LiteFold/GO huggingface dataset:
obsolete activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)
Namespace: biological_process
Definition: OBSOLETE. Any process that initiates the activity of an inactive cysteine-type endopeptidase involved in the apoptotic signaling pathway.
Synonyms: activation of cysteine-type endopeptidase activity involved in apoptotic signalling pathway; activation of initiator caspase activity
Comment: Components of the DISC (death-inducing signaling complex) may be annotated to this term. These include ligand-bound receptors such as FAS/CD95 (though care should be taken because FAS can also act as a non-apoptotic signal transducer), and signaling molecules such as FADD (FAS-associated protein with a death domain), cIAPs (cellular inhibitor of apoptosis proteins), c-FLIPs and caspases 8 and 10. Note that GO:0097296 should only be used to annotate gene products directly involved in the initiation or start up of an inactive cysteine-type endopeptidase activity involved in the apoptotic signaling pathway (also known as an initiator caspase). If the evidence provided is not sufficient to account for direct activation of this enzymatic activity, consider using the more generic terms GO:2001269 positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway or GO:0043280 positive regulation of cysteine-type endopeptidase activity involved in apoptotic process.\nThe reason for obsoletion is that this term represents a GO-CAM model.
obsolete activation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:0097297)
Namespace: biological_process
Definition: OBSOLETE. Any process that initiates the activity of an inactive cysteine-type endopeptidase involved in the execution phase of apoptosis.
Synonyms: activation of effector caspase activity
Comment: This term was obsoleted because it represents a molecular function.
regulation of nucleus size (GO:0097298)
Namespace: biological_process
Definition: Any process that modulates the size of the nucleus.
Synonyms: regulation of nuclear size; regulation of nuclear volume
obsolete cysteine-type endopeptidase activity involved in plant-type hypersensitive response (GO:0097299)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile, and contributing to plant-type hypersensitive response, the rapid, localized death of plant cells in response to invasion by a pathogen.
Synonyms: metacaspase activity involved in plant-type hypersensitive response
Comment: This term was obsoleted because it represents a GO-CAM model.
programmed necrotic cell death (GO:0097300)
Namespace: biological_process
Definition: A necrotic cell death process that results from the activation of endogenous cellular processes, such as signaling involving death domain receptors or Toll-like receptors.
Synonyms: programmed cell death by necrosis; regulated necrosis
Comment: This term may be used when annotating instances of programmed cell death characterized by necrotic morphology where the involvement of RIPK1 and/or RIPK3 is not shown. See PMID:23818611 for some examples.
obsolete regulation of potassium ion concentration by positive regulation of transcription from RNA polymerase II promoter (GO:0097301)
Namespace: biological_process
Definition: OBSOLETE. Any process that regulates the internal concentration of potassium ions at the level of a cell by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
Synonyms: cellular potassium ion homeostasis by positive regulation of transcription from RNA polymerase II promoter; potassium ion homeostasis by positive regulation of transcription from RNA polymerase II promoter
Comment: This term was obsoleted because it represents a GO-CAM model.
obsolete lipoprotein biosynthetic process via signal peptide cleavage (GO:0097304)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways by which signal peptide cleavage leads to formation of a water-soluble protein-lipid complex.
Synonyms: lipoprotein biosynthesis (signal peptide cleavage)
Comment: The reason for obsoletion is that this term represents a molecular function.
response to alcohol (GO:0097305)
Namespace: biological_process
Definition: 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 an alcohol stimulus.
Synonyms: process resulting in tolerance to alcohol
response to farnesol (GO:0097307)
Namespace: biological_process
Definition: 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 farnesol stimulus.
cellular response to farnesol (GO:0097308)
Namespace: biological_process
Definition: 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 farnesol stimulus.
obsolete cap1 mRNA methylation (GO:0097309)
Namespace: biological_process
Definition: OBSOLETE. Methylation of the ribose of the first nucleotide of a 5'-capped mRNA.
Synonyms: cap1 mRNA capping
Comment: The reason for obsoletion is that this term represents a molecular function.
obsolete cap2 mRNA methylation (GO:0097310)
Namespace: biological_process
Definition: OBSOLETE. Methylation of the ribose of the first and second nucleotides of a 5'-capped mRNA.
Synonyms: cap2 mRNA capping
Comment: The reason for obsoletion is that this term represents a molecular function.
bacterial biofilm matrix (GO:0097311)
Namespace: cellular_component
Definition: A structure lying external to bacterial cells. A biofilm is an aggregate of surface-associated bacteria, and the biofilm matrix is the envelope of polymeric substances that surrounds the bacteria.
obsolete bacterial biofilm matrix component (GO:0097312)
Namespace: cellular_component
Definition: OBSOLETE. Any constituent part of the biofilm matrix, a structure lying external to bacterial cells. A biofilm is an aggregate of surface-associated bacteria, and the biofilm matrix is the envelope of polymeric substances that surrounds the bacteria.
