Fate of "transcription regulator activity" and its remaining child terms: Difference between revisions
(Created page with "= Proposal = merge Function term into Process term ------------------------------------------------------- * GO:0030528 MF transcription regulator activity * GO:0016563...") |
|||
Line 131: | Line 131: | ||
merge Function term into Process term | merge Function term into Process term | ||
------------------------------------------------------- | ------------------------------------------------------- | ||
* GO:0030528 | * For current top level MF term: | ||
** GO:0030528 '''transcription regulator activity''' | |||
**: Existing definition already specifies DNA, so we can clearly select a "transcription, DNA-dependent" term without being concerned about the RNA-dependent type of transcription | |||
**: <font color="red">merge into one of these BP terms, which?</font>: | |||
**:*'''transcription, DNA-dependent''' (GO:0006351) | |||
**:*'''regulation of transcription, DNA-dependent''' (GO:0006355) | |||
* Three high level (not specific to a specific RNAP) terms for activators or repressors | |||
** GO:0016563 '''transcription activator activity''' | |||
**: This definition does not mention DNA specifically, but is a child of "transcription regulator activity" | |||
**: <font color="red">merge into BP term</font>: | |||
**:* '''positive regulation of transcription, DNA-dependent''' (GO:0045893) | |||
** GO:0042156 '''zinc-mediated transcriptional activator activity''' | |||
**: Def: Initiates or upregulates transcription in the presence of zinc. | |||
**: Brief look at PMID:10952993 indicates that they show MTF-1 binds DNA in the presence of zinc (EMSA), not sure if this shows direct binding to zinc, or if we care | |||
**: only existing term for any kind of regulation of transcription in relation to zinc is not appropriate | |||
**:* '''regulation of transcription from RNA polymerase II promoter in response to zinc ion starvation''' (GO:0034225) | |||
**: <font color="red">convert to BP term?</font> | |||
**:* '''positive regulation of DNA-dependent transcription in response to zinc''' | |||
** GO:0016564 '''transcription repressor activity''' | |||
**: This definition does not mention DNA specifically, but is a child of "transcription regulator activity" | |||
**: <font color="red">merge into BP term</font>: | |||
**:* '''negative regulation of transcription, DNA-dependent''' (GO:0045892) | |||
* Three terms for transcription factors for specific (eukaryotic nuclear) RNAPs | |||
** GO:0003701 '''RNA polymerase I transcription factor activity''' | |||
**: This definition does not mention DNA specifically, but is a child of "transcription regulator activity" | |||
**: <font color="red">merge into BP term</font>: | |||
**:* '''transcription from RNA polymerase I promoter''' (GO:0006360) | |||
** GO:0003702 '''RNA polymerase II transcription factor activity''' | |||
**: This definition does not mention DNA specifically, but is a child of "transcription regulator activity" | |||
**: <font color="red">merge into BP term</font>: | |||
**:* | |||
* GO: | ** GO:0003709 '''RNA polymerase III transcription factor activity''' | ||
* | **: This definition does not mention DNA specifically, but is a child of "transcription regulator activity" | ||
* | **: <font color="red">merge into BP term</font>: | ||
**:* | |||
* GO:0003711 MF transcription elongation regulator activity | * GO:0003711 MF transcription elongation regulator activity | ||
Line 170: | Line 198: | ||
* GO:0090047 positive regulation of transcription regulator activity | * GO:0090047 positive regulation of transcription regulator activity | ||
* GO:0090048 negative regulation of transcription regulator activity | * GO:0090048 negative regulation of transcription regulator activity | ||
= Supporting information = | = Supporting information = |
Revision as of 19:45, 31 March 2011
Proposal
merge Function term into Process term
- GO:0030528 MF transcription regulator activity
- GO:0016563 MF transcription activator activity
- GO:0042156 MF zinc-mediated transcriptional activator activity
- GO:0016564 MF transcription repressor activity
- GO:0003701 MF RNA polymerase I transcription factor activity
- GO:0003702 MF RNA polymerase II transcription factor activity
- GO:0003709 MF RNA polymerase III transcription factor activity
- GO:0003711 MF transcription elongation regulator activity
- GO:0008148 MF negative transcription elongation factor activity
- GO:0008159 MF positive transcription elongation factor activity
- GO:0016943 MF RNA polymerase I transcription elongation factor activity
- GO:0016944 MF RNA polymerase II transcription elongation factor activity
- GO:0016945 MF RNA polymerase III transcription elongation factor activity
- GO:0003715 MF transcription termination factor activity
- GO:0003716 MF RNA polymerase I transcription termination factor activity
- GO:0003717 MF RNA polymerase II transcription termination factor activity
- GO:0003718 MF RNA polymerase III transcription termination factor activity
- GO:0016986 MF transcription initiation factor activity
- GO:0030401 MF transcription antiterminator activity
??
