Difference between revisions of "Fate of "transcription regulator activity" and its remaining child terms"

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[[Category:Transcription]] [[Category:Ontology]]
 
= Proposal =
 
= Proposal =
  
==<font color="red">OBSOLETE (or MERGE)?</font> Function terms that are equivalent to Process terms==
+
==<font color="red">OBSOLETE (or MERGE)?</font> 19 Function terms that are equivalent to Process terms==
  
 
For this set of MF terms that are equivalent to BP terms, we are proposing to obsolete them. In previous cases, e.g. "splicing factor activity", we have merged the MF term into the '''equivalent BP term'''. Here, we are instead suggesting obsoletion with a number of options for replacement terms. We are recommending the obsoletion option for two reasons:
 
For this set of MF terms that are equivalent to BP terms, we are proposing to obsolete them. In previous cases, e.g. "splicing factor activity", we have merged the MF term into the '''equivalent BP term'''. Here, we are instead suggesting obsoletion with a number of options for replacement terms. We are recommending the obsoletion option for two reasons:
* to highlight the fact that removal of this term from MF may result in a gene having no MF annotations, or in a set of MF annotations that is incomplete
+
* to highlight the fact that removal of this term from MF may result in a gene having no MF annotations, or a set of MF annotations that is incomplete. Obsoleting instead of merging gives each group greater control over the fate of their annotations.
* we think it might be better for the non-definition dbxrefs to be reviewed and assigned to an appropriate MF term, rather than being transferred (without review) to a BP term.
+
* we think it might be better for the non-definition dbxrefs to be reviewed and assigned, if possible, to an appropriate MF term, rather than being transferred (without review) to a BP term.
  
 
For reannotation, we will be listing a number of possible terms to consider. One of the suggested replacement term is the <font color="red">'''equivalent BP term'''</font>.  
 
For reannotation, we will be listing a number of possible terms to consider. One of the suggested replacement term is the <font color="red">'''equivalent BP term'''</font>.  
  
 
* For groups that wish to '''transfer all annotations without review''', the '''equivalent BP term''' is the only appropriate destination.  
 
* For groups that wish to '''transfer all annotations without review''', the '''equivalent BP term''' is the only appropriate destination.  
* Groups wishing to reannotate to a MF term will need to go back to the original literature or other data because the existing "MF" terms are not defined in terms of how they act.  
+
* Groups wishing to reannotate to a MF term will need to go back to the original literature or other primary data because the existing "MF" terms are not defined in terms of how they act and there are multiple possibilities.  
 
*: - To assist that process, we have suggested which MF terms, and their children, might be appropriate, where such terms exist.  
 
*: - To assist that process, we have suggested which MF terms, and their children, might be appropriate, where such terms exist.  
 
*: - In some cases, we have not yet made appropriate MF terms and we ask that annotators submit SF items to request terms if they come across papers that provide insight into the mechanism of action of a given factor, e.g. a "transcription elongation factor". However, please note that a paper showing that factor X has an effect on elongation without providing insight as to HOW that is accomplished mechanistically, may only provide information appropriate for a BP annotation.
 
*: - In some cases, we have not yet made appropriate MF terms and we ask that annotators submit SF items to request terms if they come across papers that provide insight into the mechanism of action of a given factor, e.g. a "transcription elongation factor". However, please note that a paper showing that factor X has an effect on elongation without providing insight as to HOW that is accomplished mechanistically, may only provide information appropriate for a BP annotation.
 +
 +
<font color="red">'''NOTE'''</font>: The decision the group comes to regarding obsoletion versus merging for these MF terms that are equivalent to BP terms will also apply to the 6 MF->BP term merges we [http://wiki.geneontology.org/index.php/Fate_of_terms_referring_to_general/nonspecific/basal_versus_specific_transcription#Proposal proposed previously]
  
 
'''Affected terms'''
 
'''Affected terms'''
Line 41: Line 44:
 
* GO:0030401    MF      transcription antiterminator activity
 
* GO:0030401    MF      transcription antiterminator activity
  
 +
== <font color="red">OBSOLETE</font>: Regulation terms related to "transcription regulator activity" ==
 +
 +
# 3 terms to obsolete now
 +
#* GO:0090046  regulation of transcription regulator activity
 +
#* GO:0090047  positive regulation of transcription regulator activity
 +
#* GO:0090048  negative regulation of transcription regulator activity
 +
# 6 terms slated for deferred obsoletion (i.e. at the same time as the terms for binding to [http://wiki.geneontology.org/index.php/Proposal_to_obsolete_%22promoter_binding%22_and_child_terms specific promoter elements] or [http://wiki.geneontology.org/index.php/Proposal_to_obsolete_children_of_%22transcription_factor_binding%22 specific transcription factors])
 +
#* GO:0032792  negative regulation of CREB transcription factor activity
 +
#* GO:0032793  positive regulation of CREB transcription factor activity
 +
#* GO:0007228  positive regulation of hh target transcription factor activity
 +
#* GO:0032088  negative regulation of NF-kappaB transcription factor activity
 +
#* GO:0051092  positive regulation of NF-kappaB transcription factor activity
 +
#* GO:0006985  positive regulation of NF-kappaB transcription factor activity by ER overload response
 +
 +
 +
== <font color="red">OBSOLETE</font>: transcription initiation factor antagonist activity ==
  
def includes binding
 
------
 
 
* GO:0016988    MF      transcription initiation factor antagonist activity
 
* GO:0016988    MF      transcription initiation factor antagonist activity
  
  
related regulation terms
+
== FYI on: ligand-regulated transcription factor activity ==
-------------------------------------------------------
+
 
* GO:0090046    regulation of transcription regulator activity
+
* GO:0003706   MF      ligand-regulated transcription factor activity
* GO:0090047   positive regulation of transcription regulator activity
+
 
* GO:0090048    negative regulation of transcription regulator activity
+
This term is listed here because it is under the '''transcription regulator activity''' branch. Thus other changes proposed here will affect the parentage of this term. Any actions directly to this term will be coordinated with the signalling group, see the [https://sourceforge.net/tracker/?func=detail&aid=3116908&group_id=36855&atid=440764 SF item].
  
 
= Comment Period =
 
= Comment Period =
 +
 +
==<font color="red">OBSOLETE (or MERGE)?</font> 19 Function terms that are equivalent to Process terms==
 +
 +
'''Date mailed:''' 4/13/2011
 +
 +
'''Deadline for Comments:''' TBD -  Unless objections are received by <font color="red">May 3rd</font>, we will assume that you agree to this change.
 +
 +
== <font color="red">OBSOLETE</font>: Regulation terms related to "transcription regulator activity" ==
 +
 +
'''Date mailed:'''
 +
 +
'''Deadline for Comments:''' TBD -  Unless objections are received by <font color="red">May ????</font>, we will assume that you agree to this change.
 +
 +
== <font color="red">OBSOLETE</font>: transcription initiation factor antagonist activity ==
 +
 +
'''Date mailed:'''
 +
 +
'''Deadline for Comments:''' TBD -  Unless objections are received by <font color="red">May ????</font>, we will assume that you agree to this change.
 +
 +
 +
== FYI on: ligand-regulated transcription factor activity ==
  
 
'''Date mailed:'''
 
'''Date mailed:'''
  
'''Deadline for Comments:''' TBD - <font color="red"> Unless objections are received by April ??????, we will assume that you agree to this change. </font>
+
'''Deadline for Comments:'''
  
 
= Problems  =
 
= Problems  =
  
== Function terms with Process definitions ==
+
== Nineteen (19) Function terms with Process definitions ==
 
The problem with most of these terms is the same as that for
 
The problem with most of these terms is the same as that for
 
'''transcription regulator activity''' (GO:0030528). As we said in the
 
'''transcription regulator activity''' (GO:0030528). As we said in the
Line 111: Line 149:
 
* GO:0030401    transcription antiterminator activity
 
* GO:0030401    transcription antiterminator activity
  
== ligand-regulated transcription factor activity ==
 
  
* GO:0003706   MF     ligand-regulated transcription factor activity
+
== Regulation terms related to "transcription regulator activity" ==
 +
 
 +
=== Three terms for immediate obsoletion ===
 +
 
 +
* GO:0090046    regulation of transcription regulator activity
 +
* GO:0090047    positive regulation of transcription regulator activity
 +
* GO:0090048   negative regulation of transcription regulator activity
 +
 
 +
These terms are BP terms for regulation of the MF term '''transcription regulator activity''', but the term they are based on is listed above as one of the terms that is defined only in terms of process. Since the MF term is invalid, we cannot have BP terms based on it. Currently these terms are under the term '''regulation of molecular function''' (GO:0065009) and not under the term '''regulation of biological process''' (GO:0050789), we are hesitant to suggest merging these terms into the '''regulation of transcription, DNA-dependent''' terms. Thus we recommend obsoleting these terms.
 +
 
 +
Of these three terms, only the positive regulation term has any annotations [http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?gptype=all&speciesdb=all&taxid=all&evcode=all&term_assocs=direct&term=GO%3A0090047&session_id=9597amigo1302630235&action=filter via AmiGO].
  
