Fate of "transcription regulator activity" and its remaining child terms

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Revision as of 16:46, 1 April 2011 by Kchris (talk | contribs) (Supporting information)

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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)
  • 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)
  • 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: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: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

Subsets

All subsets for "transcription regulator activity"

  • Prokaryotic GO subset
  • Candida GO slim
  • GOA and proteome slim
  • PIR GO slim
  • Plant GO slim
  • Yeast GO slim

Prokaryotic GO subset

  • GO:0030528 - transcription regulator activity
  • GO:0016563 - transcription activator activity
  • GO:0016564 - transcription repressor activity
  • GO:0016986 - transcription initiation factor activity
  • GO:0016988 - transcription initiation factor antagonist activity
  • GO:0003711 - transcription elongation regulator activity
  • GO:0003715 - transcription termination factor activity
  • GO:0030401 - transcription antiterminator activity

Terms not in subsets

  • GO:0042156 zinc-mediated transcriptional activator 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:0008159 - positive transcription elongation factor activity
  • GO:0008148 - negative 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: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:0090046 - regulation of transcription regulator activity
  • GO:0090047 - positive regulation of transcription regulator activity
  • GO:0090048 - negative regulation of transcription regulator activity