fragmentation, Danio rerio
Apoptosis induced DNA fragmentation, Homo sapiens
Any process in which DNA and associated proteins are formed into a compact, orderly structure.
The cellular synthesis of RNA on a template of DNA.
regulation of transcription, DNA-dependent
Any process that modulates the frequency, rate or extent of cellular DNA-dependent transcription.
regulation of cellular transcription, DNA-dependent
regulation of gene-specific transcription
Note that protein targeting encompasses the transport of the protein to the specified location, and may also include additional steps such as protein processing.
The process of targeting specific proteins to particular membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
The directed movement of a protein from the cytoplasm to the nucleus.
establishment of protein localization to nucleus
protein transport from cytoplasm to nucleus
cellular aromatic compound metabolic process
The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
Note that amino acid and derivative metabolism should not be annotated here. Instead use the 'amino acid and derivative metabolism' node.
The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen, including (but not limited to) nitrogen fixation, nitrification, denitrification, assimilatory/dissimilatory nitrate reduction and the interconversion of nitrogenous organic matter and ammonium.
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell.
copper-induced intracellular protein transport
Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed.
The directed movement of molecules between the nucleus and the cytoplasm.
A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathways) which typically lead to rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. The process ends when the cell has died. The process is divided into a signaling pathway phase, and an execution phase, which is triggered by the former.
NRAGE signals death through JNK, Saccharomyces cerevisiae
NRAGE signals death through JNK, Drosophila melanogaster
NRIF signals cell death from the nucleus, Homo sapiens
NRAGE signals death through JNK, Xenopus tropicalis
NRIF signals cell death from the nucleus, Canis familiaris
NRAGE signals death through JNK, Oryza sativa
NRAGE signals death through JNK, Dictyostelium discoideum
NRAGE signals death through JNK, Schizosaccharomyces pombe
NRIF signals cell death from the nucleus, Mus musculus
NADE modulates death signalling, Rattus norvegicus
NRAGE signals death through JNK, Bos taurus
NRIF signals cell death from the nucleus, Xenopus tropicalis
NADE modulates death signalling, Bos taurus
NRAGE signals death through JNK, Arabidopsis thaliana
NRAGE signals death through JNK, Gallus gallus
NRIF signals cell death from the nucleus, Bos taurus
NRIF signals cell death from the nucleus, Sus scrofa
NRAGE signals death through JNK, Rattus norvegicus
NRAGE signals death through JNK, Caenorhabditis elegans
NRIF signals cell death from the nucleus, Taeniopygia guttata
NRAGE signals death through JNK, Mus musculus
NRAGE signals death through JNK, Homo sapiens
NRIF signals cell death from the nucleus, Rattus norvegicus
NADE modulates death signalling, Mus musculus
NRIF signals cell death from the nucleus, Gallus gallus
NRAGE signals death through JNK, Canis familiaris
NADE modulates death signalling, Sus scrofa
NRAGE signals death through JNK, Taeniopygia guttata
NRIF signals cell death from the nucleus, Danio rerio
NADE modulates death signalling, Canis familiaris
NADE modulates death signalling, Homo sapiens
NRAGE signals death through JNK, Sus scrofa
NRAGE signals death through JNK, Danio rerio
cellular component disassembly involved in execution phase of apoptosis
The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
cellular component disassembly involved in apoptosis
cellular component disassembly involved in apoptotic process
Apoptotic execution phase, Drosophila melanogaster
Apoptotic execution phase, Arabidopsis thaliana
Apoptotic execution phase, Xenopus tropicalis
Apoptotic execution phase, Taeniopygia guttata
Apoptotic execution phase, Plasmodium falciparum
Apoptotic execution phase, Dictyostelium discoideum
Apoptotic execution phase, Caenorhabditis elegans
Apoptotic execution phase, Schizosaccharomyces pombe
Apoptotic execution phase, Gallus gallus
Apoptotic execution phase, Canis familiaris
Apoptotic execution phase, Saccharomyces cerevisiae
Apoptotic execution phase, Rattus norvegicus
Note that in GO cellular components include whole cells (cell is_a cellular component).
The directed, self-propelled movement of a cellular component without the involvement of an external agent such as a transporter or a pore.
The orderly movement of a cell from one site to another along a substrate such as the extracellular matrix; the migrating cell forms a protrusion that attaches to the substrate.
substrate-dependent cell migration, cell extension
The formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell.
substrate-bound cell migration, cell extension
The cellular process that joins two lipid bilayers to form a single membrane.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
cytoskeletal organization and biogenesis
cytoskeleton organization and biogenesis
Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endoplasmic reticulum.
endoplasmic reticulum organization and biogenesis
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the alignment of chromosomes at the metaphase plate, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells.
The cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis.
The cell cycle process in which chromosome structure is altered from the condensed form taken on during mitosis to the relaxed disperse form held in resting cells.
The cell cycle process in which centrosome duplication and separation takes place. The centrosome cycle can operate with a considerable degree of independence from other processes of the cell cycle.
The cell cycle process in which a daughter centriole is formed perpendicular to an existing centriole. An immature centriole contains a ninefold radially symmetric array of single microtubules; mature centrioles consist of a radial array of nine microtubule triplets, doublets, or singlets depending upon the species and cell type.
Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
The binding of a cell to the extracellular matrix via adhesion molecules.
establishment or maintenance of cell polarity
Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns.
establishment and/or maintenance of cell polarity
establishment and/or maintenance of cell polarization
Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
EGFR interacts with phospholipase C-gamma, Drosophila melanogaster
EGFR interacts with phospholipase C-gamma, Xenopus tropicalis
EGFR interacts with phospholipase C-gamma, Sus scrofa
EGFR interacts with phospholipase C-gamma, Taeniopygia guttata
EGFR interacts with phospholipase C-gamma, Plasmodium falciparum
EGFR interacts with phospholipase C-gamma, Caenorhabditis elegans
EGFR interacts with phospholipase C-gamma, Oryza sativa
EGFR interacts with phospholipase C-gamma, Dictyostelium discoideum
EGFR interacts with phospholipase C-gamma, Saccharomyces cerevisiae
EGFR interacts with phospholipase C-gamma, Schizosaccharomyces pombe
EGFR interacts with phospholipase C-gamma, Homo sapiens
EGFR interacts with phospholipase C-gamma, Canis familiaris
EGFR interacts with phospholipase C-gamma, Bos taurus
EGFR interacts with phospholipase C-gamma, Arabidopsis thaliana
EGFR interacts with phospholipase C-gamma, Mycobacterium tuberculosis
EGFR interacts with phospholipase C-gamma, Gallus gallus
EGFR interacts with phospholipase C-gamma, Mus musculus
EGFR interacts with phospholipase C-gamma, Danio rerio
EGFR interacts with phospholipase C-gamma, Rattus norvegicus
A series of reactions in which a signal is passed on to downstream proteins within the cell by sequential protein phosphorylation and activation of the cascade components.
PKA-mediated phosphorylation of key metabolic factors, Taeniopygia guttata
PKA-mediated phosphorylation of key metabolic factors, Danio rerio
PKA-mediated phosphorylation of key metabolic factors, Rattus norvegicus
PKA-mediated phosphorylation of key metabolic factors, Homo sapiens
PKA-mediated phosphorylation of key metabolic factors, Dictyostelium discoideum
PKA-mediated phosphorylation of key metabolic factors, Bos taurus
PKA-mediated phosphorylation of key metabolic factors, Canis familiaris
PKA-mediated phosphorylation of key metabolic factors, Gallus gallus
PKA-mediated phosphorylation of key metabolic factors, Saccharomyces cerevisiae
PKA-mediated phosphorylation of key metabolic factors, Mus musculus
PKA-mediated phosphorylation of key metabolic factors, Schizosaccharomyces pombe
PKA-mediated phosphorylation of key metabolic factors, Sus scrofa
PKA-mediated phosphorylation of key metabolic factors, Xenopus tropicalis
The process in which a signal is passed on to downstream components within the cell through the I-kappaB-kinase (IKK)-dependent activation of NF-kappaB. The cascade begins with activation of a trimeric IKK complex (consisting of catalytic kinase subunits IKKalpha and/or IKKbeta, and the regulatory scaffold protein NEMO) and ends with the regulation of transcription of target genes by NF-kappaB. In a resting state, NF-kappaB dimers are bound to I-kappaB proteins, sequestering NF-kappaB in the cytoplasm. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing the NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
activation of the inhibitor of kappa kinase
NF-kB is activated and signals survival, Homo sapiens
TRAF6 mediated induction of TAK1 complex, Homo sapiens
The selective interaction of the transcription factor NF-kappaB with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus.
maintenance of NF-kappaB location in cytoplasm
Any process in which a protein is transported to, or maintained in, a specific location.
establishment and maintenance of protein localization
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this.
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
metabolic process resulting in cell growth
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as "apoptotic bodies"); and/or (3) its corpse (or its fragments) have been engulfed by an adjacent cell in vivo.
release of cytoplasmic sequestered NF-kappaB
The release of NF-kappaB from specific molecules in the cytoplasm to which it was bound, thereby allowing its translocation into the nucleus.
negative regulation of cytoplasmic NF-kappaB retention
negative regulation of cytoplasmic NF-kappaB sequestering
negative regulation of cytoplasmic NF-kappaB sequestration
negative regulation of cytoplasmic NF-kappaB storage
release of NF-kappaB sequestered in cytoplasm
release of NF-kappaB stored in cytoplasm
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
The controlled release of proteins from a cell.
protein secretion during cell fate commitment
protein secretion resulting in cell fate commitment
The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
The process in which a cell irreversibly increases in size in one [spatial] dimension or along one axis, resulting in the morphogenesis of the cell.