We have initiatied a [https://sourceforge.net/tracker/?func=detail&aid=3116908&group_id=36855&atid=440764 SF item] that the signalling group is also putting some thought into on how to deal with this term.
+
=== Six terms for deferred obsoletion ===
  
In addition to the problems already listed in the SF item, this term will lose all of its is_a parentage when '''transcription regulator activity''' and its other children are removed from MF. Although the definition of the term specificies that it acts on RNAP II transcription, neither the definition or placement of the term specify whether the factor acts through nucleic acid or protein binding. Because of the lack of any requirement in the definition for either DNA (or other nucleic acid) binding or protein binding, this term can not be moved under either of these two branches of transcription factor terms:
+
* GO:0032792  negative regulation of CREB transcription factor activity
* '''nucleic acid binding transcription factor activity''' (GO:0001071)
+
* GO:0032793  positive regulation of CREB transcription factor activity
* '''protein binding transcription factor activity''' (GO:0000988)
+
* GO:0007228  positive regulation of hh target transcription factor activity
 +
* GO:0032088  negative regulation of NF-kappaB transcription factor activity
 +
* GO:0051092  positive regulation of NF-kappaB transcription factor activity
 +
* GO:0006985  positive regulation of NF-kappaB transcription factor activity by ER overload response
  
Until its fate is resolved, I suppose it will have to go directly under '''molecular_function''' (GO:0003674). In order to maintain any sort of "ligand-regulated" distinction, we are going to need more specificity in terms of whether it is acting via protein binding or nucleic acid binding. We may need to obsolete this term and instantiate replacement terms with appropriate specificity.  
+
All 6 of these terms refer to specific transcription factors. Following the same logic for obsoletion of [http://wiki.geneontology.org/index.php/Proposal_to_obsolete_children_of_%22transcription_factor_binding%22 terms for binding to specific transcription factors], we feel that these terms should be obsoleted since it is not sustainable to have regulation terms for every different transcription factor. As we agreed previously for the terms for binding to [http://wiki.geneontology.org/index.php/Proposal_to_obsolete_%22promoter_binding%22_and_child_terms specific promoter elements] or [http://wiki.geneontology.org/index.php/Proposal_to_obsolete_children_of_%22transcription_factor_binding%22 terms for binding to specific transcription factors], we feel that we should also wait to obsolete these terms until a new mechanism for designating transcription factor specificity has been put in place. In the meantime, we will also not create new terms for additional specific transcription factors.
  
[http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0003706&session_id= See existing annotations.]
+
One of these terms, '''positive regulation of NF-kappaB transcription factor activity by ER overload response''' (GO:0006985) contains some information about the process which is involved in the regulation as well as the specific transcription factor that is regulated. We will create a SF item to look further at this term and what it is intended to represent in order to determine whether we need any new term(s) to represent regulation of transcription factors by this specific process. Note though that [http://wiki.geneontology.org/index.php?title=Fate_of_%22transcription_regulator_activity%22_and_its_remaining_child_terms&action=submit#Counts_for_6_BP_terms_slated_for_deferred_obsoletion as of 4/18/2011], [http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0006985&session_id= AmiGO] does not show any annotations for this term.
  
 
== transcription initiation factor antagonist activity ==
 
== transcription initiation factor antagonist activity ==
Line 143: Line 193:
 
<font color="red">Note</font>: '''sigma factor antagonist activity''' (GO:0016989) and '''anti-sigma factor antagonist activity''' (GO:0043856) are direct children of '''transcription factor binding transcription factor activity''' (GO:0000989). They need to be moved further down to reflect that sigma factors are a bacterial-type transcription factor.
 
<font color="red">Note</font>: '''sigma factor antagonist activity''' (GO:0016989) and '''anti-sigma factor antagonist activity''' (GO:0043856) are direct children of '''transcription factor binding transcription factor activity''' (GO:0000989). They need to be moved further down to reflect that sigma factors are a bacterial-type transcription factor.
  
== Regulation terms for "transcription regulator activity" ==
+
== ligand-regulated transcription factor activity ==
 +
 
 +
* GO:0003706    MF      ligand-regulated transcription factor activity
 +
 
 +
We have initiatied a [https://sourceforge.net/tracker/?func=detail&aid=3116908&group_id=36855&atid=440764 SF item] that the signalling group is also putting some thought into on how to deal with this term.
  
* GO:0090046    regulation of transcription regulator activity
+
In addition to the problems already listed in the SF item, this term will lose all of its is_a parentage when '''transcription regulator activity''' and its other children are removed from MF. Although the definition of the term specificies that it acts on RNAP II transcription, neither the definition or placement of the term specify whether the factor acts through nucleic acid or protein binding. Because of the lack of any requirement in the definition for either DNA (or other nucleic acid) binding or protein binding, this term can not be moved under either of these two branches of transcription factor terms:
* GO:0090047    positive regulation of transcription regulator activity
+
* '''nucleic acid binding transcription factor activity''' (GO:0001071)
* GO:0090048    negative regulation of transcription regulator activity
+
* '''protein binding transcription factor activity''' (GO:0000988)
  
These terms are BP terms for regulation of the MF term '''transcription regulator activity''', but the term they are based on is listed above as one of the terms that is defined only in terms of process. Since the MF term is invalid, we cannot have BP terms based on it. Currently these terms are under the term '''regulation of molecular function''' (GO:0065009) and not under the term '''regulation of biological process''' (GO:0050789), we are hesitant to suggest merging these terms into the '''regulation of transcription, DNA-dependent''' terms. Thus we recommend obsoleting these terms.  
+
Until its fate is resolved, I suppose it will have to go directly under '''molecular_function''' (GO:0003674). In order to maintain any sort of "ligand-regulated" distinction, we are going to need more specificity in terms of whether it is acting via protein binding or nucleic acid binding. We may need to obsolete this term and instantiate replacement terms with appropriate specificity.  
  
Of these three terms, only the positive regulation term has any annotations [http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?gptype=all&speciesdb=all&taxid=all&evcode=all&term_assocs=direct&term=GO%3A0090047&session_id=9597amigo1302630235&action=filter via AmiGO].
+
[http://amigo.geneontology.org/cgi-bin/amigo/term-assoc.cgi?term=GO:0003706&session_id= See existing annotations.]
  
 
= Reannotation suggestions =
 
= Reannotation suggestions =
  
==Function terms that are equivalent to Process terms==
+
==For MF terms that are equivalent to BP terms==
  
 
=== For top level MF term: GO:0030528 '''transcription regulator activity'''===
 
=== For top level MF term: GO:0030528 '''transcription regulator activity'''===
Line 260: Line 314:
 
*** <font color="red">for MF reannotation, consider:</font> whether the paper you are looking at describes HOW the termination factor acts. If the paper describes the mechanism of action by which it affects termination, please consider submitting a SF item. However, if the paper only indicates that there is an effect on termination, please consider just making a BP annotation.
 
*** <font color="red">for MF reannotation, consider:</font> whether the paper you are looking at describes HOW the termination factor acts. If the paper describes the mechanism of action by which it affects termination, please consider submitting a SF item. However, if the paper only indicates that there is an effect on termination, please consider just making a BP annotation.
  