Synonyms: biofilm matrix part
Comment: 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.
bacterial biofilm matrix surface (GO:0097313)
Namespace: cellular_component
Definition: The external part of the biofilm matrix, a structure lying external to bacterial cells. A biofilm is an aggregate of surface-associated bacteria, and the biofilm matrix is the envelope of polymeric substances that surrounds the bacteria.
apoptosome assembly (GO:0097314)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of the apoptosome, a multisubunit protein complex involved in the signaling phase of the apoptotic process.
Synonyms: apoptosome formation
response to N-acetyl-D-glucosamine (GO:0097315)
Namespace: biological_process
Definition: 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 an N-acetyl-D-glucosamine stimulus.
cellular response to N-acetyl-D-glucosamine (GO:0097316)
Namespace: biological_process
Definition: 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 an N-acetyl-D-glucosamine stimulus.
invasive growth in response to biotic stimulus (GO:0097317)
Namespace: biological_process
Definition: The growth of colonies in filamentous chains of cells as a result of a biotic stimulus. An example of this is Candida albicans forming invasive filaments in agar medium in response to a serum stimulus.
invasive growth in response to abiotic stimulus (GO:0097318)
Namespace: biological_process
Definition: The growth of colonies in filamentous chains of cells as a result of a abiotic stimulus. An example of this process is found in Candida albicans.
cell growth mode switching, filamentous to budding (GO:0097321)
Namespace: biological_process
Definition: The process in which a cell switches from growing as a filament (elongated cells attached end-to-end) to growing as a round budding cell. An example of this is observed in Candida albicans.
7SK snRNA binding (GO:0097322)
Namespace: molecular_function
Definition: Binding to a 7SK small nuclear RNA (7SK snRNA).
Synonyms: 7SK small nuclear RNA binding
B cell adhesion (GO:0097323)
Namespace: biological_process
Definition: The attachment of a B cell to another cell via adhesion molecules.
melanocyte proliferation (GO:0097325)
Namespace: biological_process
Definition: The multiplication or reproduction of melanocytes, resulting in the expansion of a cell population. A melanocyte is a pigment cell derived from the neural crest. It contains melanin-filled pigment granules, which give a brown to black appearance.
melanocyte adhesion (GO:0097326)
Namespace: biological_process
Definition: The attachment of a melanocyte to another cell via adhesion molecules.
response to antineoplastic agent (GO:0097327)
Namespace: biological_process
Definition: 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 an antineoplastic agent stimulus. An antineoplastic agent is a substance that inhibits or prevents the proliferation of neoplasms.
response to carboplatin (GO:0097328)
Namespace: biological_process
Definition: 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 carboplatin stimulus.
response to antimetabolite (GO:0097329)
Namespace: biological_process
Definition: 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 an antimetabolite stimulus. An antimetabolite is a substance which is structurally similar to a metabolite but which competes with it or replaces it, and so prevents or reduces its normal utilization.
response to cytarabine (GO:0097331)
Namespace: biological_process
Definition: 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 cytarabine stimulus.
response to antipsychotic drug (GO:0097332)
Namespace: biological_process
Definition: 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 an antipsychotic drug stimulus. Antipsychotic drugs are agents that control agitated psychotic behaviour, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect.
response to olanzapine (GO:0097333)
Namespace: biological_process
Definition: 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 an olanzapine stimulus.
response to perphenazine (GO:0097334)
Namespace: biological_process
Definition: 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 perphenazine stimulus. Perphenazine is a phenothiazine derivative having a chloro substituent at the 2-position and a 3-[4-(2-hydroxyethyl)piperazin-1-yl]propyl group at the N-10 position.
response to quetiapine (GO:0097335)
Namespace: biological_process
Definition: 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 quetiapine stimulus.
response to risperidone (GO:0097336)
Namespace: biological_process
Definition: 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 risperidone stimulus.
response to ziprasidone (GO:0097337)
Namespace: biological_process
Definition: 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 ziprasidone stimulus. Ziprasidone is a piperazine compound having 1,2-benzothiazol-3-yl- and 2-(6-chloro-1,3-dihydro-2-oxindol-5-yl)ethyl substituents attached to the nitrogen atoms.
response to clozapine (GO:0097338)
Namespace: biological_process
Definition: 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 clozapine stimulus.
glycolate transmembrane transport (GO:0097339)
Namespace: biological_process
Definition: The process in which glycolate is transported across a membrane. Glycolate is the anion of hydroxyethanoic acid (glycolic acid).