Unidimensional cell growth refers to a change in both cell size and cell shape. For cell shape changes where cell size is not affected, consider instead the term 'regulation of cell shape ; GO:0008360' and its children.
cell morphogenesis by unidimensional growth
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances.
Any process that modulates the frequency, rate or extent of signal transduction.
negative regulation of signal transduction
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
negative regulation of signaling pathway
negative regulation of signalling pathway
DTSC1 AND DTSC2 form a complex, Drosophila melanogaster
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
The cell cycle process where a cell leaves M phase. M phase is the part of the mitotic cell cycle during which mitosis and cytokinesis take place.
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
Gene Expression, Drosophila melanogaster
Gene Expression, Schizosaccharomyces pombe
Gene Expression, Saccharomyces cerevisiae
Gene Expression, Mycobacterium tuberculosis
Gene Expression, Dictyostelium discoideum
Gene Expression, Staphylococcus aureus N315
Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
regulation of macromolecule biosynthetic process
Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
regulation of intracellular protein kinase cascade
Any process that modulates the rate, frequency or extent of a series of reactions, mediated by protein kinases, which occurs as a result of a single trigger reaction or compound.
Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
negative regulation of cell communication
Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
negative regulation of intracellular protein kinase cascade
Any process that decreases the rate, frequency or extent of a series of reactions, mediated by protein kinases, which occurs as a result of a single trigger reaction or compound.
A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'.
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
A membrane-bounded vesicle found in the cytoplasm of the cell.
A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation at cellular level
cellular component organisation in other organism
cellular component organization at cellular level
cellular component organization in other organism
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
Membrane Trafficking, Arabidopsis thaliana
Membrane Trafficking, Plasmodium falciparum
Membrane Trafficking, Dictyostelium discoideum
Membrane Trafficking, Drosophila melanogaster
Membrane Trafficking, Caenorhabditis elegans
Membrane Trafficking, Saccharomyces cerevisiae
Membrane Trafficking, Xenopus tropicalis
Membrane Trafficking, Schizosaccharomyces pombe
Membrane Trafficking, Taeniopygia guttata
The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
non-developmental growth of a unicellular organism
The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
Metabolism of RNA, Plasmodium falciparum
Metabolism of RNA, Dictyostelium discoideum
Metabolism of RNA, Caenorhabditis elegans
Metabolism of RNA, Schizosaccharomyces pombe
Metabolism of RNA, Saccharomyces cerevisiae
Metabolism of RNA, Drosophila melanogaster
A permanent cessation of all vital functions: the end of life; can be applied to a whole organism or to a part of an organism.
See also the biological process term 'apoptosis ; GO:0006915'.
The orderly movement of a cell from one site to another, often during the development of a multicellular organism or multicellular structure.
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of, or within the cytoplasm of a cell.
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
Molybdenum ion transfer onto molybdopterin, Homo sapiens
transferase activity, transferring phosphorus-containing groups
Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor).
Note that this term encompasses all kinase activities, as well as activities that transfer other phosphorus-containing groups such as diphosphate or nucleotides.
Catalysis of the transfer of a nucleotidyl group to a reactant.
The directed movement of proteins into a cell or organelle.
The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
regulation of nucleobase-containing compound metabolic process
Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids.
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring.
aromatic hydrocarbon biosynthetic process
The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
The cellular process that ensures successive accurate and complete genome replication and chromosome segregation.
One of the distinct periods or stages into which the cell cycle is divided. Each phase is characterized by the occurrence of specific biochemical and morphological events.
A cellular process that results in the breakdown of a cellular component.
cellular component disassembly at cellular level
The aggregation, arrangement and bonding together of a cellular component.
cellular component assembly at cellular level
The attachment of a cell or organism to a substrate or other organism.
Any process that modulates the frequency, rate or extent of a signaling process.
Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change.
The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered.
Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process.
negative regulation of signaling process
negative regulation of signalling process
A thin sheetlike process extended by the leading edge of a crawling fibroblast; contains a dense meshwork of actin filaments.
Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
cell projection organization and biogenesis
cell surface structure organization and biogenesis
Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon.
Movement of organelles or other particles along actin filaments, or sliding of actin filaments past each other, mediated by motor proteins.
A cellular component that forms a specialized region of connection between two cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
A cell junction that forms a connection between a cell and the extracellular matrix.
A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
Thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone; usually approximately 0.1 um wide, 5-10 um long, can be up to 50 um long in axon growth cones; contains a loose bundle of about 20 actin filaments oriented with their plus ends pointing outward.
The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
Alterations undergone by nuclei at the molecular and morphological level and that contribute to the execution phase of apoptosis.
The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
The portion of the cytoskeleton that lies just beneath the plasma membrane.
The portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane.
microtubule organizing center organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microtubule organizing center, a structure from which microtubules grow.
microtubule organising center organisation
microtubule organizing center organization and biogenesis
A membrane-bounded organelle of ciliated protozoan cells that contains a diploid copy of the cell's complete genome. Sections of contiguous sequence in the macronucleus are often interrupted by internal eliminated sequences (IES), and may be permuted, in micronuclei. Genic transcription is not found in micronuclei. Some ciliate species may contain multiple micronuclei per cell.
The area of a motile cell closest to the direction of movement.
regulation of cellular metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
regulation of cellular biosynthetic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
A vesicle formed of membrane or protein, found in the cytoplasm of a cell.
A cilium which has a variable arrangement of axonemal microtubules, contains molecular motors, and beats with a characteristic whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface. Motile cilia are typically found in multiple copies on epithelial cells that line the lumenal ducts of various tissues. Motile cilia may also function as sensory organelles.
MERGED COMMENT: TARGET COMMENT: MERGED COMMENT: TARGET COMMENT: Note that this term should not be confused with 'motile primary cilium ; GO:0031512': Motile cilia are distinct from motile primary cilia (GO:0031512) that are typically present during embryogenesis in a single copy per cell, affect asymmetric body plan organization, and move in a rotational manner, as opposed to a whip-like, manner. -------------------- SOURCE COMMENT: See also the cellular component term 'cilium ; GO:0005929'. -------------------- SOURCE COMMENT: See also the cellular component term 'cilium ; GO:0005929'.
The attachment of a cell to the underlying substrate via adhesion molecules.
The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen.
The volume enclosed by the nuclear inner membrane.
Any small, fluid-filled, spherical organelle enclosed by membrane or protein.
Any small, fluid-filled, spherical organelle enclosed by a lipid bilayer.
negative regulation of NF-kappaB transcription factor activity
Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
inhibition of NF-kappaB transcription factor
Any process that modulates the frequency, rate or extent of the directed movement of substances within cells.
negative regulation of intracellular transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells.
down regulation of intracellular transport
down-regulation of intracellular transport
downregulation of intracellular transport
positive regulation of intracellular transport
Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells.
up regulation of intracellular transport
up-regulation of intracellular transport
An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition.
Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere.
maintenance of protein localization in cell
The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers.
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
The controlled release of a substance by a cell.
The process in which cellular structures, including whole cells or cell parts, are generated and organized.
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which the constituent parts function together.
Any process in which a macromolecule is transported to, or maintained in, a specific location.
regulation of intracellular protein transport
Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells.
A process in which a protein is transported to, or maintained in, a location within an organelle.
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and primer.
deoxyribonucleate nucleotidyltransferase activity
deoxyribonucleic acid polymerase activity
Elongation by Pol zeta complex, Gallus gallus
Insertion of correct bases opposite to the lesion by Pol kappa, Gallus gallus
Repair of ~27-30 bp long patch by DNA Pol Epsilon, Gallus gallus
Insertion of correct bases opposite to the lesion by Pol eta, Gallus gallus
substrate adhesion-dependent cell spreading
The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate.
cell spreading during cell substrate adhesion
substrate adhesion dependent cell spreading
A process in which a protein is transported to, or maintained in, a location within the nucleus.
Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
cellular nitrogen compound metabolic process
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
Metabolism of amino acids and derivatives, Schizosaccharomyces pombe
Metabolism of amino acids and derivatives, Arabidopsis thaliana
Metabolism of amino acids and derivatives, Oryza sativa
Metabolism of amino acids and derivatives, Caenorhabditis elegans
Metabolism of amino acids and derivatives, Gallus gallus
Metabolism of amino acids and derivatives, Escherichia coli
Metabolism of amino acids and derivatives, Sus scrofa
Metabolism of amino acids and derivatives, Saccharomyces cerevisiae
Metabolism of amino acids and derivatives, Staphylococcus aureus N315
Metabolism of amino acids and derivatives, Rattus norvegicus
Metabolism of amino acids and derivatives, Xenopus tropicalis
Metabolism of amino acids and derivatives, Plasmodium falciparum
Metabolism of amino acids and derivatives, Drosophila melanogaster
Metabolism of amino acids and derivatives, Mycobacterium tuberculosis
Metabolism of amino acids and derivatives, Mus musculus
Metabolism of amino acids and derivatives, Homo sapiens
Metabolism of amino acids and derivatives, Danio rerio
Metabolism of amino acids and derivatives, Bos taurus
Metabolism of amino acids and derivatives, Taeniopygia guttata
Metabolism of amino acids and derivatives, Canis familiaris
Metabolism of amino acids and derivatives, Dictyostelium discoideum
cellular macromolecule biosynthetic process
The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells.
cellular biopolymer biosynthetic process
nucleobase-containing compound biosynthetic process
The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid anabolism
nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis
nucleobase, nucleoside, nucleotide and nucleic acid formation
nucleobase, nucleoside, nucleotide and nucleic acid synthesis
nucleobase-containing compound catabolic process
The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid breakdown
nucleobase, nucleoside, nucleotide and nucleic acid catabolic process
nucleobase, nucleoside, nucleotide and nucleic acid catabolism
nucleobase, nucleoside, nucleotide and nucleic acid degradation
The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
intracellular signal transduction pathway
signal transduction via intracellular signaling cascade
signal transmission via intracellular cascade
A region of a chromosome at which a DNA double-strand break has occurred. DNA damage signaling and repair proteins accumulate at the lesion to respond to the damage and repair the DNA to form a continuous DNA helix.
