Gene Ontology Definition Changes
Files used:
- file 1 (old): 12:08:2011 16:34, cvs revision 1.2181
- file 2 (new): 19:08:2011 16:54, cvs revision 1.2200
- Database: unknown DB type, unknown DB release name
Terms with changed definitions
GO:0000418 : DNA-directed RNA polymerase IV complex
OLD: RNA polymerase IV is a multisubunit RNA polymerase complex found in the nucleus of plants. In addition to RNA polymerases I, II, and III, the essential RNA polymerases present in all eukaryotes, plants have two additional nuclear RNA polymerases, Pol IV and Pol V, that play nonredundant roles in siRNA-directed DNA methylation and gene silencing. Pol IV is required for siRNA production and Pol V is required for generating noncoding transcripts at target loci. Pol IV is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. The largest and second-largest subunits of Pol IV are the catalytic subunits and share similarity with the corresponding subunits of other eukaryotic and bacterial multisubunit RNA polymerases.
NEW: RNA polymerase IV is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol IV is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. The largest and second-largest subunits of Pol IV are the catalytic subunits and share similarity with the corresponding subunits of other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase V, while the largest subunit is found only in RNAP IV complex.
GO:0000419 : DNA-directed RNA polymerase V complex
(was DNA-directed RNA polymerase IVb complex)
OLD: RNA polymerase IVb is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensus sequence as well as other sequences. The remainder of the complex is composed of smaller subunits.
NEW: RNA polymerase V is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol V is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensus sequence as well as other sequences. The remainder of the complex is composed of smaller subunits.
GO:0000785 : chromatin
OLD: The ordered and organized complex of DNA and protein that forms the chromosome.
NEW: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
GO:0000789 : cytoplasmic chromatin
OLD: The ordered and organized complex of DNA and protein that forms the chromosome in the cytoplasm.
NEW: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the cytoplasm.
GO:0000790 : nuclear chromatin
OLD: The ordered and organized complex of DNA and protein that forms the chromosome in the nucleus.
NEW: The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
GO:0000988 : protein binding transcription factor activity
OLD: Interacting selectively and non-covalently with two or more protein molecules, or a protein and another macromolecule or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
NEW: Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
GO:0000989 : transcription factor binding transcription factor activity
OLD: Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
NEW: Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
GO:0000990 : core RNA polymerase binding transcription factor activity
OLD: Interacting selectively and non-covalently with an RNA polymerase and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
NEW: Interacting selectively and non-covalently with an RNA polymerase in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
GO:0000991 : core RNA polymerase II binding transcription factor activity
OLD: Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
NEW: Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
GO:0000995 : core RNA polymerase III binding transcription factor activity
OLD: Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
NEW: Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
GO:0001007 : RNA polymerase III transcription factor binding transcription factor activity
OLD: Interacting selectively and non-covalently with an RNA polymerase III transcription factor, which may be a single protein or a complex, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
NEW: Interacting selectively and non-covalently with an RNA polymerase III transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
GO:0001076 : RNA polymerase II transcription factor binding transcription factor activity
OLD: Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
NEW: Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
0 annotations
GO:0001082 : RNA polymerase I transcription factor binding transcription factor activity
OLD: Interacting selectively and non-covalently with an RNA polymerase I transcription factor, which may be a single protein or a complex, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
NEW: Interacting selectively and non-covalently with an RNA polymerase I transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
GO:0001083 : RNA polymerase II basal transcription factor binding transcription factor activity
OLD: Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor, which may be a single protein or a complex, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
NEW: Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
0 annotations
GO:0002192 : IRES-dependent translational initiation
OLD: The process where translation initiation recruits the 40S ribosomal\n\nsubunits via an internal ribosome entry segment (IRES) before an AUG codon is encountered in an appropriate sequence context to initiate mRNA translation.
NEW: The process where translation initiation recruits the 40S ribosomal subunits via an internal ribosome entry segment (IRES) before an AUG codon is encountered in an appropriate sequence context to initiate mRNA translation.