- GO:0003706 MF ligand-regulated transcription factor activity
def includes binding
- GO:0016988 MF transcription initiation factor antagonist activity
related regulation terms
- GO:0090046 regulation of transcription regulator activity
- GO:0090047 positive regulation of transcription regulator activity
- GO:0090048 negative regulation of transcription regulator activity
Comment Period
Date mailed:
Deadline for Comments: TBD - Unless objections are received by April ??????, we will assume that you agree to this change.
Problems
in progress
Function terms with Process definitions
The problem with most of these terms is the same as that for transcription regulator activity (GO:0030528). As we said in the [http://wiki.geneontology.org/index.php/Proposals_to_overhaul_transcription_in_GO_-_2010#transcription_regulator_activity_-_GO:0030528 original proposal], the term "transcription regulator activity" is the highest level Function term for transcription and it is essentially identical to a Process term. It conveys exactly the same information as the Process term regulation of transcription and it does NOT convey any information about the molecular nature of the regulator activity. In addition, it is grouping the child terms below it based on involvement in a common Process, not based on having a common Function and it currently includes functions based on binding DNA and functions based on interacting with other proteins.
MF: transcription regulator activity - GO:0030528 Current definition: Plays a role in regulating transcription; may bind a promoter or enhancer DNA sequence or interact with a DNA-binding transcription factor.
BP: regulation of transcription - GO:0045449 Current definition: Any process that modulates the frequency, rate or extent of the synthesis of either RNA on a template of DNA or DNA on a template of RNA.
This problem applies to most of the MF terms that still remain under transcription regulator activity (GO:0030528). All of these terms have definitions that specify only process information; thus we feel that they need to be merged into process terms.
- GO:0030528 transcription regulator activity
- GO:0003701 RNA polymerase I transcription factor activity
- GO:0003702 RNA polymerase II transcription factor activity
- GO:0003709 RNA polymerase III transcription factor activity
- GO:0016563 transcription activator activity
- GO:0042156 zinc-mediated transcriptional activator activity
- GO:0016564 transcription repressor activity
- GO:0003711 transcription elongation regulator activity
- GO:0008148 negative transcription elongation factor activity
- GO:0008159 positive transcription elongation factor activity
- GO:0016943 RNA polymerase I transcription elongation factor activity
- GO:0016944 RNA polymerase II transcription elongation factor activity
- GO:0016945 RNA polymerase III transcription elongation factor activity
- GO:0003715 transcription termination factor activity
- GO:0003716 RNA polymerase I transcription termination factor activity
- GO:0003717 RNA polymerase II transcription termination factor activity
- GO:0003718 RNA polymerase III transcription termination factor activity
- GO:0016986 transcription initiation factor activity
- GO:0030401 transcription antiterminator activity
what about this one?
Issues for these terms:
- GO:0003706 MF ligand-regulated transcription factor activity
rework, or merge into another MF term?
def includes binding
- GO:0016988 MF transcription initiation factor antagonist activity
Regulation terms for "transcription regulator activity"
- GO:0090046 regulation of transcription regulator activity
- GO:0090047 positive regulation of transcription regulator activity
- GO:0090048 negative regulation of transcription regulator activity
Reannotation suggestions
merge Function term into Process term
- For current top level MF term:
- GO:0030528 transcription regulator activity
- Existing definition already specifies DNA, so we can clearly select a "transcription, DNA-dependent" term without being concerned about the RNA-dependent type of transcription
- merge into one of these BP terms, which?:
- transcription, DNA-dependent (GO:0006351)
- regulation of transcription, DNA-dependent (GO:0006355)
- GO:0030528 transcription regulator activity
- Three high level (not specific to a specific RNAP) terms for activators or repressors
- GO:0016563 transcription activator activity
- This definition does not mention DNA specifically, but is a child of "transcription regulator activity"
- merge into BP term:
- positive regulation of transcription, DNA-dependent (GO:0045893)
- GO:0042156 zinc-mediated transcriptional activator activity
- Def: Initiates or upregulates transcription in the presence of zinc.
- Brief look at PMID:10952993 indicates that they show MTF-1 binds DNA in the presence of zinc (EMSA), not sure if this shows direct binding to zinc, or if we care
- only existing term for any kind of regulation of transcription in relation to zinc is not appropriate
- regulation of transcription from RNA polymerase II promoter in response to zinc ion starvation (GO:0034225)
- convert to BP term?