See also the biological process term 'cell growth ; GO:0016049'.
The increase in size or mass of an entire organism, a part of an organism or a cell.
Self-propelled movement of a cell or organism from one location to another.
regulation of protein import into nucleus
Any process that modulates the frequency, rate or extent of movement of proteins from the cytoplasm to the nucleus.
regulation of protein import into cell nucleus
regulation of protein transport from cytoplasm to nucleus
positive regulation of protein import into nucleus
Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus.
activation of protein import into nucleus
positive regulation of protein import into cell nucleus
positive regulation of protein transport from cytoplasm to nucleus
positive regulation of protein-nucleus import
stimulation of protein import into nucleus
up regulation of protein import into nucleus
up-regulation of protein import into nucleus
upregulation of protein import into nucleus
negative regulation of protein import into nucleus
Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus.
down regulation of protein import into nucleus
down-regulation of protein import into nucleus
downregulation of protein import into nucleus
inhibition of protein import into nucleus
negative regulation of protein import into cell nucleus
negative regulation of protein transport from cytoplasm to nucleus
negative regulation of protein-nucleus import
regulation of NF-kappaB import into nucleus
Any process that modulates the frequency, rate or extent of the transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
regulation of NF-kappaB import into cell nucleus
regulation of NF-kappaB transport from cytoplasm to nucleus
positive regulation of NF-kappaB import into nucleus
Any process that activates or increases the frequency, rate or extent of transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
activation of NF-kappaB import into nucleus
positive regulation of NF-kappaB import into cell nucleus
positive regulation of NF-kappaB transport from cytoplasm to nucleus
positive regulation of NF-kappaB-nucleus import
stimulation of NF-kappaB import into nucleus
up regulation of NF-kappaB import into nucleus
up-regulation of NF-kappaB import into nucleus
upregulation of NF-kappaB import into nucleus
negative regulation of NF-kappaB import into nucleus
Any process that stops, prevents, or reduces the frequency, rate or extent of the transfer of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
down regulation of NF-kappaB import into nucleus
down-regulation of NF-kappaB import into nucleus
downregulation of NF-kappaB import into nucleus
inhibition of NF-kappaB import into nucleus
negative regulation of NF-kappaB import into cell nucleus
negative regulation of NF-kappaB transport from cytoplasm to nucleus
negative regulation of NF-kappaB-nucleus import
NF-kappaB transport from cytoplasm to nucleus
The directed movement of NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters, from the cytoplasm into the nucleus, across the nuclear membrane.
Any complex of actin, myosin, and accessory proteins.
Polarized growth from one end of a cell.
regulation of transcription factor import into nucleus
Any process that modulates the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
regulation of transcription factor import into cell nucleus
regulation of transcription factor transport from cytoplasm to nucleus
regulation of transcription factor-nucleus import
transcription factor import into nucleus
The directed movement of a transcription factor from the cytoplasm to the nucleus.
transcription factor import into cell nucleus
transcription factor transport from cytoplasm to nucleus
negative regulation of transcription factor import into nucleus
Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
down regulation of transcription factor import into nucleus
down-regulation of transcription factor import into nucleus
downregulation of transcription factor import into nucleus
inhibition of transcription factor import into nucleus
negative regulation of transcription factor import into cell nucleus
negative regulation of transcription factor transport from cytoplasm to nucleus
negative regulation of transcription factor-nucleus import
positive regulation of transcription factor import into nucleus
Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
activation of transcription factor import into nucleus
positive regulation of transcription factor import into cell nucleus
positive regulation of transcription factor transport from cytoplasm to nucleus
positive regulation of transcription factor-nucleus import
stimulation of transcription factor import into nucleus
up regulation of transcription factor import into nucleus
up-regulation of transcription factor import into nucleus
upregulation of transcription factor import into nucleus
cytoplasmic sequestering of transcription factor
The selective interaction of a transcription factor with specific molecules in the cytoplasm, thereby inhibiting its translocation into the nucleus.
cytoplasmic retention of transcription factor
cytoplasmic sequestration of transcription factor
cytoplasmic storage of transcription factor
maintenance of transcription factor protein location in cytoplasm
retention of transcription factor in cytoplasm
sequestering of transcription factor in cytoplasm
sequestration of transcription factor in cytoplasm
storage of transcription factor in cytoplasm
transcription factor binding, cytoplasmic sequestering
A prolongation or process extending from a cell, e.g. a flagellum or axon.
A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
regulation of I-kappaB kinase/NF-kappaB cascade
Any process that modulates an I-kappaB kinase/NF-kappaB induced cascade.
negative regulation of I-kappaB kinase/NF-kappaB cascade
Any process that stops, prevents, or reduces the frequency, rate or extent of an I-kappaB kinase/NF-kappaB induced cascade.
down regulation of I-kappaB kinase/NF-kappaB cascade
down-regulation of I-kappaB kinase/NF-kappaB cascade
downregulation of I-kappaB kinase/NF-kappaB cascade
inhibition of I-kappaB kinase/NF-kappaB cascade
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.
Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
intracellular membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
intracellular membrane-enclosed organelle
intracellular non-membrane-bounded organelle
Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes.
intracellular non-membrane-enclosed organelle
The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen.
Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules.
negative regulation of sequence-specific DNA binding transcription factor activity
Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
down regulation of transcription factor activity
down-regulation of transcription factor activity
downregulation of transcription factor activity
inhibition of transcription factor activity
negative regulation of transcription factor activity
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.
cellular component biogenesis at cellular level
negative regulation of molecular function
Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
positive regulation of molecular function
Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
transcription regulatory region DNA binding
Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
The chemical reactions and pathways by which individual cells transform chemical substances.
The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells.
The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
cellular macromolecule metabolic process
The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells.
cellular macromolecule catabolic process
The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells.
cellular nitrogen compound catabolic process
The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds.
cellular nitrogen compound biosynthetic process
The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds.
A dendrite arising from another dendrite.
Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane.
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
Any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.
Any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
Any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice.
Any constituent part of the Golgi apparatus, a compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack.
Any constituent part of the endoplasmic reticulum, the irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae.
Any constituent part of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. Also note that cilia and eukaryotic flagella are deemed to be equivalent.
Any constituent part of the cytoplasm, all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
A constituent part of an intracellular organelle, an organized structure of distinctive morphology and function, occurring within the cell. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton but excludes the plasma membrane.
Any constituent part of the cell cortex, the region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
Any constituent part of the nucleoplasm, that part of the nuclear content other than the chromosomes or the nucleolus.
Any constituent part of a cell projection, a prolongation or process extending from a cell, e.g. a flagellum or axon.
Any constituent part of a cell, the basic structural and functional unit of all organisms.
A biological process that involves only one organism.
A signaling process occurring within a single organism.
The process of directing proteins towards the nucleus, usually using signals contained within the protein.
Any process that is carried out at the cellular level, occurring within a single organism.
The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore, involving a single organism.
A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition, involving only one organism.
The cell cycle process by which a cell commits to entering the next cell cycle phase.
The cell cycle process by which a cell commits to entering the next mitotic cell cycle phase.
The mitotic cell cycle phase transition whose occurrence commits the cell from the G0 quiescent state to the G1 phase. Under certain conditions, cells exit the cell cycle during G1 and remain in the G0 state as nongrowing, non-dividing (quiescent) cells. Appropriate stimulation of such cells induces them to return to G1 and resume growth and division. The G0 to G1 transition is accompanied by many changes in the program of gene expression.
The joining of two or more lipid bilayer membranes that surround a cell.
The directed movement of a protein to a specific location.
Any process in which a protein is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of proteins that do move away.
A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
regulation of nucleocytoplasmic transport
Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm.
negative regulation of nucleocytoplasmic transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances between the cytoplasm and the nucleus.
down regulation of nucleocytoplasmic transport
down-regulation of nucleocytoplasmic transport
downregulation of nucleocytoplasmic transport
inhibition of nucleocytoplasmic transport
positive regulation of nucleocytoplasmic transport
Any process that activates or increases the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm.
activation of nucleocytoplasmic transport
stimulation of nucleocytoplasmic transport
up regulation of nucleocytoplasmic transport
up-regulation of nucleocytoplasmic transport
upregulation of nucleocytoplasmic transport
The controlled release of a substance by a cell or a tissue.
The directed movement of substances within a cell.
The creation of two or more organelles by division of one organelle.
The process whose specific outcome is the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate.
positive regulation of biological process
Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
positive regulation of physiological process
negative regulation of biological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
negative regulation of physiological process
Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
negative regulation of cellular physiological process
Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
negative regulation of response to stimulus
Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus.
The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
Any process in which a chromosome is transported to, or maintained in, a specific location.
establishment and maintenance of chromosome localization
establishment and maintenance of chromosome position
Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
regulation of cellular physiological process
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
regulation of sequence-specific DNA binding transcription factor activity
Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
regulation of transcription factor activity
Activation of the AP-1 family of transcription factors, Danio rerio
Activation of the AP-1 family of transcription factors, Homo sapiens
Activation of the AP-1 family of transcription factors, Schizosaccharomyces pombe
Activation of the AP-1 family of transcription factors, Rattus norvegicus
Activation of the AP-1 family of transcription factors, Taeniopygia guttata
Activation of the AP-1 family of transcription factors, Xenopus tropicalis
Activation of the AP-1 family of transcription factors, Bos taurus
Activation of the AP-1 family of transcription factors, Canis familiaris
Activation of the AP-1 family of transcription factors, Drosophila melanogaster
Activation of the AP-1 family of transcription factors, Gallus gallus
Activation of the AP-1 family of transcription factors, Mus musculus
Activation of the AP-1 family of transcription factors, Sus scrofa
positive regulation of sequence-specific DNA binding transcription factor activity
Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
activation of transcription factor activity
positive regulation of transcription factor activity
stimulation of transcription factor activity
up regulation of transcription factor activity
up-regulation of transcription factor activity
upregulation of transcription factor activity
positive regulation of NF-kappaB transcription factor activity
Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
activation of NF-kappaB transcription factor
TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Mus musculus
TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Rattus norvegicus
TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Sus scrofa
TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Bos taurus
TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Xenopus tropicalis
TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Danio rerio
TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Homo sapiens
TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Canis familiaris
TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Taeniopygia guttata
TAK1 activates NFkB by phosphorylation and activation of IKKs complex, Drosophila melanogaster
The directed movement of substances into, out of, or within the nucleus.