 +
== For regulation terms for "transcription regulator activity" ==
  
 +
* '''regulation of transcription regulator activity''' (GO:0090046)
 +
*: - existing term to consider: '''regulation of sequence-specific DNA binding transcription factor activity''' (GO:0051090)
 +
* '''positive regulation of transcription regulator activity''' (GO:0090047)
 +
*: - existing term to consider: '''positive regulation of sequence-specific DNA binding transcription factor activity''' (GO:0051091)
 +
* '''negative regulation of transcription regulator activity''' (GO:0090048)
 +
*: - existing term to consider: '''negative regulation of sequence-specific DNA binding transcription factor activity''' (GO:0043433)
 +
* <font color="red">For all three of these terms</font>:
 +
** Consider if the paper would support annotation to a regulation term for a specific RNAP. If so, please make a SF item regarding creation of such a term.
 +
** Also consider if what you need would be regulation of '''protein binding transcription factor activity''' or any of its child terms instead. If so, please make a SF item regarding creation of such a term.
  
??
+
== For "transcription initiation factor antagonist activity" ==
-----
 
* GO:0003706    MF      ligand-regulated transcription factor activity
 
  
def includes binding
+
* '''transcription initiation factor antagonist activity''' (GO:0016988)
------
+
*: - For reannotation, there are not yet any terms created for "antagonist activities" of any specific eukaryotic transcription systems (for bacterial RNAP, there were already specific terms; these have been moved to more appropriate places in the new MF tree for transcription factor functions).
* GO:0016988    MF      transcription initiation factor antagonist activity
+
*: - To help you think about what types of terms we think we could make for such functions (if they are adequately supported by the evidence), please look at:
 +
*:* '''RNA polymerase II basal transcription factor binding transcription factor activity''' (GO:0001083) and child terms for ideas about the classes of transcription factor binding we are representing. Basically, we have limited specific terms in GO to the basal transcription factors because these are highly conserved and integral to preinitiation complex (PIC) formation. We will not be making terms for every specific transcription factor that exists.
 +
*:* '''RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription''' (GO:0001078) for ideas about the types of MF-BP link terms we are willing to make
 +
*: - If you have evidence supporting creation of a term that binds a specific RNAP II basal transcription factor in order to negatively regulate transcription, please create a SF item about making such a term.
 +
*: - If the paper you are annotating shows only that the gene to be annotated is involved in negative regulation without specifically showing how, consider making a BP annotation.
  
 
+
<font color="red">Note</font>: '''sigma factor antagonist activity''' (GO:0016989) and '''anti-sigma factor antagonist activity''' (GO:0043856) are direct children of '''transcription factor binding transcription factor activity''' (GO:0000989). They need to be moved further down to reflect that sigma factors are a bacterial-type transcription factor.
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 =
 
= Supporting information =
Line 281: Line 342:
 
==Annotation counts==
 
==Annotation counts==
  
 +
=== Counts for terms to be obsoleted now ===
 
via GOOSE (Berkeley BOP) on 3/30/2011
 
via GOOSE (Berkeley BOP) on 3/30/2011
  
 +
 +
==== Summary of GO annotation counts, by annotation source ====
 
<pre>
 
<pre>
=== Summary of GO annotation counts, by source ===
 
 
 
Source............      non-IEA IEA    Grand Total
 
Source............      non-IEA IEA    Grand Total
 
..............ASAP      9      -      9
 
..............ASAP      9      -      9
Line 316: Line 378:
 
</pre>
 
</pre>
  
 +
 +
==== Summary of GO annotation counts, by term ====
 
<pre>
 
<pre>
=== Summary of GO annotation counts, by term ===
 
 
 
GO Term......................................................  aspect  non-IEA IEA    Grand Total
 
GO Term......................................................  aspect  non-IEA IEA    Grand Total
 
.............................transcription regulator activity  MF      1238    62032  63270
 
.............................transcription regulator activity  MF      1238    62032  63270
Line 355: Line 417:
 
Grand Total..................................................          6021    96995  103016
 
Grand Total..................................................          6021    96995  103016
 
</pre>
 
</pre>
 +
 +
=== Counts for 6 BP terms slated for deferred obsoletion ===
 +
via GOOSE (EBI) on 4/18/2011
 +
 +
==== by term ====
 +
<pre>
 +
GO Term.......................................................  non-IEA IEA    Grand Total
 +
.....negative regulation of CREB transcription factor activity  16      4      20
 +
negative regulation of NF-kappaB transcription factor activity  166    74      240
 +
.....positive regulation of CREB transcription factor activity  6      2      8
 +
positive regulation of hh target transcription factor activity  14      6      20
 +
positive regulation of NF-kappaB transcription factor activity  294    256    550
 +
.........positive regulation of NF-kappaB transcription factor  0      0      0
 +
                activity by ER overload response
 +
 +
Grand Total...................................................  496    342    838
 +
</pre>
 +
 +
==== by annotation source ====
 +
<pre>
 +
Source..        non-IEA IEA    Grand Total
 +
.......FB      7      -      7
 +
......MGI      128    -      128
 +
......PDB      39      -      39
 +
......RGD      112    28      140
 +
UniProtKB      205    314    519
 +
.......WB      2      -      2
 +
.....ZFIN      3      -      3
 +
Grand Total    496    342    838
 +
</pre>
 +
  
 
== Subsets ==
 
== Subsets ==

Latest revision as of 15:43, 23 April 2014

Contents

Proposal

OBSOLETE (or MERGE)? 19 Function terms that are equivalent to Process terms

For this set of MF terms that are equivalent to BP terms, we are proposing to obsolete them. In previous cases, e.g. "splicing factor activity", we have merged the MF term into the equivalent BP term. Here, we are instead suggesting obsoletion with a number of options for replacement terms. We are recommending the obsoletion option for two reasons:

  • to highlight the fact that removal of this term from MF may result in a gene having no MF annotations, or a set of MF annotations that is incomplete. Obsoleting instead of merging gives each group greater control over the fate of their annotations.
  • we think it might be better for the non-definition dbxrefs to be reviewed and assigned, if possible, to an appropriate MF term, rather than being transferred (without review) to a BP term.

For reannotation, we will be listing a number of possible terms to consider. One of the suggested replacement term is the equivalent BP term.

  • For groups that wish to transfer all annotations without review, the equivalent BP term is the only appropriate destination.
  • Groups wishing to reannotate to a MF term will need to go back to the original literature or other primary data because the existing "MF" terms are not defined in terms of how they act and there are multiple possibilities.
    - To assist that process, we have suggested which MF terms, and their children, might be appropriate, where such terms exist.
    - In some cases, we have not yet made appropriate MF terms and we ask that annotators submit SF items to request terms if they come across papers that provide insight into the mechanism of action of a given factor, e.g. a "transcription elongation factor". However, please note that a paper showing that factor X has an effect on elongation without providing insight as to HOW that is accomplished mechanistically, may only provide information appropriate for a BP annotation.

NOTE: The decision the group comes to regarding obsoletion versus merging for these MF terms that are equivalent to BP terms will also apply to the 6 MF->BP term merges we proposed previously

Affected terms

  • 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

OBSOLETE: Regulation terms related to "transcription regulator activity"

  1. 3 terms to obsolete now
    • GO:0090046 regulation of transcription regulator activity
    • GO:0090047 positive regulation of transcription regulator activity
    • GO:0090048 negative regulation of transcription regulator activity
  2. 6 terms slated for deferred obsoletion (i.e. at the same time as the terms for binding to specific promoter elements or specific transcription factors)
    • GO:0032792 negative regulation of CREB transcription factor activity
    • GO:0032793 positive regulation of CREB transcription factor activity
    • GO:0007228 positive regulation of hh target transcription factor activity
    • GO:0032088 negative regulation of NF-kappaB transcription factor activity
    • GO:0051092 positive regulation of NF-kappaB transcription factor activity
    • GO:0006985 positive regulation of NF-kappaB transcription factor activity by ER overload response


OBSOLETE: transcription initiation factor antagonist activity

  • GO:0016988 MF transcription initiation factor antagonist activity


FYI on: ligand-regulated transcription factor activity

  • GO:0003706 MF ligand-regulated transcription factor activity

This term is listed here because it is under the transcription regulator activity branch. Thus other changes proposed here will affect the parentage of this term. Any actions directly to this term will be coordinated with the signalling group, see the SF item.