GO:0003682 : chromatin binding
OLD: Interacting selectively and non-covalently with chromatin, the network of fibers of DNA and protein that make up the chromosomes of the eukaryotic nucleus during interphase.
NEW: Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
GO:0004764 : shikimate 3-dehydrogenase (NADP+) activity
(was shikimate 5-dehydrogenase activity)
OLD: Catalysis of the reaction: shikimate + NADP+ = 5-dehydroshikimate + NADPH + H+.
NEW: Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
GO:0005006 : epidermal growth factor-activated receptor activity
(was epidermal growth factor receptor activity)
OLD: Combining with an epidermal growth factor to initiate a change in cell activity.
NEW: Combining with an epidermal growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity.
GO:0005007 : fibroblast growth factor-activated receptor activity
(was fibroblast growth factor receptor activity)
OLD: Combining with fibroblast growth factor to initiate a change in cell activity.
NEW: Combining with a fibroblast growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity.
GO:0005008 : hepatocyte growth factor-activated receptor activity
(was hepatocyte growth factor receptor activity)
OLD: Combining with hepatocye growth factor to initiate a change in cell activity.
NEW: Combining with hepatocyte growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity.
GO:0005009 : insulin-activated receptor activity
(was insulin receptor activity)
OLD: Combining with insulin to initiate a change in cell activity.
NEW: Combining with insulin and transmitting the signal across the plasma membrane to initiate a change in cell activity.
GO:0005010 : insulin-like growth factor-activated receptor activity
(was insulin-like growth factor receptor activity)
OLD: Combining with an insulin-like growth factor to initiate a change in cell activity.
NEW: Combining with insulin-like growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity.
GO:0005017 : platelet-derived growth factor-activated receptor activity
(was platelet-derived growth factor receptor activity)
OLD: Combining with platelet-derived growth factor to initiate a change in cell activity.
NEW: Combining with platelet-derived growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity.
GO:0005021 : vascular endothelial growth factor-activated receptor activity
(was vascular endothelial growth factor receptor activity)
OLD: Combining with vascular endothelial growth factor to initiate a change in cell activity.
NEW: Combining with vascular endothelial growth factor and transmitting the signal across the plasma membrane to initiate a change in cell activity.
GO:0007175 : negative regulation of epidermal growth factor-activated receptor activity
(was negative regulation of epidermal growth factor receptor activity)
OLD: Any process that stops, prevents, or reduces the frequency, rate or extent of EGF receptor activity.
NEW: Any process that stops, prevents, or reduces the frequency, rate or extent of EGF-activated receptor activity.
GO:0007176 : regulation of epidermal growth factor-activated receptor activity
(was regulation of epidermal growth factor receptor activity)
OLD: Any process that modulates the frequency, rate or extent of EGF receptor activity.
NEW: Any process that modulates the frequency, rate or extent of EGF-activated receptor activity.
GO:0016485 : protein processing
OLD: Any protein maturation process achieved by the cleavage of peptide bonds.
NEW: Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
GO:0016568 : chromatin modification
OLD: The alteration of DNA or protein in chromatin, which may result in changing the chromatin structure.
NEW: The alteration of DNA, protein, or sometimes RNA, in chromatin, which may result in changing the chromatin structure.
GO:0030266 : quinate 3-dehydrogenase (NAD+) activity
(was quinate 5-dehydrogenase activity)
OLD: Catalysis of the reaction: quinate + NAD+ = 5-dehydroquinate + NADH + H+.
NEW: Catalysis of the reaction: (-)-quinate + NAD+ = (-)-3-dehydroquinate + NADH + H+.
GO:0031497 : chromatin assembly
OLD: The assembly of DNA, histone proteins, and other associated proteins into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
NEW: The assembly of DNA, histone proteins, other associated proteins, and sometimes RNA, into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
GO:0031498 : chromatin disassembly
OLD: The controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, and other proteins.