Import of PIC to the Host Nucleus, Homo sapiens
The directed movement of substances into the nucleus.
snRNP nuclear import and release, Xenopus tropicalis
snRNP nuclear import and release, Mus musculus
snRNP nuclear import and release, Homo sapiens
snRNP nuclear import and release, Danio rerio
regulation of nitrogen compound metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds.
regulation of nitrogen metabolic process
Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location.
establishment and maintenance of cellular component location
establishment and maintenance of localization
establishment and maintenance of position
establishment and maintenance of substance location
establishment and maintenance of substrate location
The selective interaction of a protein with specific molecules in the cytoplasm, thereby inhibiting its transport into other areas of the cell.
maintenance of protein location in cytoplasm
positive regulation of protein transport
Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
negative regulation of protein transport
Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
The directed movement of a cell, substance or cellular entity, such as a protein complex or organelle, to a specific location.
Any process in which a cell, substance or cellular entity, such as a protein complex or organelle, is maintained in a location and prevented from moving elsewhere.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA.
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information.
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized.
The replication of a centrosome, a structure comprised of a pair of centrioles and peri-centriolar material from which a microtubule spindle apparatus is organized.
Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis excludes nuclear division; in prokaryotes, there is little difference between cytokinesis and cell division. Note that there is no relationship between this term and 'nuclear division ; GO:0000280' because cell division can take place without nuclear division (as in prokaryotes) and vice versa (as in syncytium formation by mitosis without cytokinesis.
The process resulting in the physical partitioning and separation of a cell into daughter cells.
establishment of chromosome localization
The directed movement of a chromosome to a specific location.
establishment of chromosome localisation
The alignment of chromosomes at the metaphase plate, a plane halfway between the poles of the spindle.
The alteration of chromosome structure from the condensed form to a relaxed disperse form.
The cell cycle 'gap' phase which is the interval between the completion of DNA segregation (usually by mitosis or meiosis) and the beginning of DNA synthesis.
The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation (usually by mitosis or meiosis).
The cell cycle phase, following G1, during which DNA synthesis takes place.
The cell cycle phase, following prophase or prometaphase in higher eukaryotes, during which chromosomes become aligned on the equatorial plate of the cell.
The cell cycle phase which is the first stage of M phase of meiosis and mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell.
The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when prophase of meiosis or mitosis begins. During interphase the cell readies itself for meiosis or mitosis and the replication of its DNA occurs.
The cell cycle phase following cytokinesis which begins with G1 phase, proceeds through S phase and G2 phase and ends when mitotic prophase begins. During interphase the cell readies itself for mitosis and the replication of its DNA occurs.
Any process in which an organelle is transported to, and/or maintained in, a specific location.
establishment and maintenance of organelle localization
A localization process that takes place at the cellular level; as a result of a cellular localization process, a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within or in the membrane of a cell.
establishment and maintenance of cellular localization
establishment and maintenance of localization in cell or cell membrane
The directed movement of a substance or cellular entity, such as a protein complex or organelle, to a specific location within, or in the membrane of, a cell.
establishment of intracellular localization
establishment of localization within cell
Any process in which a substance or cellular entity, such as a protein complex or organelle, is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere.
maintenance of intracellular localization
The directed movement of an organelle to a specific location.
Any process in which a cell is transported to, and/or maintained in, a specific location.
establishment and maintenance of cell localization
establishment and maintenance of localization of cell
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell.
regulation of macromolecule metabolic process
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell.
developmental growth involved in morphogenesis
The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape.
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
The membrane organization process that joins two lipid bilayers to form a single membrane.
The endoplasmic reticulum organization process that results in the structure of the endoplasmic reticulum being oriented in the cell.
Any process that modulates a measurable attribute of any biological process, quality or function.
Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc.
Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding.
An organelle lumen that is part of an intracellular organelle.
A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix.
regulation of establishment of protein localization
Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location.
regulation of establishment of protein localisation
The actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in contraction of all or part of the cell body.
Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule.
The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon.
The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
organic molecular entity metabolic process
cellular component organization or biogenesis
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component.
cellular component organisation or biogenesis
cellular component organisation or biogenesis at cellular level
cellular component organization or biogenesis at cellular level
The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
Any cellular metabolic process involving nucleic acids.
nucleic acid phosphodiester bond hydrolysis
The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
positive regulation of intracellular protein transport
Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells.
negative regulation of intracellular protein transport
Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure.
A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. The execution phase ends when the cell has died.
An arrangement of closely apposed microtubules running parallel to each other.
Any constituent part of a neuron, the basic cellular unit of nervous tissue. A typical neuron consists of a cell body (often called the soma), an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
regulation of protein localization to nucleus
Any process that modulates the frequency, rate or extent of protein localization to nucleus.
regulation of protein localisation to nucleus
regulation of protein localization in cell nucleus
regulation of protein localization in nucleus
organic cyclic compound metabolic process
The chemical reactions and pathways involving organic cyclic compound.
organic cyclic compound catabolic process
The chemical reactions and pathways resulting in the breakdown of organic cyclic compound.
organic cyclic compound biosynthetic process
The chemical reactions and pathways resulting in the formation of organic cyclic compound.
Interacting selectively and non-covalently with heterocyclic compound.
The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon.
organic molecular entity catabolic process
The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon.
organic molecular entity biosynthetic process
regulation of cellular macromolecule biosynthetic process
Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process.
regulation of cellular biopolymer biosynthetic process
regulation of cellular macromolecule anabolism
regulation of cellular macromolecule biosynthesis
regulation of cellular macromolecule formation
regulation of cellular macromolecule synthesis
Any process that modulates the frequency, rate or extent of RNA biosynthetic process.
A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities.
A physical quality inhering in a bearer by virtue of the bearer's scalar absolute value of the rate of change of the bearer's position.
A scalar optical property that is the intensity, value or amount of perceived light.
Color brightness refers to the intensity, lightness or value of the light present. Think of this as a dimmer switch.
A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time.
A quality inhering in a bearer by virtue of the bearer's possessing or displaying a distinctive feature in type or degree or effect or force.
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc).
Shapes are invariant on size transformations. Shapes can be subdivided into 2D and 3D shapes, We can also make a distinction between shapes of complete self-connected objects, and shapes of parts of objects.
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence.
A spatial quality inhering in a bearer by virtue of the bearer's exhibiting repetition of placement of its parts.
TODO: define this or obsolete it and move children somewhere else.
A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average.
A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude.
A 1-D extent quality which is equal to the distance between two points.
A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity.
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time.
An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population.
A quality of a process which ends earlier than the natural end time or reference process.
TODO: the definition is incorrect. See absent.
A spatial pattern inhering in a bearer by virtue of the bearer's magnitude of or the relationships between its repeated parts lack consistency.
An intensity which is less than moderate in type or degree or effect or force.
An intensity which is extremely bad or unpleasant in type or degree or effect or force.
A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center.
A pattern quality inhering in a bearer by virtue of the bearer's having a repeatable or predictable placement.
A quality inhering in a bearer by virtue of the bearer's deviation from normal or average.
A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average.
A duration quality of a process which is relatively high.
A duration quality of a process which is relatively low.
A quality of a process which starts later than the natural start time or the reference process.
A length quality which is relatively large.
A length quality which is relatively small.
A size quality which is relatively high.
A symmetry quality inhering in a bearer by virtue of the bearer's lacking symmetry.
A positional quality inhering in a bearer by virtue of the bearer's having two sides; two-sided.
A structural quality inhering in a bearer by virtue of the bearer's consisting of blebbing of the nucleus and DNA fragmentation due to the cell undergoing a specific form of programmed cell death termed apoptosis.
A color brightness which is relatively high.
A quality of a single process inhering in a bearer by virtue of the bearer's being uninterrupted in time, sequence, substance, or extent.
A viability quality inhering in a population by virtue of the bearer's long term survival inability.
A viability quality inhering in a bearer or a population by virtue of the bearer's ability to survive or the long term survival ability of a given population.
A 1-D extent quality which is equal to the dimension through an object as opposed to its length or width.
A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
A 1-D extent quality which is equal to the distance from one side of an object to another side which is opposite.
This term is for curator easiness - we might consider obsoleting this but we have to consider how curators are going to represent them if we do.
A structural quality inhering in a bearer by virtue of the bearer's lacking organisation.
A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section.
A pattern quality of inhering in a bearer by virtue of the correspondence in size, shape, and relative position of the bearer's parts on opposite sides of a dividing line or median plane or about a center or axis.
A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.
A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
See comments of relational quality of a physical entity.
A quality which inheres in a continuant.
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
multiply inhering quality of a physical entity
A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation.
An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light.
A quality inhering in a bearer by virtue of the bearer's disposition to varying or changing.
A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point.
A 2-D extent quality inhering in a bearer by virtue of the bearer's two dimensional extent.
A symmetry quality inhering in a bearer by virtue of the bearer's having equal proportion around a central point or axis.
A surface feature shape quality inhering in a bearer by virtue of the bearer's having spines, thorns or similar thin projections on its surface.