Comment Period

OBSOLETE (or MERGE)? 19 Function terms that are equivalent to Process terms

Date mailed: 4/13/2011

Deadline for Comments: TBD - Unless objections are received by May 3rd, we will assume that you agree to this change.

OBSOLETE: Regulation terms related to "transcription regulator activity"

Date mailed:

Deadline for Comments: TBD - Unless objections are received by May ????, we will assume that you agree to this change.

OBSOLETE: transcription initiation factor antagonist activity

Date mailed:

Deadline for Comments: TBD - Unless objections are received by May ????, we will assume that you agree to this change.


FYI on: ligand-regulated transcription factor activity

Date mailed:

Deadline for Comments:

Problems

Nineteen (19) 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 are essentially identical to BP terms. We are recommending obsoleting these terms with the suggested replacement terms including an equivalent BP term to which all annotations could be transferred without review and, where possible, any appropriate MF terms which should be considered in reannotation from the original literature or data.

  • 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


Regulation terms related to "transcription regulator activity"

Three terms for immediate obsoletion

  • GO:0090046 regulation of transcription regulator activity
  • GO:0090047 positive regulation of transcription regulator activity
  • GO:0090048 negative regulation of transcription regulator activity

These terms are BP terms for regulation of the MF term transcription regulator activity, but the term they are based on is listed above as one of the terms that is defined only in terms of process. Since the MF term is invalid, we cannot have BP terms based on it. Currently these terms are under the term regulation of molecular function (GO:0065009) and not under the term regulation of biological process (GO:0050789), we are hesitant to suggest merging these terms into the regulation of transcription, DNA-dependent terms. Thus we recommend obsoleting these terms.

Of these three terms, only the positive regulation term has any annotations via AmiGO.

Six terms for deferred obsoletion

  • GO:0032792 negative regulation of CREB transcription factor activity
  • GO:0032793 positive regulation of CREB transcription factor activity
  • GO:0007228 positive regulation of hh target transcription factor activity
  • GO:0032088 negative regulation of NF-kappaB transcription factor activity
  • GO:0051092 positive regulation of NF-kappaB transcription factor activity
  • GO:0006985 positive regulation of NF-kappaB transcription factor activity by ER overload response

All 6 of these terms refer to specific transcription factors. Following the same logic for obsoletion of terms for binding to specific transcription factors, we feel that these terms should be obsoleted since it is not sustainable to have regulation terms for every different transcription factor. As we agreed previously for the terms for binding to specific promoter elements or terms for binding to specific transcription factors, we feel that we should also wait to obsolete these terms until a new mechanism for designating transcription factor specificity has been put in place. In the meantime, we will also not create new terms for additional specific transcription factors.

One of these terms, positive regulation of NF-kappaB transcription factor activity by ER overload response (GO:0006985) contains some information about the process which is involved in the regulation as well as the specific transcription factor that is regulated. We will create a SF item to look further at this term and what it is intended to represent in order to determine whether we need any new term(s) to represent regulation of transcription factors by this specific process. Note though that as of 4/18/2011, AmiGO does not show any annotations for this term.

transcription initiation factor antagonist activity

  • GO:0016988 MF transcription initiation factor antagonist activity

This term isn't even defined in a way that is consistent with its own name:

Def: The function of binding to a transcription factor and stopping, preventing 
or reducing the rate of its transcriptional activity.

We are also not representing "initiation factors" as a class in the MF ontology. Historically, this term was originally the parent term of sigma factor antagonist activity (GO:0016989). While we can keep the sigma factor terms as defining a specific class of molecules that act in a specific way, we cannot define all initiation factors as acting via a specific mechanism, so we cannot keep this term.

We recommend obsoleting with some suggestions for terms to consider, as well as considering to request additional terms as we have not yet created very many MF terms that have the positive or negative regulation or transcription aspects encoded within them, though we have done this in some areas are will create more as appropriate.

See existing annotations.

Note: sigma factor antagonist activity (GO:0016989) and anti-sigma factor antagonist activity (GO:0043856) are direct children of transcription factor binding transcription factor activity (GO:0000989). They need to be moved further down to reflect that sigma factors are a bacterial-type transcription factor.

ligand-regulated transcription factor activity

  • GO:0003706 MF ligand-regulated transcription factor activity

We have initiatied a SF item that the signalling group is also putting some thought into on how to deal with this term.

In addition to the problems already listed in the SF item, this term will lose all of its is_a parentage when transcription regulator activity and its other children are removed from MF. Although the definition of the term specificies that it acts on RNAP II transcription, neither the definition or placement of the term specify whether the factor acts through nucleic acid or protein binding. Because of the lack of any requirement in the definition for either DNA (or other nucleic acid) binding or protein binding, this term can not be moved under either of these two branches of transcription factor terms:

  • nucleic acid binding transcription factor activity (GO:0001071)
  • protein binding transcription factor activity (GO:0000988)

Until its fate is resolved, I suppose it will have to go directly under molecular_function (GO:0003674). In order to maintain any sort of "ligand-regulated" distinction, we are going to need more specificity in terms of whether it is acting via protein binding or nucleic acid binding. We may need to obsolete this term and instantiate replacement terms with appropriate specificity.

See existing annotations.

Reannotation suggestions

For MF terms that are equivalent to BP terms

For top level MF term: GO:0030528 transcription regulator activity

  • transcription regulator activity (GO:0030528)
    • equivalent BP term = transcription, DNA-dependent (GO:0006351)
      • Existing definition already specifies DNA, so we can focus on "transcription, DNA-dependent" terms without being concerned about the RNA-dependent type of transcription.
      • For the equivalent process term, we considered both transcription, DNA-dependent (GO:0006351) and regulation of transcription, DNA-dependent (GO:0006355) and we looked at some existing annotations to transcription regulator activity to consider which of these two terms would be most appropriate to transfer them to. While the majority of annotations (from both MGI and SGD) are "regulatory" transcription factors, the SGD set of annotations, which was small enough to look at in its entirety, includes annotations for basal transcription factors and RNA polymerase subunits, via both manual and computational methods. Thus, we felt that the term has been used so broadly that it would be better to select the more general term.
    • for MF reannotation, consider:
      • nucleic acid binding transcription factor activity (GO:0001071) and child terms
      • protein binding transcription factor activity (GO:0000988) and child terms
      • Annotators for eukaryotic organisms, should specifically look to see if they can make the annotation specific to a particular RNA polymerase. If the paper does not specifically mention an RNA polymerase and talks only about regulation of specific genes, you should consider if you can make the annotation specific to RNAP II, particularly if the genes are nuclear (not organellar) protein-coding genes. There are so few exceptions to the generalization that RNAP II transcribes mRNAs for nuclear-encoded protein coding genes, that unless you are annotating Trypanosome genes, it is extremely likely that anyone discussing transcription of a protein coding genes is talking about RNAP II, but if they are more interested in the regulator than the RNAP (many researchers are), they may not mention that it is RNAP II.

For other high level terms, not specific to a particular RNAP

Comments on selection of equivalent BP term

  • These definitions do not mention DNA specifically, but the terms are direct children of "transcription regulator activity".
  • Based on a quick glance at some of the annotations and the logic we used for the merge of the transcription BP terms into the transcription, DNA-dependent BP terms, we think this is reasonable, i.e. that there will be very little which should actually be annotated to a transcription, RNA-dependent term instead.