- positive regulation of DNA-dependent transcription in response to zinc
- GO:0016564 transcription repressor activity
- This definition does not mention DNA specifically, but is a child of "transcription regulator activity"
- merge into BP term:
- negative regulation of transcription, DNA-dependent (GO:0045892)
- GO:0016563 transcription activator activity
- Three terms for transcription factors for specific (eukaryotic nuclear) RNAPs
- GO:0003701 RNA polymerase I transcription factor activity
- This definition does not mention DNA specifically, but is a child of "transcription regulator activity"
- merge into BP term:
- transcription from RNA polymerase I promoter (GO:0006360)
- GO:0003702 RNA polymerase II transcription factor activity
- This definition does not mention DNA specifically, but is a child of "transcription regulator activity"
- merge into BP term:
- GO:0003701 RNA polymerase I transcription factor activity
- GO:0003709 RNA polymerase III transcription factor activity
- This definition does not mention DNA specifically, but is a child of "transcription regulator activity"
- merge into BP term:
- GO:0003709 RNA polymerase III transcription factor activity
- GO:0003711 MF transcription elongation regulator activity
- GO:0008148 MF negative transcription elongation factor activity
- GO:0008159 MF positive transcription elongation factor activity
- GO:0016943 MF RNA polymerase I transcription elongation factor activity
- GO:0016944 MF RNA polymerase II transcription elongation factor activity
- GO:0016945 MF RNA polymerase III transcription elongation factor activity
- GO:0003715 MF transcription termination factor activity
- GO:0003716 MF RNA polymerase I transcription termination factor activity
- GO:0003717 MF RNA polymerase II transcription termination factor activity
- GO:0003718 MF RNA polymerase III transcription termination factor activity
- GO:0016986 MF transcription initiation factor activity
- GO:0030401 MF transcription antiterminator activity
??
- GO:0003706 MF ligand-regulated transcription factor activity
def includes binding
- GO:0016988 MF transcription initiation factor antagonist activity
related regulation terms
- GO:0090046 regulation of transcription regulator activity
- GO:0090047 positive regulation of transcription regulator activity
- GO:0090048 negative regulation of transcription regulator activity
Supporting information
Annotation counts via GOOSE (Berkeley BOP) on 3/30/2011
== Summary of GO annotation counts, by source == Source............ non-IEA IEA Grand Total ..............ASAP 9 - 9 .............AspGD 17 51 68 ...............CGD 71 35 106 .........dictyBase 36 33 69 ............EcoCyc 337 30 367 .........EcoliWiki 146 40 186 ...........Ensembl - 208 208 ................FB 374 126 500 GeneDB_Pfalciparum 4 - 4 .....GeneDB_Spombe 56 7 63 ....GeneDB_Tbrucei 4 - 4 ........GR_protein 306 - 306 ..........JCVI_CMR 314 - 314 ...............MGI 888 345 1233 ..............NCBI 2 - 2 ...............PDB 4 753 757 .........PseudoCAP 142 - 142 ............RefSeq - 129 129 ...............RGD 763 478 1241 ...............SGD 186 54 240 ...............SGN 1 - 1 ..............TAIR 315 79 394 ..........TIGR_CMR 299 - 299 .........UniProtKB 1650 93884 95534 ................WB 36 167 203 ..............ZFIN 61 576 637 Grand Total....... 6021 96995 103016
== Summary of GO annotation counts, by term == GO Term...................................................... aspect non-IEA IEA Grand Total .............................transcription regulator activity MF 1238 62032 63270 .............................transcription activator activity MF 2354 6847 9201 .............zinc-mediated transcriptional activator activity MF 10 7 17 .............................transcription repressor activity MF 1554 9353 10907 ...............RNA polymerase I transcription factor activity MF 32 12 44 ..............RNA polymerase II transcription factor activity MF 383 3913 4296 .............RNA polymerase III transcription factor activity MF 49 13 62 ..................transcription elongation regulator activity MF 69 8348 8417 ............negative transcription elongation factor activity MF 12 7 19 ............positive transcription elongation factor activity MF 23 150 173 ....RNA polymerase I transcription elongation factor activity MF - - - ...RNA polymerase II transcription elongation factor activity MF 54 125 179 ..RNA polymerase III transcription elongation factor activity MF - - - ....................transcription termination factor activity MF 80 5011 5091 ...RNA polymerase I transcription termination factor activity MF 17 4 21 ..RNA polymerase II transcription termination factor activity MF 5 3 8 .RNA polymerase III transcription termination factor activity MF 2 - 2 .....................transcription initiation factor activity MF 39 699 738 ........................transcription antiterminator activity MF 43 420 463 ...............ligand-regulated transcription factor activity MF 39 33 72 ..........transcription initiation factor antagonist activity MF 3 4 7 .............. regulation of transcription regulator activity BP - - - ......positive regulation of transcription regulator activity BP 15 14 29 ......negative regulation of transcription regulator activity BP - - - Grand Total.................................................. 6021 96995 103016