A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism.
A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes.
A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes.
A monadic quality of continuant that exists at the cellular level of organisation.
A cellular quality inhering in a bearer by virtue of bearer's number of nuclei.
A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei.
A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus.
A structural quality inhering in a bearer by virtue of whether the bearer includes all its components.
A broken quality inhering in a bearer by virtue of the bearer's being broken open.
A pattern inhering in a surface by virtue of the bearer's being marked by the presence of dots, punctures, points or pits.
The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts.
extra or missing physical or functional parts
A quality of a process inhering in a bearer by virtue of the bearer's lacking a processual part as specified by the additional entity.
A mass which is lower than normal or average.
A mass which is higher than normal or average.
A quality of a process inhering in a bearer by virtue of the bearer's processual parts.
A morphological quality inhering in a bearer by virtue of the bearer's being distorted in form.
A spatial pattern inhering in a bearer by virtue of the bearer's being gathered or tending to gather into a mass or whole.
A positional quality inhering in a bearer by virtue of the bearer's being distributed or spread over a considerable extent.
A size quality inhering in an bearer by virtue of the bearer's extension in one dimension.
A size quality inhering in an bearer by virtue of the bearer's extension in two dimensions.
A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions.
A quality that inheres in an bearer by virtue of how that bearer interacts with radiation.
A spatial quality inhering in a bearer by virtue of the bearer's being extended on all sides of another entity simultaneously.
A shape quality inhering in a bearer by virtue of the bearer's having three angles.
A shape quality inhering in a bearer by virtue of the bearer's forming two equal obtuse triangles with a short side in common.
Gradually enlarged at the base, like the head of an arrow.
A physical quality inhering in a bearer by virtue of the bearer's participation in movement.
A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus.
A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell.
This quality either inheres directly in the surface, or in the entity that has the surface. For example, to say that a particular fly wing is curved is shorthand for saying the wing has a surface which is curved.
A variability quality inhering in a bearer by virtue of whether the bearer exhibits shape variation or change.
A variability quality inhering in a bearer by virtue of whether the bearer exhibits size variation or change.
A variability of size which is relatively high.
A shape quality inhering in a bearer by virtue of the bearer's being partly divided into a determinate number of regions.
A quality that inheres in an entire organism or part of an organism.
The bearer of this quality has_part < n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly. This case includes the limit case, where the bearer lacks all parts of the specified type.
A quality of physical entities inhering in a bearer by virtue of the bearer's lacking a physical part as specified by the additional entity.
Example: [E=organism Q=lacks_all_parts_of_type E2=Wing] - applies to an organism. A relational quality in which the bearer entity has no parts of the specified type. The bearer of this quality has_part = 0 of the indicated entity type, where a comparable organism usually has at least 1 part of the same type. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e lacks all parts of type X at time t, then there exists no instances x of X at t such that x part_of e that has no wings, where wings are normally present in that organism type. In OWL this is equivalent to a restriction on the OBO_REL:has_part relation with cardinality=0, i.e has_part 0 E2.
Example: [E=hand Q=has_fewer_parts_of_type E2=digit] - applies to an organism that has no less fingers than is normal for organisms of that type.
The bearer of this quality has_part < n AND has_part > 0 of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part. Formally: If a bearer entity e has fewer parts of type X at time t, then the number of instances x of X at t such that x part_of e is < n, where n is either the normal number for comparable entities, or n is stated explicitly.
In polydactyly, the bearer of the quality is the hand, and the entity type being counted is 'finger'. In EQ syntax, E=hand, Q=<this> E2=finger.
The bearer of this quality has_part > n of the indicated entity type, where n is the normal amount for a comparable organism. Note that the bearer of the quality is the whole, not the part.
A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity.
A shape quality inhering in a bearer by virtue of the bearer's being arranged like rays or radii; radiating from a common center.
A positional quality inhering in a bearer by virtue of the bearer's being at the edge or boundary of a related entity.
A lobed quality inhering in a bearer by virtue of the bearer's being divided into or having two lobes.
A quality inhering in a bearer that is shaped in the form of a fan.
A structural quality inhering in a bearer by virtue of the bearer's being arranged in a systematic fashion.
A positional quality inhering in a bearer by virtue of the bearer's being located in a position equidistant from edges.
A quality that has a value that is increased compared to normal or average.
A quality that has a value that is decreased compared to normal or average.
A quality of a process that has a value that is decreased compared to normal or average.
A quality of an object that has a value that is decreased compared to normal or average.
A quality of a process that has a value that is increased compared to normal or average.
A quality of an object that has a value that is increased compared to normal or average.
A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt
A temporal distribution pattern of process occurrences within a regulation/reference process.
The temporal relation between the end of the process with respect to a reference process.
The temporal relation between the start of the process with respect to a reference process.
Having a shape that resembles a many-lobed "berry," such as a raspberry.
cell population
A phenotype observation at the level of a population of cells
phenotype
An observation where the phenotype is described in terms of a biological process, a cell population, a whole cell or a subcellular structure that bears a particular quality.
cell morphology phenotype
A phenotype observation at the level of the whole cell relating to the cell's shape, size or structure
cell morphology
cell process phenotype
A phenotype observation at the level of a cellular process
cell component number phenotype
An increase or decrease in the number of specified components within a cell
cell component number
cell component size phenotype
A phenotype observation at the level of a cellular component relating to the components size
cell component size
cell component shape phenotype
A phenotype observation at the level of a cellular component relating to the components shape
cell component shape
cell component structure phenotype
A phenotype observation at the level of a cellular component relating to the components structure
cell component structure
cell viability phenotype
A phenotype relating to the ability of a cell survive or to develop normally
cell viability
viable cell phenotype
A cell phenotype where the cell is viable
viable cell
inviable cell phenotype
A cell phenotype where the cell is not viable
inviable cell
cell nucleation phenotype
A phenotype observation at the level of the whole cell relating to the cell's nucleation
cell nucleation
mononuclear cell phenotype
mononuclear cell
multinucleated cell phenotype
A phenotype observation where a cell is multinucleate, e.g. have more than one nucleus per cell
multinucleated cell
cytoskeletal phenotype
A phenotype observation at the level of any constituent part of the cytoskeleton, a cellular scaffolding or skeleton that maintains cell shape, enables some cell motion (using structures such as flagella and cilia), and plays important roles in both intra-cellular transport (e.g. the movement of vesicles and organelles) and cellular division. Includes constituent parts of intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice.
endoplasmic reticulum phenotype
A phenotype observation at the level of any constituent part of the endoplasmic reticulum, the irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae.
golgi phenotype
A phenotype observation at the level of any constituent part of the Golgi apparatus, a compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack
mitochondrion phenotype
A phenotype observation at the level of any constituent part of a mitochondrion, a semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells.
nuclear phenotype
A phenotype observation at the level of any constituent part of the nucleus, a membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated.
organelle shape phenotype
A phenotype observation at the level of a cellular organelle relating to the organelle's shape
organelle shape
nucleus shape phenotype
A phenotype observation at the level of the nucleus relating to the ratios of distances between its features (points, edges, surfaces and also holes etc).
cell adhesion phenotype
A phenotype where the attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules is observed
cell cycle phenotype
A phenotype observation at the level of a cell cycle
cell death phenotype
A phenotype where the cell death process process is observed
cell membrane organisation phenotype
A phenotype observation of a process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
cell migration phenotype
A phenotype of a cell involving its translation from one location to another
cell growth phenotype
A phenotype observation of the process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
chromosome segregation phenotype
A phenotype observation of the process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the alignment of chromosomes at the metaphase plate, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
metabolic process phenotype
A phenotype observation of chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
organelle localization phenotype
A phenotype observations where any process in which an organelle is transported to, and/or maintained in, a specific location.
regulation of metabolic process phenotype
A phenotype observation where a process modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism.
regulation of signal transduction phenotype
A phenotype observation of a process that modulates the frequency, rate or extent of signal transduction.
transport phenotype
A phenotype observation of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
increased cell component number phenotype
An increased number of specified cellular components relative to normal
increased cell component number
decreased cell component number phenotype
A decrease in number of specified cellular components relative to normal
decreased cell component number
apoptotic DNA fragmentation phenotype
A phenotype observation where the cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments.
apoptotic DNA fragmentation
apoptotic cell shape phenotype
apoptotic cell shape
dispersed outline with blobby protrusions
A phenotype observation at the level of the cell shape where the cell is apoptotic
aggregated cells in population
Groups of cells gathered or tending to gather into a mass or whole.
altered cell number in population
Number of cells in a population phenotype
cell number in population
increased cell numbers
The population has an increased number of cells with respect to normal
decreased cell numbers
The population has a decreased number of cells with respect to normal
increased number of cells in S phase mitosis
cell population by process phenotype
A population of cells where a specifcied biological process is occuring or is observed.
cell population process
increased cell numbers in G1
more cells in G2M
fewer cells in G1
fewer cells in G2M
fewer cells in S
decreased number of focal adhesion phenotype
A phenotype observation at the level of focal adhesions where the components number has decreased.
decreased number of focal adhesion
centrally located focal adhesion phenotype
A phenotype observation where the focal adhesion is located in a position equidistant from the edges of the cell
centrally located focal adhesion
cell component position phenotype
A phenotype observation at the level of a cellular component relating to the components position in the cell
cell component position
peripheral focal adhesion phenotype
A phenotype observation where the focal adhesions's position is at the edge or boundary of a related entity.
peripheral focal adhesion
decreased number of filopodia phenotype
A phenotype observation at the level of filopodia where the components number has decreased.
decreased number of filopodia
decreased number of microtubules phenotype
A phenotype observation at the level of microtubules where the components number has decreased.