Terms

  • GO:0016563 transcription activator activity
    • equivalent BP term = positive regulation of transcription, DNA-dependent (GO:0045893)
    • for MF reannotation, consider:
      • nucleic acid binding transcription factor activity (GO:0001071) and child terms
      • protein binding transcription factor activity (GO:0000988) and child terms
    • Annotators for eukaryotic organisms, should specifically look to see if they can make the annotation specific to a particular RNA polymerase. If the paper does not specifically mention an RNA polymerase and talks only about regulation of specific genes, you should consider if you can make the annotation specific to RNAP II, particularly if the genes are nuclear (not organellar) protein-coding genes. There are so few exceptions to the generalization that RNAP II transcribes mRNAs for nuclear-encoded protein coding genes, that unless you are annotating Trypanosome genes, it is extremely likely that anyone discussing transcription of a protein coding genes is talking about RNAP II, but if they are more interested in the regulator than the RNAP (many researchers are), they may not mention that it is RNAP II.
  • GO:0016564 transcription repressor activity
    • equivalent BP term = negative regulation of transcription, DNA-dependent (GO:0045892)
    • for MF reannotation, consider:
      • nucleic acid binding transcription factor activity (GO:0001071) and child terms
      • protein binding transcription factor activity (GO:0000988) and child terms
    • Annotators for eukaryotic organisms, should specifically look to see if they can make the annotation specific to a particular RNA polymerase. If the paper does not specifically mention an RNA polymerase and talks only about regulation of specific genes, you should consider if you can make the annotation specific to RNAP II, particularly if the genes are nuclear (not organellar) protein-coding genes. There are so few exceptions to the generalization that RNAP II transcribes mRNAs for nuclear-encoded protein coding genes, that unless you are annotating Trypanosome genes, it is extremely likely that anyone discussing transcription of a protein coding genes is talking about RNAP II, but if they are more interested in the regulator than the RNAP (many researchers are), they may not mention that it is RNAP II.
  • GO:0003711 transcription elongation regulator activity
    • equivalent BP term = regulation of transcription elongation, DNA-dependent (GO:0032784)
    • for MF reannotation, consider: whether the paper you are looking at describes HOW the elongation factor acts. If the paper describes the mechanism of action by which it affects elongation, please consider submitting a SF item. However, if the paper only indicates that there is an effect on elongation, please consider just making a BP annotation.
  • GO:0008148 negative transcription elongation factor activity
    • equivalent BP term = negative regulation of transcription elongation, DNA-dependent (GO:0032785)
    • for MF reannotation, consider: whether the paper you are looking at describes HOW the elongation factor acts. If the paper describes the mechanism of action by which it affects elongation, please consider submitting a SF item. However, if the paper only indicates that there is an effect on elongation, please consider just making a BP annotation.
  • GO:0008159 positive transcription elongation factor activity
    • equivalent BP term = positive regulation of transcription elongation, DNA-dependent (GO:0032786)
    • for MF reannotation, consider: whether the paper you are looking at describes HOW the elongation factor acts. If the paper describes the mechanism of action by which it affects elongation, please consider submitting a SF item. However, if the paper only indicates that there is an effect on elongation, please consider just making a BP annotation.
  • GO:0016986 transcription initiation factor activity
    • equivalent BP term = transcription initiation, DNA-dependent (GO:0006352)
    • for MF reannotation, consider:
      • nucleic acid binding transcription factor activity (GO:0001071) and child terms
      • protein binding transcription factor activity (GO:0000988) and child terms
      • such as core RNA polymerase binding promoter specificity activity (GO:0000996), and child terms (for bacterial type enzymes, including mitochondrial and some plastid RNAPs)
  • GO:0003715 transcription termination factor activity
    • equivalent BP term = transcription termination, DNA-dependent (GO:0006353)
    • for MF reannotation, consider: whether the paper you are looking at describes HOW the termination factor acts. If the paper describes the mechanism of action by which it affects termination, please consider submitting a SF item. However, if the paper only indicates that there is an effect on termination, please consider just making a BP annotation.
  • GO:0030401 transcription antiterminator activity
    • equivalent BP term = ??? transcription antitermination (GO:0031564) or regulation of transcription termination, DNA-dependent (GO:0031554)
      - I could use some guidance from prokaryotic annotators on whether the more specific term with a more comparable name is appropriate or whether it is necessary to go up to the more general term. Via AmiGO, I think all existing annotations are for prokaryotic genes.
      - Note that we think there is a structural issue in BP, that "transcription antitermination" should be a sibling rather than a child of "transcriptional attenuation"
    • for MF reannotation, consider: requesting RNAP specific children under one of these terms
      • DNA binding transcription antitermination factor activity (GO:0001073)
      • RNA binding transcription antitermination factor activity (GO:0001072)

Terms for transcription factors for specific (eukaryotic nuclear) RNAPs

These terms all mention specific eukaryotic nuclear RNA polymerases, so there is no confusion with respect to DNA-dependent vs RNA-dependent (they are all under the DNA-dependent branch).

  • Three terms for specific RNAPs, but not specific to which part of the transcription cycle is affected:
    - The definitions of these terms say "Functions to initiate or regulate RNA polymerase ____ transcription." Thus these definitions encompass both the basal and regulatory factors required for preinitiation complex (PIC) assembly as well as any factors which might regulate transcription by one of these RNAPs. Thus we think that the general terms are a better option than the regulation terms. Since PIC assembly is part of initiation, most of the MF terms I am suggesting relate to the initiation portions of the transcription cycle. However, if the gene you are reannotating affects elongation of termination, please see the reannotation suggestions for the elongation and termination terms below.
    • GO:0003701 RNA polymerase I transcription factor activity
      • equivalent BP term = transcription from RNA polymerase I promoter (GO:0006360)
      • for MF reannotation, consider:
        • sequence-specific DNA binding RNA polymerase I transcription factor activity (GO:0001167) and child terms
        • requesting a more specific term under protein binding transcription factor activity (GO:0000988)
    • GO:0003702 RNA polymerase II transcription factor activity
      • equivalent BP term =: transcription from RNA polymerase II promoter (GO:0006366)
      • for MF reannotation, consider:
        • sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981) and child terms
        • the RNAP II specific terms under protein binding transcription factor activity (GO:0000988), particularly:
          - core RNA polymerase II binding transcription factor activity (GO:0000991)
          - RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)
    • GO:0003709 RNA polymerase III transcription factor activity
      • equivalent BP term =: transcription from RNA polymerase III promoter (GO:0006383)
      • for MF reannotation, consider:
        • sequence-specific DNA binding RNA polymerase III transcription factor activity (GO:0001034) and child terms
        • the RNAP II specific terms under protein binding transcription factor activity (GO:0000988), particularly:
          - core RNA polymerase III binding transcription factor activity (GO:0000995)
          - RNA polymerase III transcription factor binding transcription factor activity (GO:0001007)
  • RNAP specific terms for "elongation factor activity"
    - These three terms are all children of transcription elongation regulator activity (GO:0003711) and the definitions specify "Any activity that modulates the rate of transcription elongation, the addition of ribonucleotides to an RNA molecule catalyzed by RNA polymerase _____ following transcription initiation.", which would seem to suggest selecting "regulation of transcription elongation" terms as the equivalents. However, I think this term has been used for a mix of things that are directly part of the transcription machinery and things that exert their effects more indirectly, so I have selected the "transcription elongation" terms. In addition, it doesn't look like we have regulation of transcription elongation terms for RNAPs I or III.
    • RNA polymerase I transcription elongation factor activity (GO:0016943)
      • equivalent BP term =: transcription elongation from RNA polymerase I promoter (GO:0006362)
      • for MF reannotation, consider: whether the paper you are looking at describes HOW the elongation factor acts. If the paper describes the mechanism of action by which it affects elongation, please consider submitting a SF item. However, if the paper only indicates that there is an effect on elongation, please consider just making a BP annotation.
    • RNA polymerase II transcription elongation factor activity (GO:0016944)
      • equivalent BP term =: transcription elongation from RNA polymerase II promoter (GO:0006368)
      • for MF reannotation, consider: whether the paper you are looking at describes HOW the elongation factor acts. If the paper describes the mechanism of action by which it affects elongation, please consider submitting a SF item. However, if the paper only indicates that there is an effect on elongation, please consider just making a BP annotation.
    • RNA polymerase III transcription elongation factor activity (GO:0016945)
      • equivalent BP term =: transcription elongation from RNA polymerase III promoter (GO:0006385)
      • for MF reannotation, consider: whether the paper you are looking at describes HOW the elongation factor acts. If the paper describes the mechanism of action by which it affects elongation, please consider submitting a SF item. However, if the paper only indicates that there is an effect on elongation, please consider just making a BP annotation.
  • RNAP specific terms for "termination factor activity"
    - These three terms are all children of transcription termination, DNA-dependent (GO:0006353) and the definitions specify "Any activity that brings about termination of transcription by RNA polymerase ____." which is broad enough to encompass activities that are part of the transcription machinery as well as purely regulatory activities, so we have chosen the "transcription termination" terms, rather than regulatory terms. In addition, it doesn't look like we have regulation of transcription elongation terms for RNAPs I, II, or III.
    • RNA polymerase I transcription termination factor activity (GO:0003716)
      • equivalent BP term =: termination of RNA polymerase I transcription (GO:0006363)
      • for MF reannotation, consider: whether the paper you are looking at describes HOW the termination factor acts. If the paper describes the mechanism of action by which it affects termination, please consider submitting a SF item. However, if the paper only indicates that there is an effect on termination, please consider just making a BP annotation.
    • RNA polymerase II transcription termination factor activity (GO:0003717)
      • equivalent BP term =: termination of RNA polymerase II transcription (GO:0006369)
      • for MF reannotation, consider: whether the paper you are looking at describes HOW the termination factor acts. If the paper describes the mechanism of action by which it affects termination, please consider submitting a SF item. However, if the paper only indicates that there is an effect on termination, please consider just making a BP annotation.
    • RNA polymerase III transcription termination factor activity (GO:0003718)
      • equivalent BP term =: termination of RNA polymerase III transcription (GO:0006386)
      • for MF reannotation, consider: whether the paper you are looking at describes HOW the termination factor acts. If the paper describes the mechanism of action by which it affects termination, please consider submitting a SF item. However, if the paper only indicates that there is an effect on termination, please consider just making a BP annotation.