NEW: The controlled breakdown of chromatin from a higher order structure into its simpler subcomponents, DNA, histones, other proteins, and sometimes RNA.
0 annotations
GO:0031551 : regulation of brain-derived neurotrophic factor-activated receptor activity
(was regulation of brain-derived neurotrophic factor receptor activity)
OLD: Any process that modulates the frequency, rate or extent of brain-derived neurotrophic factor receptor activity.
NEW: Any process that modulates the frequency, rate or extent of brain-derived neurotrophic factor-activated receptor activity.
0 annotations
GO:0031552 : negative regulation of brain-derived neurotrophic factor-activated receptor activity
(was negative regulation of brain-derived neurotrophic factor receptor activity)
OLD: Any process that stops, prevents, or reduces the frequency, rate or extent of brain-derived neurotrophic factor receptor activity.
NEW: Any process that stops, prevents, or reduces the frequency, rate or extent of brain-derived neurotrophic factor-activated receptor activity.
0 annotations
GO:0031553 : positive regulation of brain-derived neurotrophic factor-activated receptor activity
(was positive regulation of brain-derived neurotrophic factor receptor activity)
OLD: Any process that activates or increases the frequency, rate or extent of brain-derived neurotrophic factor receptor activity.
NEW: Any process that activates or increases the frequency, rate or extent of brain-derived neurotrophic factor-activated receptor activity.
0 annotations
GO:0033709 : D-arabinitol dehydrogenase, D-ribulose forming (NADP+) activity
OLD: Catalysis of the reactions: D-arabinitol + NADP+ = D-ribulose + NADPH + H+.
NEW: Catalysis of the reaction: D-arabinitol + NADP+ = D-ribulose + NADPH + H+.
GO:0035561 : regulation of chromatin binding
OLD: Any process that modulates the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA and protein that make up the chromosomes of the eukaryotic nucleus during interphase.
NEW: Any process that modulates the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
GO:0035562 : negative regulation of chromatin binding
OLD: Any process that stops or reduces the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA and protein that make up the chromosomes of the eukaryotic nucleus during interphase.
NEW: Any process that stops or reduces the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
GO:0035563 : positive regulation of chromatin binding
OLD: Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA and protein that make up the chromosomes of the eukaryotic nucleus during interphase.
NEW: Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
GO:0035625 : epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway
(was epidermal growth factor receptor transactivation by G-protein coupled receptor signaling pathway)
OLD: The process in which an epidermal growth factor receptor is activated via signaling events from a G-protein coupled receptor. This is an example of cross-talk between the EGFR and GPCR signaling pathways.
NEW: The process in which an epidermal growth factor-activated receptor is activated via signaling events from a G-protein coupled receptor. This is an example of cross-talk between the EGF and GPCR signaling pathways.
GO:0042790 : transcription of nuclear large rRNA transcript from RNA polymerase I promoter
(was transcription of nuclear rRNA large RNA polymerase I transcript)
OLD: The synthesis of the large ribosomal RNA (rRNA) transcript which encodes several rRNAs, e.g. in mammals 28S, 18S and 5.8S, from a nuclear DNA template.
NEW: The synthesis of the large ribosomal RNA (rRNA) transcript which encodes several rRNAs, e.g. in mammals 28S, 18S and 5.8S, from a nuclear DNA template transcribed by RNA polymerase I.
GO:0042813 : Wnt-activated receptor activity
(was Wnt receptor activity)
OLD: Combining with a member of the Wnt family of signaling molecules to initiate a change in cell activity.
NEW: Combining with a Wnt protein and transmitting the signal across the plasma membrane to initiate a change in cell activity.
0 annotations
GO:0043957 : acryloyl-CoA reductase (NADP+) activity
(was acrylyl-CoA reductase (NADPH) activity)
OLD: Catalysis of the reaction: acrylyl-CoA + NADPH + H+ = propionyl-CoA + NADP+.
NEW: Catalysis of the reaction: acryloyl-CoA + NADPH + H+ = propionyl-CoA + NADP+.