decreased number of microtubules
decreased number of dendritic branches phenotyope
A phenotype observation at the level of dendritic branches where the components number has decreased.
cells with projections
increased number of cell projections phenotype
An increase in number of any cell projection relative to normal
increased number of cell projections
increased number of cells in population with projections
decreased number of cell projections phenotype
A phenotype observation at the level of cell projections where the components number has decreased.
decreased number of cell projections
decreased number of cells in population with projections
increased number of filopodia
A phenotype observation at the level of filopodia where the components number has increased.
elongated cell phenotype
A phenotype observation at the level of the cell shape where the cell is elongated, with a length notably greater than its width
elongated cell
elongated cells in population
Cells in population with a length notably greater than their width
increased number of lamellipodia phenotype
A phenotype observation at the level of lamellipodia where the components number has increased.
increased number of lamellipodia
decreased number of lamellipodia phenotype
A phenotype observation at the level of lamellipodia where the components number has decreased.
decreased number of lamellipodia
increased lamellipodia cells in population phenotype
decreased lamellipodia cells in population phenotype
cell ploidy phenotype
A phenotype observation at the level of the whole cell relating to the cell's ploidy
cell ploidy
polyploid cell phenotype
A cell phenotype with more than two homologous sets of chromosomes.
polyploid cell
S phase mitotic phenotype
A phenotype observation at the level of athe S phase of the mitotic cell cycle
G1 phase mitotic phenotype
A phenotype observation at the level of a G1 phase of the mitotic cell cycle
G2/M transition phenotype
A phenotype observation at the level of the G2/M transition of the mitotic cell cycle
cell cycle phase phenotype
A phenotype observation at the level of a cell cycle phase
increased number of polyploid cells in population
increased number of focal adhesion phenotype
A phenotype observation at the level of focal adhesions where the components number has increased.
increased number of focal adhesion
increased number of nucleoli phenotype
A phenotype observation at the level of nucleoli where the components number has increased.
increased number of nucleoli
A phenotype observation at the level of nucleoli where the components number has decreased.
decreased number of nucleoli
more cells with decreased number of nucleoli
more cells with increased number of nucleoli
increased number of nucleoli in population phenotype
increased number of microtubules phenotype
A phenotype observation at the level of microtubules where the components number has increased.
increased number of microtubules
phagosomes phenotype
phagosomes
A phenotype observation at the level of the phagosomes, a membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
phagosomes absent phenotype
A phenotype observation where phagosomes are absent
phagosomes absent
actin filament phenotype
A phenotype observation at the level of the actin filaments, a filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells.
increased number of actin filament phenotype
A phenotype observation at the level of actin filaments where the components number has increased.
increased number of actin filament
decreased number of actin filament phenotype
A phenotype observation at the level of actin filaments where the components number has decreased.
decreased number of actin filament
increased number of actin filament cells in population
decreased number of actin filament cells
decreased number of actin filament phenotypes in population
centered cytoskeleton phenotype
A phenotype observation where the cytoskeleton is located in a position equidistant from the edges of the cell
centered cytoskeleton
centered nucleus phenotype
A phenotype observation where the nucleus is located in a position equidistant from the edges of the cell
centered nucleus
dispersed nucleus phenotype
A phenotype observation where the nucleus is distributed or spread over a considerable extent.
dispersed nucleus
apoptopic nucleus phenotype
A phenotype observation at the level of nucleus consisting of blebbing of the nucleus and DNA fragmentation due to the cell undergoing a specific form of programmed cell death termed apoptosis.
apoptopic nucleus
deformed nucleus
A phenotype observation where the nucleus is distorted in form
peripheral nucleus phenotype
A phenotype observation where the nucleus's position is at the edge or boundary of a related entity.
peripheral nucleus
peripheral cytoskeleton phenotype
A phenotype observation where the cytoskeleton's position is at the edge or boundary of a related entity.
peripheral cytoskeleton
abnormal cell shape phenotype
A phenotype observation at the level of the cell shape where the shape is abnormal
abnormal cell shape
bilobed nucleus phenotype
A lobed quality inhering in a nucleus by virtue of the nucleus being divided into or having two lobes.
bilobed nucleus
round cell phenotype
A phenotype observation at the level of the cell shape where the cell is round
round cell
elongated focal adhesion
A phenotype observation of the length of the focal adhesion is notably higher than the width.
elongated nucleus
A phenotype observation of the length of the nucleus is notably higher than the width.
arrow shaped cell phenotype
A phenotype observation at the level of the cell shape where the cell is arrow shaped, with a wide front and a sharp tail, displaying monopolar cell growth
triangular shaped cell phenotype
A phenotype observation at the level of the cell shape where the cell has a triangular shape, with a wide front and a sharp tail, displaying cell motility
triangular shaped cell
round nucleus phenotype
A phenotype observation where the shape of the nucleus has every part of the surface or the circumference equidistant from the center.
round nucleus
nuclear body phenotype
A phenotype observation at the level of the nuclear body, an extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
nuclear body
increased nuclear body size phenotype
A phenotype observation where the nuclear body size is relatively high.
increased nuclear body size
decreased nuclear body size phenotype
A phenotype observation where the nuclear body size is relatively low.
decreased nuclear body size
A phenotype observation at the level of the cell size where a cell is larger with respect to normal/wild-type
increased cell size
A phenotype observation at the level of the cell size where a cell is smaller with respect to normal/wild-type
small cell
decreased golgi volume phenotype
A phenotype observation at the level of the golgi where the golgi's volume has decreased.
decreased golgi volume
increased golgi volume phenotype
A phenotype observation at the level of the golgi where the golgi's volume has increased.
increased golgi volume
decreased cilium length phenotype
A phenotype observation at the level of a cilium where the components length has decreased.
decreased cilium length
increased cilium length phenotype
A phenotype observation at the level of a cilium where the components length has increased.
increased cilium length
decreased size of focal adhesion phenotype
A phenotype observation where the size of the focal adhesion has decreased.
decreased size of focal adhesion
increased size of focal adhesion phenotype
A phenotype observation where the size of the focal adhesion has increased.
increased size of focal adhesion
decreased focal adhesion area phenotype
A phenotype observation where the area of the focal adhesion has decreased.
decreased focal adhesion area
increased focal adhesion area phenotype
A phenotype observation where the area of the focal adhesion has increased.
increased focal adhesion area
decreased focal adhesion length phenotype
A phenotype observation where the length of the focal adhesion has decreased.
decreased focal adhesion length
increased focal adhesion length phenotype
A phenotype observation where the length of the focal adhesion has increased.
increased focal adhesion length
increased nucleus size phenotype
A phenotype observation where the size of the nucleus has increased
increased nucleus size
decreased nucleus size phenotype
A phenotype observation where the size of the nucleus has decreased
decreased nucleus size
increased nuclei size in G1 phenotype
A phenotype of a cell that has both an increased nuclei size phenotypes and a G1 phase phenotype
increased nuclei size in G1
decreased nuclei size in G1 phenotype
A phenotype of a cell that has both a decreased nuclei size phenotypes and a G1 phase phenotype
decreased nuclei size in G1
increased thickness of dendritic branches phenotype
A phenotype observation where the thickness of the dendritic branches has increased.
increased thickness of dendritic branches
decreased thickness of dendritic branches
A phenotype observation where the thickness of the dendritic branches has decreased.
disorganized microtubules phenotype
A phenotype observation where the microtublue structure is disorganised
disorganized microtubules
podosome phenotype
A phenotype observation at the level of podosomes, an actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell.
podosome
radial cytoskeleton phenotype
A phenotype observation where the cytoskeleton is symmetric, having equal proportions around a central point or axis.
radial cytoskeleton
phenotypes by organelle
Phenotype observation organised by specific named organelles.
fragmented endoplasmic reticulum phenotype
A phenotype observation where the structure of the endoplasmic reticulum is fragmented or broken.
fragmented endoplasmic reticulum
fragmented golgi phenotype
A phenotype observation at the level of the golgi where the golgi's structure is broken
fragmented golgi
fragmented mitochondria phenotype
A phenotype observation where the structure of the mitochondria is fragmented or broken.
fragmented mitochondria
bright nuclei phenotype
A phenotype observation where the nuclear's color brightness is relatively high.
bright nuclei
fragmented nucleus phenotype
A phenotype observation where the structure of the nucleus is fragmented or broken.
fragmented nucleus
graped micronucleus phenotype
A phenotype observation where nuclear envelopes form around single chromosomes or small sets of chromosomes. Forming a grape like structure
Mitocheck Publication: http://www.ncbi.nlm.nih.gov/pubmed/20360735 Micronucleation, i.e. presumably nuclear envelopes around single chromosomes or small sets of chromosomes.
graped micronucleus
abnormal nucleus shape phenotype
A phenotype observation where the shape of the nucleus is abnormal
decreased nuclei size in G2/M phenotype
A phenotype observation at the level of the G2/M transition of the mitotic cell cycle where the nuclei are decreased in size with respect to normal
decreased nuclei size in G2/M
absence of cellular component phenotype
A phenotype observation at the level of a cellular component where the cell component is absent
absence of cellular component
cell population viability
A phenotype of a cell population relating to the ability of the cells to live and develop normally
increased cell viability in population
increased number of viable cell phenotype in a population
decreased cell viability in population
decreased number of viable cell phenotype in a population
cell population by morphology
A population phenotype relating to the size, shape or structure of the cells within a population
cell population morphology
absence of cytokinesis phenotype
A phenotype that results in the absence of cytokinesis
absence of cytokinesis
cytokinesis phenotype
A phenotype observation at the level of cytokinesis
cell division phenotype
A phenotype observation of the process resulting in the physical partitioning and separation of a cell into daughter cells.
increased rate of cell division phenotype
A phenotype where the cell division process occurs at a higher rate
increased rate of cell division
decreased rate of cell division phenotype
A phenotype where the cell division process occurs at a lower rate
decreased rate of cell division
telomerase activity phenotype
A phenotype observation of the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes extension of the 3'- end of a DNA strand by one deoxynucleotide at a time using an internal RNA template that encodes the telomeric repeat sequence.
decreased telomerase activity phenotype
A phenotype observation where the occurane of telomerase activity is decreased
decreased telomerase activity
increased telomerase activity phenotype
A phenotype observation where the occurane of telomerase activity is increased
increased telomerase activity
G0/1 arrested phenotype
(from GO) Under certain conditions, cells exit the cell cycle during G1 and remain in the G0 state as nongrowing, non-dividing (quiescent) cells.