For regulation terms for "transcription regulator activity"

  • regulation of transcription regulator activity (GO:0090046)
    - existing term to consider: regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)
  • positive regulation of transcription regulator activity (GO:0090047)
    - existing term to consider: positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)
  • negative regulation of transcription regulator activity (GO:0090048)
    - existing term to consider: negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)
  • For all three of these terms:
    • Consider if the paper would support annotation to a regulation term for a specific RNAP. If so, please make a SF item regarding creation of such a term.
    • Also consider if what you need would be regulation of protein binding transcription factor activity or any of its child terms instead. If so, please make a SF item regarding creation of such a term.

For "transcription initiation factor antagonist activity"

  • transcription initiation factor antagonist activity (GO:0016988)
    - For reannotation, there are not yet any terms created for "antagonist activities" of any specific eukaryotic transcription systems (for bacterial RNAP, there were already specific terms; these have been moved to more appropriate places in the new MF tree for transcription factor functions).
    - To help you think about what types of terms we think we could make for such functions (if they are adequately supported by the evidence), please look at:
    • RNA polymerase II basal transcription factor binding transcription factor activity (GO:0001083) and child terms for ideas about the classes of transcription factor binding we are representing. Basically, we have limited specific terms in GO to the basal transcription factors because these are highly conserved and integral to preinitiation complex (PIC) formation. We will not be making terms for every specific transcription factor that exists.
    • RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078) for ideas about the types of MF-BP link terms we are willing to make
    - If you have evidence supporting creation of a term that binds a specific RNAP II basal transcription factor in order to negatively regulate transcription, please create a SF item about making such a term.
    - If the paper you are annotating shows only that the gene to be annotated is involved in negative regulation without specifically showing how, consider making a BP annotation.

Note: sigma factor antagonist activity (GO:0016989) and anti-sigma factor antagonist activity (GO:0043856) are direct children of transcription factor binding transcription factor activity (GO:0000989). They need to be moved further down to reflect that sigma factors are a bacterial-type transcription factor.

Supporting information

Annotation counts

Counts for terms to be obsoleted now

via GOOSE (Berkeley BOP) on 3/30/2011


Summary of GO annotation counts, by annotation 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

Counts for 6 BP terms slated for deferred obsoletion

via GOOSE (EBI) on 4/18/2011

by term

GO Term.......................................................  non-IEA IEA     Grand Total
.....negative regulation of CREB transcription factor activity  16      4       20
negative regulation of NF-kappaB transcription factor activity  166     74      240
.....positive regulation of CREB transcription factor activity  6       2       8
positive regulation of hh target transcription factor activity  14      6       20
positive regulation of NF-kappaB transcription factor activity  294     256     550
.........positive regulation of NF-kappaB transcription factor  0       0       0
                activity by ER overload response

Grand Total...................................................  496     342     838

by annotation source

Source..        non-IEA IEA     Grand Total
.......FB       7       -       7
......MGI       128     -       128
......PDB       39      -       39
......RGD       112     28      140
UniProtKB       205     314     519
.......WB       2       -       2
.....ZFIN       3       -       3
Grand Total     496     342     838


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


Sample of existing annotations to transcription regulator activity

downloaded from SGD April 2011

Manual annotations for S. cerevisiae genes

Gene                            Annot
Name    Evidence        Date    Source  Description
BRE2    ISS             4/2/03  SGD     Subunit of COMPASS (Set1C) complex, which methylates Lys4 of histone H3 and functions in silencing at telomeres
ASK10   TAS             3/11/03 SGD     Component of RNA polymerase II holoenzyme, phosphorylated in response to oxidative stress
RLF2    IMP             2/16/05 SGD     Largest subunit (p90) of the Chromatin Assembly Complex (CAF-1) with Cac2p and Msi1p that assembles newly synthesized histones onto recently replicated DNA
DEP1    IMP             2/9/06  SGD     Transcriptional modulator involved in regulation of structural phospholipid biosynthesis genes and metabolically unrelated genes, as well as maintenance of telomeres, mating efficiency, and sporulation
BDF1    ISS|IMP         3/11/03 SGD     Protein involved in transcription initiation at TATA-containing promoters
UME6    IMP|IDA         2/26/02 SGD     Key transcriptional regulator of early meiotic genes, binds URS1 upstream regulatory sequence, couples metabolic responses to nutritional cues with initiation and progression of meiosis, forms complex with Ime1p, and also with Sin3p-Rpd3p
UME6    IMP|IDA         2/26/02 SGD     Key transcriptional regulator of early meiotic genes, binds URS1 upstream regulatory sequence, couples metabolic responses to nutritional cues with initiation and progression of meiosis, forms complex with Ime1p, and also with Sin3p-Rpd3p
IME1    TAS             3/11/03 SGD     Master regulator of meiosis that is active only during meiotic events, activates transcription of early meiotic genes through interaction with Ume6p, degraded by the 26S proteasome following phosphorylation by Ime2p
MSI1    IMP             2/16/05 SGD     Subunit of chromatin assembly factor I (CAF-1), negative regulator of the RAS/cAMP pathway via sequestration of Npr1p kinase
LAP3    IDA             9/30/02 SGD     Cysteine aminopeptidase with homocysteine-thiolactonase activity
SUS1    IDA             2/17/09 SGD     Protein involved in mRNA export coupled transcription activation and elongation
GTS1    IDA|IPI         4/14/08 SGD     Arf3p GTPase Activating Protein (GAP) that localizes to endocytic patches
RTG2    IDA             5/8/03  SGD     Sensor of mitochondrial dysfunction
LRE1    IDA             10/1/02 SGD     Protein involved in control of cell wall structure and stress response
CAC2    IMP             2/16/05 SGD     Component of the chromatin assembly complex (with Rlf2p and Msi1p) that assembles newly synthesized histones onto recently replicated DNA, required for building functional kinetochores, conserved from yeast to humans