Synonyms: glycolate membrane transport
Comment: Note that this term is not intended for use in annotating lateral movement within membranes.
obsolete inhibition of cysteine-type endopeptidase activity (GO:0097340)
Namespace: biological_process
Definition: OBSOLETE. Any process that prevents the activation of an inactive cysteine-type endopeptidase.
Synonyms: inhibition of caspase activity; prevention of caspase activity; prevention of cysteine-type endopeptidase activity
Comment: The reason for obsoletion is that this term represents regulation of a molecular function.
zymogen inhibition (GO:0097341)
Namespace: biological_process
Definition: Any process that prevents the proteolytic processing of an inactive enzyme to an active form.
Synonyms: prevention of zymogen activation
ripoptosome (GO:0097342)
Namespace: cellular_component
Definition: A protein complex whose core components are the receptor-interacting serine/threonine-protein kinases RIPK1 and RIPK3 (also called RIP1 and RIP3). Formation of the ripoptosome can induce an extrinsic apoptotic signaling pathway or a necroptotic signaling pathway. The composition of this protein complex may depend on several factors including nature of the signal, cell type and more.
Synonyms: necrosome; TNFR1 complex II; Tnfr1-CII
Comment: It has been shown that receptor-mediated necroptotic signaling pathway requires assembly of a ripoptosome protein complex consisting of caspase-8, caspase-10, Fas-associated death domain protein (FADD), casp8 and FADD-like apoptosis regulator (CFLAR) as well as the two receptor-interacting serine/threonine-protein kinases RIPK1 and RIPK3 (PMID:21737330). Optionally, depending on the receptor activated, this complex may contain TLR3 adaptor protein TRIF (PMID:21737330).
ripoptosome assembly (GO:0097343)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a set of components to form a ripoptosome, a protein complex whose formation can induce an extrinsic apoptotic signaling pathway or a necroptotic signaling pathway. The composition of this protein complex may depend on several factors including nature of the signal, cell type and more.
obsolete Rix1 complex (GO:0097344)
Namespace: cellular_component
Definition: OBSOLETE. A protein complex that comprises Rix1p, Ipi1p and Ipi3p, and is required for processing of ITS2 sequences from 35S pre-rRNA. The Rix1 complex has been identified in budding yeast and fission yeast, and members of this complex are conserved in higher eukaryotes.
Synonyms: IPI complex
Comment: redundant, this is the non-catalytic core of Rixosome
mitochondrial outer membrane permeabilization (GO:0097345)
Namespace: biological_process
Definition: The process by which the mitochondrial outer membrane becomes permeable to the passing of proteins and other molecules from the intermembrane space to the cytosol as part of the apoptotic signaling pathway.
Synonyms: mitochondrial outer membrane permeabilization during apoptotic cell death; mitochondrion outer membrane permeabilization; MOMP
Comment: BAX and BAK are involved in this process, as reviewed in PMID:21760595 (the human proteins have UniProt symbols Q07812 and Q16611 respectively).
INO80-type complex (GO:0097346)
Namespace: cellular_component
Definition: A chromatin remodeling protein complex initially purified from S. cerevisiae and containing more than 10 subunits, including the SWR1-related complexes. INO80 (inositol requiring 80)-type complexes have diverse functions, including promoting transcriptional activation and DNA repair.
TAM protein secretion complex (GO:0097347)
Namespace: cellular_component
Definition: A heterooligomeric protein complex that spans the bacterial periplasm and enables the secretion of adhesin proteins in Gram-negative bacteria. In Citrobacter rodentium, Salmonella enterica and Escherichia coli, the TAM complex consists of an Omp85-family protein, TamA, in the outer membrane and TamB in the inner membrane.
Synonyms: translocation and assembly module protein complex
host cell endocytic vesicle membrane (GO:0097348)
Namespace: cellular_component
Definition: The lipid bilayer surrounding a host cell endocytic vesicle.
neutrophil clearance (GO:0097350)
Namespace: biological_process
Definition: The selective elimination of senescent neutrophils from the body by autoregulatory mechanisms.
toxin sequestering activity (GO:0097351)
Namespace: molecular_function
Definition: Binding to a toxin to prevent it from interacting with other partners or to inhibit its localization to the area of the cell or complex where it is active.
Synonyms: toxin-antitoxin pair type I binding; toxin-antitoxin pair type II binding
Comment: There may be more than one antitoxin to a toxic protein. Instances of this activity are known only in prokaryotes, where the toxic protein may be a ribonuclease, a DNA gyrase, or other.
autophagosome maturation (GO:0097352)
Namespace: biological_process
Definition: Removal of PI3P and Atg8/LC3 after the closure of the phagophore and before the fusion with the endosome/lysosome (e.g. mammals and insects) or vacuole (yeast), and that very likely destabilizes other Atg proteins and thus enables their efficient dissociation and recycling.