A phenotype of a cell that is arrested at the G0/1 transition
G0/1 arrested
polarized endoplasmic reticulum phenotype
A phenotype observation where the endoplasmic reticulum is oriented in the cell with extremities at either end of the main axis.
polarized endoplasmic reticulum
molecular component phenotype
A phenotype observation at the level of a molecular component of a cell
cell DNA phenotype
A phenotype observation at the level of the cell DNA
misshapen DNA
A phenotyoe observation where the nucleus has an irregular shape that is not ovoid.
site of double-strand break phenotype
A phenotype observation at the level of the site of double-strand break, a region of a chromosome at which a DNA double-strand break has occurred.
site of double-strand break
decreased number of site of double-strand break phenotype
A phenotype observation at the level of double strand breaks where the components number has decreased.
decreased number of site of double-strand break
increased number of site of double-strand break phenotype
A phenotype observation where the number of double-strand breaks has increased
increased number of site of double-strand break
cell-matrix adhesion phenotype
increased cell component size phenotype
A phenotype observation at the level of a cellular component where the components size has increased.
increased cell component size
decreased cell component size phenotype
A phenotype observation at the level of a cellular component where the components size has decreased.
decreased cell component size
cell spreading phenotype
substrate adhesion-dependent cell spreading phenotype
A phenotype observation where the morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate.
cellular development phenotype
A phenotype observation of a biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
decreased number of axons phenotype
A phenotype observation at the level of axons where the components number has decreased.
decreased number of axons
increased number of axons phenotype
A phenotype observation at the level of axons where the components number has increased.
increased number of axons
mitotic process phenotype
A phenotype observation at the level of the mitotic cell cycle
arrested process phenotype
A phenotype of a cell where a particular process is arrested, or ends earlier in time than expected
arrested process
M phase arrested phenotype
A phenotype of a cell where the M phase of mitotic cell cycle process is arrested, or ends earlier in time than expected
M phase arrested
mitosis delayed phenotype
A phenotype observation where mitosis is delayed
mitosis delayed
G2 arrested phenotype
A phenotype of a cell is arrested in G2 pahse of the cell cycle.
G2 arrested
S phase arrested phenotype
A phenotype of a cell where the S pahse process is arrested, or ends earlier in time than expected
S phase arrested
increased duration of exit from mitosis phenotype
increased duration of exit from mitosis
A phenotype observation where the duration of the exit from mitosis is increased
decreased duration of exit from mitosis phenotype
decreased duration of exit from mitosis
G2 phase mitotic phenotype
A phenotype observation at the level of a G2 phase of the mitotic cell cycle
mitotic metaphase phenotype
A phenotype observation at the level of the mitotic metaphase of the cell cycle
increased number of mitotic metaphase cells in population phenotype
decreased number of mitotic metaphase cells in population phenotype
abnormal cell cycle phenotype
A phenotype where the cell cycle is in some way abnormal
abnormal cell cycle
binuclear cell phenotype
binuclear cell
A phenotype observation where a cell is binucleate, e.g. have two nuclei per cell
increased duration of mitotic chromosome condensation phenotype
A phenotype observation where the duration of the mitotic chromosome condensation is increased
increased duration of mitotic chromosome condensation
decreased duration of mitotic chromosome condensation phenotype
A phenotype observation where the duration of the mitotic chromosome condensation is decreased
decreased duration of mitotic chromosome condensation
absence of mitotic chromosome decondensation phenotype
A phenotype resulting from the absence of mitotic chromosome decondensation
absence of mitotic chromosome decondensation
absence of mitotic process phenotype
A phenotype resulting in the absence of mitotic process
absence of mitotic process
mitotic chromosome condensation phenotype
A phenotype observation at the level of mitotic chromosome condensation
mitotic chromosome decondensation phenotype
A phenotype observation at the level of mitotic chromosome decondensation
mitotic chromosome decondensation
cell apoptosis phenotype
A phenotype where the apoptosis process is observed
increased number of apoptosis phenotypes in population
decreased number of apoptosis phenotypes in population
increased axon thickness phenotype
A phenotype observation where the thickness of the axon has increased.
increased axon thickness
decresed axon thickness phenotype
A phenotype observation where the thickness of the axon has decreased.
decresed axon thickness
increased axon length phenotype
A phenotype observation at the level of a axon where the components length has increased.
increased axon length
decreased axon length phenotype
A phenotype observation at the level of a axon where the components length has decreased.
decreased axon length
plasma membrane fusion occurance phenotype
plasma membrane fusion occurance
increased rate of cell migration process phenotype
A phenotype where the cell migration process occurs at an increased rate, typically observed as a faster moving cell
increased rate of cell migration process
decreased rate of cell migration process phenotype
A phenotype where the cell migration process occurs at an redcued rate, typically observed as a slower moving cell
decreased rate of cell migration process
cell movement phenotype
A phenotype observation at the level of the whole cell relating to the cell's movement
cell movement
increased cell movement phenotype
A phenotype observation at the level of the cell movement where cell movement is increased
increased cell movement
increased cell movement speed
A phenotype observation at the level of the cell movement where the cell moves faster than normal/wild type.
increased cell movement distance
A phenotype observation at the level of the cell movement where the distance travelled by the cell is increased. The distance is measured as the euclidean distance between start and end point of the cell trajectory.
decreased cell movement phenotype
A phenotype observation at the level of the cell movement where cell movement is decreased
decreased cell movement
decreased cell movement distance
A phenotype observation at the level of the cell movement where the distance travelled by the cell is decreased. The distance is measured as the euclidean distance between start and end point of the cell trajectory.
decreased cell movement speed
A phenotype observation at the level of the cell movement where the cell moves slower than normal/wild type.
increased number of cells in population phenotype
actin-mediated cell contraction phenotype
A phenotype of a cell contraction caused by an actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in contraction of all or part of the cell body.
actin-mediated cell contraction
cell component movement phenotype
A phenotype where the directed, self-propelled movement of a cellular component without the involvement of an external agent such as a transporter or a pore is observed
cell component movement
cell secretion phenotype
A phenotype observation of the controlled release of a substance by a cell.
increased rate of protein secretion
A phenotype observation where the rate of release of proteins from a cell is increased
decreased rate of protein secretion
A phenotype observation where the rate of release of proteins from a cell is decreased
nuclear morphology phenotype
A phenotype observation at the level of the nucleus relating to the nuclear morphology
nuclear morphology
golgi morphology phenotype
A phenotype observation at the level of the golgi relating to the golgi's morphology
golgi morphology
cilium phenotype
A phenotype observation at the level of the cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface.
cilium morphology phenotype
A phenotype observation at the level of a cilium relating to the components shape, size or structure
cilium morphology
single cell phenotype
A phenotype observation at the level of a single or whole cell.
cellular component phenotype
A phenotype observation at the level of a cellular component
geometric cell phenotype
A phenotype observation at the level of the cell shape where the cell has a geometric shape with straight edges
geometric cell
apoptotic DNA
Fragmented and condensed DNA during or following apoptosis
more cells in M phase
fewer cells in M phase
decreased occurrence of mitotic cells in population
M phase mitotic phenotype
A phenotype observation at the level of the M phase of the mitotic cell cycle
asymmetric lamellipodia phenotype
A phenotype observation where more lamellipoda is localised to one side of the cell with respect to the other
asymmetric lamellipodia
star shaped cell phenotype
A phenotype observation at the level of the cell shape where the cell has a star-like or bristly shape
star shaped cell
spiny shaped cell phenotype
spiny shaped cell
increased variability of cell size in population
A population of cells where the cells exhibit a high variability of size
increased variability of cell shape in population
A population of cells where the cells exhibit a high variability of shape
cortical actin cytoskeleton phenotype
A phenotype observation at the level of the cortical actin cytoskeleton, the portion of the actin cytoskeleton, comprising filamentous actin and associated proteins, that lies just beneath the plasma membrane.
increased cortical actin cytoskeleton mass phenotype
A phenotype observation at the level of the cortical actin cytoskeleton where the components mass has increased.
increased cortical actin cytoskeleton mass
decreased cortical actin cytoskeleton mass phenotype
A phenotype observation at the level of the cortical actin cytoskeleton where the components mass has decreased.
decreased cortical actin cytoskeleton mass
disorganised cortical actin cytoskeleton phenotype
A phenotype observation at the level of the cortical actin cytoskeleton where the component shows an irregular organization
disorganised cortical actin cytoskeleton
increased lamellipodia width phenotype
increased lamellipodia width
A phenotype observation at the level of a lamellipodia where the components width has increased.
decreased lamellipodia width phenotype
A phenotype observation at the level of a lamellipodia where the components width has decreased.
decreased lamellipodia width
fan-shaped lamellipodia phenotype
A phenotype observation where the lamellipodia is shaped in the form of a fan.
fan-shaped lamellipodia
lamellipodium phenotype
A phenotype observation at the level of a cell with an increased amount of lamellipodia.
cell projection phenotype
A phenotype observation at the level of a cellular component relating to a prolongation or process extending from a cell, e.g. a cilium, lamellipodium or axon.
filopodium phenotype
A phenotype observation at the level of the filopodium; a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast.