Computational annotations for S. cerevisiae genes

Gene                                                                    Annot
Name    Ev Code With (or) From                                  Date    Source          Description
YOX1    IEA     EBI:IPR017970                                   1/10/11 InterPro        Homeodomain-containing transcriptional repressor, binds to Mcm1p and to early cell cycle boxes (ECBs) in the promoters of cell cycle-regulated genes expressed in M/G1 phase
YHP1    IEA     EBI:IPR017970                                   1/10/11 InterPro        One of two homeobox transcriptional repressors (see also Yox1p), that bind to Mcm1p and to early cell cycle box (ECB) elements of cell cycle regulated genes, thereby restricting ECB-mediated transcription to the M/G1 interval
PHO2    IEA     EBI:IPR017970                                   1/10/11 InterPro        Homeobox transcription factor
RPA12   IEA     EBI:IPR001222                                   1/10/11 InterPro        RNA polymerase I subunit A12.2
RPB9    IEA     EBI:IPR001222                                   1/10/11 InterPro        RNA polymerase II subunit B12.6
TYE7    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Serine-rich protein that contains a basic-helix-loop-helix (bHLH) DNA binding motif
MAF1    IEA     EBI:IPR017152                                   1/10/11 InterPro        Negative regulator of RNA polymerase III
INO2    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Component of the heteromeric Ino2p/Ino4p basic helix-loop-helix transcription activator that binds inositol/choline-responsive elements (ICREs), required for derepression of phospholipid biosynthetic genes in response to inositol depletion
HAP4    IEA     EBI:IPR018287                                   1/10/11 InterPro        Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression
HMRA1   IEA     EBI:IPR017970                                   1/10/11 InterPro        Silenced copy of a1 at HMR
DST1    IEA     EBI:IPR001222|EBI:IPR010990                     1/10/11 InterPro        General transcription elongation factor TFIIS, enables RNA polymerase II to read through blocks to elongation by stimulating cleavage of nascent transcripts stalled at transcription arrest sites
HIR1    IEA     EBI:IPR011494|EBI:IPR019015                     1/10/11 InterPro        Subunit of the HIR complex, a nucleosome assembly complex involved in regulation of histone gene transcription
YAP7    IEA     EBI:IPR018287                                   1/10/11 InterPro        Putative basic leucine zipper (bZIP) transcription factor
PHO4    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Basic helix-loop-helix (bHLH) transcription factor of the myc-family
CDC36   IEA     EBI:IPR007282                                   1/10/11 InterPro        Component of the CCR4-NOT complex, which has multiple roles in regulating mRNA levels including regulation of transcription and destabilizing mRNAs by deadenylation
RTG1    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Transcription factor (bHLH) involved in interorganelle communication between mitochondria, peroxisomes, and nucleus
YKR023W IEA     EBI:IPR009349                                   1/10/11 InterPro        Putative protein of unknown function
RPL7A   IEA     EBI:IPR005998                                   1/10/11 InterPro        Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins
HIR2    IEA     EBI:IPR011494                                   1/10/11 InterPro        Subunit of the HIR complex, a nucleosome assembly complex involved in regulation of histone gene transcription
NOT5    IEA     EBI:IPR007282|EBI:IPR007207|EBI:IPR012270       1/10/11 InterPro        Subunit of the CCR4-NOT complex, which is a global transcriptional regulator with roles in transcription initiation and elongation and in mRNA degradation
RTG3    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Basic helix-loop-helix-leucine zipper (bHLH/Zip) transcription factor that forms a complex with another bHLH/Zip protein, Rtg1p, to activate the retrograde (RTG) and TOR pathways
RPL7B   IEA     EBI:IPR005998                                   1/10/11 InterPro        Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Ap and has similarity to E. coli L30 and rat L7 ribosomal proteins
HMS1    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Basic helix-loop-helix (bHLH) protein with similarity to myc-family transcription factors
CBF1    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Helix-loop-helix protein that binds the motif CACRTG, which is present at several sites including MET gene promoters and centromere DNA element I (CDEI)
TAF5    IEA     EBI:IPR007582                                   1/10/11 InterPro        Subunit (90 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification
INO4    IEA     EBI:IPR001092|EBI:IPR011598                     1/10/11 InterPro        Transcription factor required for derepression of inositol-choline-regulated genes involved in phospholipid synthesis
RPC11   IEA     EBI:IPR001222                                   1/10/11 InterPro        RNA polymerase III subunit C11
NOT3    IEA     EBI:IPR007282|EBI:IPR007207|EBI:IPR012270       1/10/11 InterPro        Subunit of the CCR4-NOT complex, which is a global transcriptional regulator with roles in transcription initiation and elongation and in mRNA degradation
SUA7    IEA     EBI:IPR000812                                   1/10/11 InterPro        Transcription factor TFIIB, a general transcription factor required for transcription initiation and start site selection by RNA polymerase II
BRF1    IEA     EBI:IPR000812                                   1/10/11 InterPro        TFIIIB B-related factor, one of three subunits of RNA polymerase III transcription initiation factor TFIIIB, binds TFIIIC and TBP and recruits RNA pol III to promoters, amino-terminal half is homologous to TFIIB

Non-definition dbxrefs

GO:0030528 transcription regulator activity

  • COG:K
  • HAMAP:MF_01132
  • HAMAP:MF_01181
  • InterPro:IPR000812
  • InterPro:IPR001092
  • InterPro:IPR001222
  • InterPro:IPR005559
  • InterPro:IPR005998
  • InterPro:IPR006377
  • InterPro:IPR006417
  • InterPro:IPR006699
  • InterPro:IPR006793
  • InterPro:IPR006794
  • InterPro:IPR006923
  • InterPro:IPR006957
  • InterPro:IPR007127
  • InterPro:IPR007207
  • InterPro:IPR007282
  • InterPro:IPR007324
  • InterPro:IPR007448
  • InterPro:IPR007576
  • InterPro:IPR007582
  • InterPro:IPR007668
  • InterPro:IPR007684
  • InterPro:IPR007738
  • InterPro:IPR007790
  • InterPro:IPR007933
  • InterPro:IPR008095
  • InterPro:IPR008116
  • InterPro:IPR008246
  • InterPro:IPR008247
  • InterPro:IPR008329
  • InterPro:IPR008648
  • InterPro:IPR009170
  • InterPro:IPR009184
  • InterPro:IPR009349
  • InterPro:IPR010213
  • InterPro:IPR010214
  • InterPro:IPR010533
  • InterPro:IPR011075
  • InterPro:IPR011494
  • InterPro:IPR011520
  • InterPro:IPR011598
  • InterPro:IPR011663
  • InterPro:IPR012270
  • InterPro:IPR012642
  • InterPro:IPR012925
  • InterPro:IPR016375
  • InterPro:IPR016481
  • InterPro:IPR017152
  • InterPro:IPR017923
  • InterPro:IPR017970
  • InterPro:IPR018287
  • InterPro:IPR019015
  • JCVI_TIGRFAMS:TIGR00244
  • JCVI_TIGRFAMS:TIGR02702
  • JCVI_TIGRFAMS:TIGR02844
  • JCVI_TIGRFAMS:TIGR02974
  • Pfam:PF00010
  • Pfam:PF01096
  • Pfam:PF03859
  • Pfam:PF03979
  • Pfam:PF04065
  • Pfam:PF04153
  • Pfam:PF04198
  • Pfam:PF04309
  • Pfam:PF04353
  • Pfam:PF04487
  • Pfam:PF04494
  • Pfam:PF04589
  • Pfam:PF04606
  • Pfam:PF04704
  • Pfam:PF04838
  • Pfam:PF04873
  • Pfam:PF05044
  • Pfam:PF05098
  • Pfam:PF05269
  • Pfam:PF05459
  • Pfam:PF06221
  • Pfam:PF06529
  • Pfam:PF07545
  • Pfam:PF07569
  • Pfam:PF07702
  • Pfam:PF07739
  • Pfam:PF07988
  • Pfam:PF08711
  • Pfam:PF09453
  • Pfam:PF10297
  • PIRSF:PIRSF002395
  • PIRSF:PIRSF003028
  • PIRSF:PIRSF005259
  • PIRSF:PIRSF005290
  • PIRSF:PIRSF006171
  • PIRSF:PIRSF006198
  • PIRSF:PIRSF006373
  • PIRSF:PIRSF016548
  • PIRSF:PIRSF036385
  • PIRSF:PIRSF037240
  • PRINTS:PR00685
  • PRINTS:PR01719
  • PRINTS:PR01743
  • ProDom:PD007170
  • PROSITE:MF_01909
  • PROSITE:PS00027
  • PROSITE:PS00466
  • PROSITE:PS50888
  • PROSITE:PS51133
  • PROSITE:PS51319
  • PROSITE:PS51437
  • SMART:SM00353
  • SMART:SM00440
  • SMART:SM00866