Synonyms: autophagic vacuole fusion; autophagic vacuole maturation; autophagosome fusion
prenylation (GO:0097354)
Namespace: biological_process
Definition: The covalent attachment of a prenyl group to a molecule; geranyl, farnesyl, or geranylgeranyl groups may be added.
protein localization to heterochromatin (GO:0097355)
Namespace: biological_process
Definition: Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into heterochromatin.
Synonyms: protein localisation to heterochromatin
perinucleolar compartment (GO:0097356)
Namespace: cellular_component
Definition: The perinucleolar compartment (PNC) is a subnuclear structure associated with, but structurally distinct from, the nucleolus. The PNC contains large amounts of the heterogeneous nuclear ribonucleoprotein complex (hnRNP) called hnRNP 1 (PTB). Many RNA binding proteins as well as RNA polymerase III transcripts are highly enriched in this compartment. PTB and pol III transcripts are required for the integrity of the PNC.
Synonyms: perinucleolar region
D-leucyl-tRNA(Leu) deacylase activity (GO:0097358)
Namespace: molecular_function
Definition: Catalysis of the reaction: D-leucyl-tRNA(Leu) = D-leucine + tRNA(Leu). Removal of a D-leucine from a charged tRNA(Leu).
UDP-glucosylation (GO:0097359)
Namespace: biological_process
Definition: The covalent attachment of a UDP-glucose residue to a substrate molecule.
chorionic trophoblast cell proliferation (GO:0097360)
Namespace: biological_process
Definition: The multiplication or reproduction of chorionic trophoblast cells, resulting in the expansion of their population.
cytosolic [4Fe-4S] assembly targeting complex (GO:0097361)
Namespace: cellular_component
Definition: A protein complex capable of condensing two 2Fe-2S clusters into one 4Fe-4S center in the cytoplasm and nucleus. In humans it consists of MMS19, CIAO1, CIAO2A/CIAO2B, CIAO3. MMS19, CIAO1 and CIAO2A/CIAO2B form a tight 'core' complex, whereas CIAO3 is an 'external' component of this complex.
Synonyms: CIA complex; CIA targeting complex; cytosolic iron-sulfur protein assembly complex
MCM8-MCM9 complex (GO:0097362)
Namespace: cellular_component
Definition: A hexameric protein complex composed of MCM8 and MCM9 and involved in homologous recombination repair following DNA interstrand cross-links.
protein O-acetylglucosaminyltransferase activity (GO:0097363)
Namespace: molecular_function
Definition: Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + [protein]-L-serine = UDP + [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine, or UDP-N-acetyl-D-glucosamine + [protein]-L-threonine = UDP + [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-threonine.
Synonyms: O-GlcNAc transferase; O-linked N-acetylglucosaminyltransferase; OGTase; protein O-GlcNAc transferase activity; UDP-N-acetyl-D-glucosamine:protein-O-beta-N-acetyl-D-glucosaminyl transferase
obsolete stretch-activated, monoatomic cation-selective, calcium channel activity involved in regulation of action potential (GO:0097364)
Namespace: molecular_function
Definition: OBSOLETE. Enables the transmembrane transfer of a calcium ion by a channel that opens in response to a mechanical stress in the form of stretching, and contributing to the regulation of action potential.
Synonyms: stretch-activated, cation-selective, calcium channel activity involved in regulation of action potential
Comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
obsolete stretch-activated, monoatomic cation-selective, calcium channel activity involved in regulation of cardiac muscle cell action potential (GO:0097365)
Namespace: molecular_function
Definition: OBSOLETE. OBSOLETE. Enables the transmembrane transfer of a calcium ion by a channel that opens in response to a mechanical stress in the form of stretching, and contributing to the regulation of action potential in a cardiac muscle cell.
Synonyms: stretch-activated, cation-selective, calcium channel activity involved in regulation of cardiac muscle cell action potential
Comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
response to bronchodilator (GO:0097366)
Namespace: biological_process
Definition: 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 bronchodilator stimulus. A bronchodilator is a chemical that causes an increase in the expansion of a bronchus or bronchial tubes.
Synonyms: response to bronchodilator agent; response to broncholytic agent
Comment: Note that this term is in the subset of terms that should not be used for direct manual annotation of gene products. It was created to be used for cross-referencing by other ontologies. Direct annotations to this term may be amended during annotation QC.
carbohydrate derivative binding (GO:0097367)
Namespace: molecular_function
Definition: Binding to a carbohydrate derivative.
establishment of Sertoli cell barrier (GO:0097368)
Namespace: biological_process
Definition: Establishment of a structure near the basement membrane in adjacent Sertoli cells of the seminiferous epithelium for maintaining spermatogenesis. The structure consists of tight junctions, basal ectoplasmic specializations, and desmosome-like junctions.
Synonyms: establishment of blood-testis barrier; establishment of BTB; establishment of SCB