filopodium
layered cells in population
Cells not stopping at confluence and growing on top of each other in layers
actin cytoskeleton phenotype
A phenotype observation at the level of the actin cytoskeleton, the part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
actin cytoskeleton
increased actin cytoskeleton mass phenotype
A phenotype observation at the level of a actin cytoskeleton where the components mass has increased
increased actin cytoskeleton mass
decreased actin cytoskeleton mass phenotype
A phenotype observation at the level of a actin cytoskeleton where the components mass has decreased.
decreased actin cytoskeleton mass
aggregated microtubules phenotype
A phenotype observation where microtubules form clump-like structures as opposed to filaments
aggregated microtubules
microtubules nuclear bracket phenotype
A phenotype observation where the microtubules form two crescent shaped brackets around the nucleus
microtubules nuclear bracket
microtubules nuclear ring phenotype
A phenotype observation where the microtubules form a ring around the nucleus
microtubules nuclear ring
increased amount of stress fibers phenotype
A phenotype observation at the level of any stress fibers where the components number has increased.
increased amount of stress fibers
punctate actin foci phenotype
A phenotype observation where actin is observed as small patches or spots all over the cell
punctate actin foci
increased amount of punctate actin foci phenotype
A phenotype observation where a cell has an increased amount of actin observed as small patches or spots all over the cell
increased amount of punctate actin foci
cell layer phenotype
A phenotype of a culture in which cells grow as a monolayer that is attached to the culture substrate.
loss of cell monolayer
Loss of sheet like monolayer leading to empty patches
increased actin localised to the nucleus
A phenotype observation where many actin filaments are observed in or around the nucleus
increased actin localised to the cytoplasm
A phenotype observation where many actin filaments are observed in the cytoplasm
increased amount of stress fibers located in the cell cortex phenotype
Increased amount of actin stress fibers in the cortical area
A phenotype observation at the level of stress fibers localized to the cell cortex where the components number has increased.
increased amount of stress fibers located in the cell cortex
increased amount of transverse stress fibers
Increased amount of actin stress fibers, forming transverse arcs located in the cell cortex
A phenotype observation at the level of stress fibers where the components number has increased and formed transverse arcs which are located in the cell cortex
increased amount of zig-zag stress fibers
A phenotype observation at the level of stress fibers where the components number has increased and formed a zig zag pattern across the cell
Increased amount of actin stress fibers, with zig-zag pattern across the cell
more multinucleate cells
no cells phenotype
no cells
actin nuclear ring phenotype
actin nuclear ring
cell component morphology phenotype
A phenotype observation at the level of a cellular component relating to the components shape, size or structure
cell component morphology
cell cycle arrested phenotype
cell cycle arrested
metaphase arrested phenotype
A phenotype of a cell arrested in mitotic metaphase
metaphase arrested
delayed process phenotype
A phenotype of a cell where a particular process is delayed
delayed process
metaphase delayed phenotype
A phenotype of a cell where mitotic metaphase is delayed
metaphase delayed
impaired cell migration
A phenotype where the cell migration is impaired
increased duration of cell migration process phenotype
A phenotype where the cell migration process occurs for longer, typically observed as a cell moving a further distance
increased duration of cell migration process
decreased duration of cell migration process phenotype
A phenotype where the cell migration process duration is reduced, typically observed as a cell moving a shorter distance
decreased duration of cell migration process
exit from mitosis phenotype
A phenotype observation at the level of the exit from mitosis
exit from mitosis
absence of cell process phenotype
A phenotype observation at the level of a cellular process where the cell process is absent
absence of cell process
abnormal cell growth phenotype
A phenotype observation of the process in which the cell growth is abnormal
abnormal cell growth
cell growth arrested phenotype
A phenotype observation of the process in which the cell growth is arrested
cell growth arrested
mild decrease in rate of protein secretion
A phenotype observation where the rate of release of proteins from a cell is mildly decreased
strong decrease in rate of protein secretion
A phenotype observation where the rate of release of proteins from a cell is severly decreased
increased cell spreading phenotype
A phenotype observation where there is an increased occurance of cell spreading
increased cell spreading
mild increase of cell spreading phenotype
A phenotype observation where there is a mild increase of cell spreading
mild increase of cell spreading
strong increase of cell spreading phenotype
A phenotype observation where there is a severe increase in cell spreading
strong increase of cell spreading
decreased cell spreading phenotype
A phenotype observation where there is a decreased occurance of cell spreading
decreased cell spreading
absence of cell spreading phenotype
A phenotype observation where cell spreading is absent
absence of cell spreading
spread cell morphology phenotype
A phenotype observation where a cell shows a thin and large projected areas, with developed matrix adhesions at the cell periphery, as opposed to round cells with no or few adhesion sites
spread cell morphology
abnormal chromosome segregation phenotype
abnormal chromosome segregation
A phenotype observation of the process in which the chromosome segregation is abnormal
mitotic prophase phenotype
A phenotype observation at the level of the mitotic prophase of the cell cycle
increased duration of mitotic prophase phenotype
A phenotype observation where the duration of the mitotic prophase of the cell cycle is increased
increased duration of mitotic prophase
decreased duration of mitotic prophase phenotype
A phenotype observation where the duration of the mitotic prophase of the cell cycle is decreased
decreased duration of mitotic prophase
decreased frequency of negative regulation of NF-kappaB transcription factor activity phenotype
A phenotype observation where the frequency of a process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB is decreased.
decreased number of oscillations; the amplitude of the first peak is comparable to control, although the duration may be increased; the time of the second and third peaks is delayed, due to greater interval times between termination and initiation of nuclear translocation responses
decreased frequency of negative regulation of NF-kappaB transcription factor activity
increased frequency of negative regulation of NF-kappaB transcription factor activity phenotype
A phenotype observation where the frequency of a process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB is increased.
increased frequency of negative regulation of NF-kappaB transcription factor activity
increased number of oscillations; the amplitude of the second and third peak is increased and nuclear translocation responses occur at increased intervals.
cytoplasmic sequestering of NF-kappaB phenotype
cytoplasmic sequestering of NF-kappaB
abnormal release of cytoplasmic sequestered NF-kappaB phenotype
A phenotype observation where the release of NF-kappaB from specific molecules in the cytoplasm to which it was bound, thereby allowing its translocation into the nucleus, is abnormal.
contains all cases that are significantly different from the rest, but don't share any clear commonalities. NF-kB oscillation patterns are not synchronized within a cell population, oscillation amplitude and frequency follow erratic patterns
abnormal release of cytoplasmic sequestered NF-kappaB
regulation of process phenotype
A phenotype observation where any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule.
bright nuclear body phenotype
A phenotype obervation where the nuclear body's color brightness is relatively high.
bright nuclear body
round focal adhesion
A phenotype observation where the shape of the focal adhesion has every part of the surface or the circumference equidistant from the center.
mitosis arrested
A phenotype of a cell that is arrested at mitosis
increased cell size in population
A population of cells where there is an increased number of large cells in the population
pyknotic nuclear phenotype
A phenotype observation at the level of the nucleus underoging Pyknosis, or karyopyknosis, consisting of the irreversible condensation of chromatin in the nucleus of a cell undergoing necrosis or apoptosis.
prometaphase arrested phenotype
A phenotype of a cell arrested in mitotic prometaphase
prometaphase arrested
prometaphase delayed phenotype
A phenotype of a cell where mitotic prometaphase is delayed
prometaphase delayed
increased variability of nuclear shape in population
A population of cells where the nuclei exhibit a high variability of shape
decreased rate of intracellular protein transport phenotype
A phenotype observation where the rate of intracellular protein transport is decreased
decreased rate of intracellular protein transport
absence of mitotic metaphase process phenotype
A phenotype resulting in the absence of mitotic metaphase process
absence of mitotic metaphase
mitotic metaphase plate congression phenotype
A phenotype observation at the level of the cell cycle process in which chromosomes are aligned at the metaphase plate, a plane halfway between the poles of the mitotic spindle, during mitosis.
mitotic metaphase plate congression
increased substrate-dependent cell migration, cell extension phenotype
A phenotype where an increased formation of a cell surface protrusion, such as a lamellipodium or filopodium, at the leading edge of a migrating cell is observed.
increased protrusive activity
increased substrate-dependent cell migration, cell extension
increased substrate-dependent cell migration phenotype
A phenotype where an increased occurrence of the orderly movement of a cell from one site to another along a substrate such as the extracellular matrix is observed.
increased substrate-dependent cell migration
increased microtubule-based processes phenotype
A phenotype where an increased occurance of any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins, is observed.
increased monopolar cell elongation phenotype
A phenotype observation of the process in which a cell increases in size due to polarized growth from one end of a cell.
increased monopolar cell elongation
decreased monopolar cell elongation phenotype
A phenotype observation of the process in which a cell decreases in size due to polarized growth from one end of a cell.
decreased monopolar cell elongation
mild actin-mediated cell contraction phenotype
A phenotype of a cell contraction caused by an actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in mild contraction of all or part of the cell body.
mild actin-mediated cell contraction
cell component localisation phenotype
A phenotype where any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in a specific location is observed
cell component localisation
A phenotype observation where the shape of the nucleus resembles a many-lobed berry, such as a raspberry.
A phenotype of a cell where the rate of DNA amplification is increased
increased rate of DNA amplification
A phenotype observation where a cell has an increased amount of DNA
increased amount of DNA
centriole replication phenotype
A phenotype of a cell in which the biological process resulting in a doubling of the number of centrioles in the cell is affected
centriole replication
increased centriole replication phenotype
A phenotype of a cell in which the biological process resulting in a the number of centrioles is increased
increased centriole replication
decreased centriole replication phenotype
A phenotype of a cell in which the biological process resulting in a the number of centrioles is decreased
decreased centriole replication
protein localization to cellular component phenotype