GO:0016563 transcription activator activity

  • HAMAP:MF_01449
  • InterPro:IPR004120
  • InterPro:IPR004247
  • InterPro:IPR004619
  • InterPro:IPR004956
  • InterPro:IPR004998
  • InterPro:IPR005022
  • InterPro:IPR005205
  • InterPro:IPR005206
  • InterPro:IPR006711
  • InterPro:IPR006712
  • InterPro:IPR006897
  • InterPro:IPR006898
  • InterPro:IPR006899
  • InterPro:IPR007031
  • InterPro:IPR007532
  • InterPro:IPR007786
  • InterPro:IPR007911
  • InterPro:IPR007944
  • InterPro:IPR008013
  • InterPro:IPR008851
  • InterPro:IPR009508
  • InterPro:IPR010113
  • InterPro:IPR011399
  • InterPro:IPR011420
  • InterPro:IPR011665
  • InterPro:IPR011789
  • InterPro:IPR012787
  • InterPro:IPR012794
  • InterPro:IPR020357
  • InterPro:IPR023559
  • JCVI_TIGRFAMS:TIGR01481
  • JCVI_TIGRFAMS:TIGR01716
  • JCVI_TIGRFAMS:TIGR02051
  • JCVI_TIGRFAMS:TIGR02424
  • MIPS_funcat:11.02.03.04.01
  • MultiFun:3.1.2.2
  • Pfam:PF02959
  • Pfam:PF02998
  • Pfam:PF03274
  • Pfam:PF03309
  • Pfam:PF03326
  • Pfam:PF03355
  • Pfam:PF03584
  • Pfam:PF03585
  • Pfam:PF04441
  • Pfam:PF04617
  • Pfam:PF04618
  • Pfam:PF04812
  • Pfam:PF04813
  • Pfam:PF04814
  • Pfam:PF04947
  • Pfam:PF05094
  • Pfam:PF05247
  • Pfam:PF05280
  • Pfam:PF05349
  • Pfam:PF05793
  • Pfam:PF06573
  • Pfam:PF07180
  • Pfam:PF07573
  • Pfam:PF07741
  • PIRSF:PIRSF003159
  • PIRSF:PIRSF036354
  • ProDom:PD007233
  • ProDom:PD011171
  • ProDom:PD015582
  • ProDom:PD016592
  • ProDom:PD081346
  • ProDom:PD355092
  • PROSITE:MF_00725
  • PROSITE:MF_01274
  • Reactome:9388

GO:0042156 zinc-mediated transcriptional activator activity

  • JCVI_TIGRFAMS:TIGR02043

GO:0016564 transcription repressor activity

  • HAMAP:MF_00081
  • HAMAP:MF_00440
  • HAMAP:MF_00475
  • HAMAP:MF_00621
  • HAMAP:MF_00744
  • HAMAP:MF_01180
  • HAMAP:MF_01277
  • HAMAP:MF_01449
  • HAMAP:MF_01563
  • InterPro:IPR003796
  • InterPro:IPR004409
  • InterPro:IPR005569
  • InterPro:IPR006986
  • InterPro:IPR006988
  • InterPro:IPR006989
  • InterPro:IPR007412
  • InterPro:IPR009718
  • InterPro:IPR010078
  • InterPro:IPR010248
  • InterPro:IPR010312
  • InterPro:IPR010575
  • InterPro:IPR010712
  • InterPro:IPR010744
  • InterPro:IPR011350
  • InterPro:IPR011373
  • InterPro:IPR012712
  • InterPro:IPR013335
  • InterPro:IPR013573
  • InterPro:IPR014160
  • JCVI_TIGRFAMS:TIGR01321
  • JCVI_TIGRFAMS:TIGR01481
  • JCVI_TIGRFAMS:TIGR01529
  • JCVI_TIGRFAMS:TIGR01848
  • JCVI_TIGRFAMS:TIGR02040
  • JCVI_TIGRFAMS:TIGR02054
  • JCVI_TIGRFAMS:TIGR02655
  • JCVI_TIGRFAMS:TIGR02698
  • JCVI_TIGRFAMS:TIGR02793
  • JCVI_TIGRFAMS:TIGR02944
  • JCVI_TIGRFAMS:TIGR03298
  • MIPS_funcat:11.02.03.04.03
  • MultiFun:3.1.2.3
  • Pfam:PF03869
  • Pfam:PF04316
  • Pfam:PF04902
  • Pfam:PF04904
  • Pfam:PF04905
  • Pfam:PF06018
  • Pfam:PF06613
  • Pfam:PF06953
  • Pfam:PF06971
  • Pfam:PF07022
  • Pfam:PF08362
  • PIRSF:PIRSF000197
  • PIRSF:PIRSF003196
  • PIRSF:PIRSF003228
  • ProDom:PD012582
  • ProDom:PD342192
  • PROSITE:MF_00440
  • PROSITE:MF_00475

GO:0003711 transcription elongation regulator activity

  • HAMAP:MF_00105
  • InterPro:IPR001062
  • InterPro:IPR001437
  • InterPro:IPR006358
  • InterPro:IPR006359
  • InterPro:IPR006645
  • InterPro:IPR010215
  • InterPro:IPR010216
  • InterPro:IPR012243
  • InterPro:IPR016492
  • InterPro:IPR017071
  • InterPro:IPR017072
  • InterPro:IPR018151
  • InterPro:IPR022691
  • JCVI_TIGRFAMS:TIGR01385
  • JCVI_TIGRFAMS:TIGR01461
  • JCVI_TIGRFAMS:TIGR01462
  • Pfam:PF01272
  • Pfam:PF02357
  • Pfam:PF03449
  • PIRSF:PIRSF006092
  • PIRSF:PIRSF006704
  • PIRSF:PIRSF036945
  • PIRSF:PIRSF036947
  • PRINTS:PR00338
  • PROSITE:PS00829
  • PROSITE:PS00830
  • SMART:SM00738

GO:0008159 positive transcription elongation factor activity

  • InterPro:IPR009287
  • PIRSF:PIRSF025023

GO:0016986 transcription initiation factor activity

  • HAMAP:MF_01909
  • InterPro:IPR003228
  • InterPro:IPR004823
  • InterPro:IPR007900
  • InterPro:IPR011442
  • Pfam:PF02969
  • Pfam:PF03847
  • Pfam:PF05236
  • Pfam:PF07571
  • SMART:SM00803

GO:0003715 transcription termination factor activity

  • HAMAP:MF_01884
  • InterPro:IPR004665
  • InterPro:IPR011112
  • InterPro:IPR011113
  • InterPro:IPR011605
  • JCVI_TIGRFAMS:TIGR00767
  • JCVI_TIGRFAMS:TIGR00922
  • JCVI_TIGRFAMS:TIGR01953
  • Pfam:PF07497
  • Pfam:PF07498
  • PROSITE:MF_00073
  • PROSITE:MF_01884
  • Rfam:RF00519
  • SMART:SM00959

GO:0030401 transcription antiterminator activity

  • HAMAP:MF_00779
  • InterPro:IPR010534
  • JCVI_TIGRFAMS:TIGR01951
  • Pfam:PF06530

GO:0003701 RNA polymerase I transcription factor activity

  • InterPro:IPR016629
  • PIRSF:PIRSF015161

GO:0003702 RNA polymerase II transcription factor activity

  • InterPro:IPR000814
  • InterPro:IPR002853
  • InterPro:IPR003166
  • InterPro:IPR003194
  • InterPro:IPR003195
  • InterPro:IPR003196
  • InterPro:IPR003923
  • InterPro:IPR004598
  • InterPro:IPR004855
  • InterPro:IPR006289
  • InterPro:IPR006809
  • InterPro:IPR009083
  • InterPro:IPR009088
  • InterPro:IPR011039
  • InterPro:IPR011442
  • InterPro:IPR013028
  • InterPro:IPR015871
  • InterPro:IPR015872
  • InterPro:IPR016656
  • InterPro:IPR017919
  • Pfam:PF00352
  • Pfam:PF02186
  • Pfam:PF02268
  • Pfam:PF02269
  • Pfam:PF02270
  • Pfam:PF02751
  • Pfam:PF03153
  • Pfam:PF03540
  • Pfam:PF03849
  • Pfam:PF04719
  • Pfam:PF07571
  • PIRSF:PIRSF009415
  • PIRSF:PIRSF016398
  • PIRSF:PIRSF017246
  • PRINTS:PR00686
  • PRINTS:PR01443
  • ProDom:PD009224
  • PROSITE:MF_00408
  • PROSITE:PS00351
  • PROSITE:PS51344
  • PROSITE:PS51351
  • SMART:SM00531

GO:0016944 RNA polymerase II transcription elongation factor activity

  • InterPro:IPR019464
  • Pfam:PF10390