GO:0043958 : acryloyl-CoA reductase activity
OLD: Catalysis of the reaction: reduced electron transferring flavoprotein + NADH + acrylyl-CoA = NAD+ + oxidized electron transferring flavoprotein + propionyl-CoA.
NEW: Catalysis of the reaction: acryloyl-CoA + NADH + H+ + a reduced electron-transfer flavoprotein = propionyl-CoA + NAD+ + an oxidized electron-transfer flavoprotein.
GO:0045741 : positive regulation of epidermal growth factor-activated receptor activity
(was positive regulation of epidermal growth factor receptor activity)
OLD: Any process that activates or increases the frequency, rate or extent of epidermal growth factor receptor activity.
NEW: Any process that activates or increases the frequency, rate or extent of EGF-activated receptor activity.
GO:0052632 : citrate hydro-lyase (cis-aconitate-forming) activity
OLD: Catalysis of the reactions: citrate = cis-aconitate + H2O.
NEW: Catalysis of the reaction: citrate = cis-aconitate + H2O.
0 annotations
GO:0052662 : zeaxanthin epoxidase activity
OLD: Catalysis of the reactions: zeaxanthin + NAD(P)H + H+ + O2 = antheraxanthin + NAD(P)+ + H2O.
NEW: Catalysis of the reaction: zeaxanthin + NAD(P)H + H+ + O2 = antheraxanthin + NAD(P)+ + H2O.
0 annotations
GO:0060175 : brain-derived neurotrophic factor-activated receptor activity
(was brain-derived neurotrophic factor receptor activity)
OLD: Combining with brain-derived neurotrophic factor, to block apoptosis in neurons and promote nerve growth, or to initiate a change in cell activity.
NEW: Combining with a brain-derived neurotrophic factor and transmitting the signal across the plasma membrane to initiate a change in cell activity.
GO:0070613 : regulation of protein processing
OLD: Any process that modulates the frequency, rate or extent of protein processing, the posttranslational modification of a protein leading to the attainment of the full functional capacity of the protein.
NEW: Any process that modulates the frequency, rate or extent of protein processing, any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein.
0 annotations
GO:0072043 : regulation of pre-tubular aggregate formation by cell-cell signaling
OLD: Any process that mediates the transfer of information from one cell to another that modulates the rate, frequency, or extent of pre-tubular aggregate formation. Pre-tubular aggregate formation is the cell adhesion process in which mammary mesenchyme cells adhere to one another in the initial stages of the formation of the pre-tubular aggregate, the earliest recognizable structure of the kidney.
NEW: Any process that mediates the transfer of information from one cell to another that modulates the rate, frequency, or extent of pre-tubular aggregate formation. Pre-tubular aggregate formation is the cell adhesion process in which mesenchymal cells adhere to one another in the initial stages of the formation of the pre-tubular aggregate, the earliest recognizable structure of the kidney.
0 annotations
GO:0072689 : MCM complex assembly
OLD: The aggregation, arrangement and bonding together of a set of components to form an MCM complex, a hexameric protein complex required for the initiation and regulation of DNA replication.
NEW: The aggregation, arrangement and bonding together of a set of components to form an MCM complex, a hexameric protein complex required for the initiation and regulation of DNA replication.
0 annotations
GO:0080184 : response to phenylpropanoid
OLD: Any process that results in a change in state or activity of a cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as the result of a phenylpropanoid stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. A phenylpropoanoid is any of secondary metabolites with structures based on a phenylpropane skeleton. The class includes phenylpropanoid esters, flavonoids, anthocyanins, coumarins and many small phenolic molecules. Phenylpropanoids are also precursors of lignin.
NEW: Any process that results in a change in state or activity of a cell or organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as the result of a phenylpropanoid stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. A phenylpropanoid is any of secondary metabolites with structures based on a phenylpropane skeleton. The class includes phenylpropanoid esters, flavonoids, anthocyanins, coumarins and many small phenolic molecules. Phenylpropanoids are also precursors of lignin.