View source for Proposal to obsolete "promoter binding" and child terms

[[Category:Transcription]]
= Proposal =

# obsolete: '''promoter binding''' (GO:0010843)
# obsolete these terms representing binding to specific DNA motifs:
#* all current children of promoter binding:
#** cAMP response element binding - GO:0035497
#** carbohydrate response element binding - GO:0035538
#** E-box binding - GO:0070888
#** estrogen response element binding - GO:0034056
#** juvenile hormone response element binding - GO:0070594
#** mitochondrial heavy strand promoter anti-sense binding - GO:0070362
#** mitochondrial heavy strand promoter sense binding - GO:0070364
#** mitochondrial light strand promoter anti-sense binding - GO:0070361
#** mitochondrial light strand promoter sense binding - GO:0070363
#** serum response element binding - GO:0010736
#** sterol response element binding - GO:0032810
#** vitamin D response element binding - GO:0070644
#* obsolete this child term of DNA regulatory region binding (GO:0044212)
#** purine-rich negative regulatory element binding (GO:0032422)

These obsolations were all proposed in the [[http://wiki.geneontology.org/index.php/Proposals_to_overhaul_transcription_in_GO_-_2010#transcription_factor_activity_-_GO:0003700_.26_promoter_binding_-_GO:0010843 original proposal]].


=Comment Period=

Comment period ends on March 24, 2011.

<font color="red">Unless objections are received by March 24, we will assume that you agree to this change.</font>


=Summary of Actions Taken=

* '''promoter binding''' (GO:0010843) was obsoleted on 5/11/2011, with '''transcription regulatory region DNA binding''' (GO:0044212) listed as a consider term.
* Its child terms referring to specific promoter motifs were moved to be direct children of '''transcription regulatory region DNA binding''' (GO:0044212).

= Problems =

== Reason to obsolete '''promoter binding''' (GO:0010843)==

The word promoter is used in different ways such that it is not
possible to define it consistently. In RNA polymerase II literature,
most though not all researchers seem to include transcription factor
binding sites; in prokaryotes, the promoter is limited to what is
recognized by basal factors and thus is comparable to the RNA pol II
core promoter in eukaryotes.


== Reason to obsolete these terms representing binding to specific DNA motifs==

All of these represent binding to specific sequence motifs. It is
beyond the scope of GO to capture the thousands of individual sequence
motifs that exist. We are working with Karen Eilbeck of SO to make
sure that GO and SO are in synch with respect to how promoter motifs
are defined and even SO is planning only to represent general classes
of motifs, not every specific one. Thus, we feel that the appropriate
level of detail for GO to capture for promoters is whether it is a
basal/core promoter element (generally done by a basal transcription
factor), a binding site for a transcription factor that binds in the
core promoter proximal region (the majority of the "gene-specific
regulatory" transcription factors), or an enhancer binding site (also
bound by regulatory transcription factors). Thus we would like to
indicate the types of binding to general types of motifs as indicated
in the structure above. These existing terms that indicate very
specific motifs, we feel should be obsoleted.

= Reannotation suggestions = 

== For reannotation of '''promoter binding'''==


<font color="red">consider</font>  this term or its children:
* '''transcription regulatory region DNA binding''' (GO:0044212)

Further suggestions:
* Please consider whether you want to indicate '''sequence-specific DNA binding''' versus any '''DNA binding''' which may not be sequence specific. 
* Note that terms specific to the regulatory regions of specific RNA polymerases have been created. 
* For example '''RNA polymerase II core promoter proximal region sequence-specific DNA binding''' (GO:0000978), specifies sequence-specific binding to the region adjacent to the core promoter of the RNAP II regulatory region; this would be the appropriate term for the majority of RNAP II transcription factors, provided the evidence is sufficient.
* Do NOT assume that you can transfer all annotations from '''promoter binding''' to the term '''core promoter binding''' (GO:0001047) or one of its children. Particularly for RNAP II, we have seen the word "promoter" used for both the "core promoter" and the "core promoter proximal region". 
* If you want to transfer all annotations without review, then we think only the highest level term '''transcription regulatory region DNA binding''' (GO:0044212) is appropriate. 
* If cursory review makes it clear that the binding is, for example, to a regulatory region for RNAP II, please consider the term '''RNA polymerase II regulatory region DNA binding''' (GO:0001012) or '''RNA polymerase II regulatory region sequence-specific DNA binding''' (GO:0000977)

== For reannotation of the four mitochondrial terms==
* mitochondrial heavy strand promoter anti-sense binding - GO:0070362
* mitochondrial heavy strand promoter sense binding - GO:0070364
* mitochondrial light strand promoter anti-sense binding - GO:0070361
* mitochondrial light strand promoter sense binding - GO:0070363

<font color="red">consider</font> this term or its children:
* '''GO:0001018 - mitochondrial RNA polymerase regulatory region DNA binding'''

==For reannotation of purine-rich negative regulatory element binding (GO:0032422)==
<font color="red">consider</font> one of these terms:
* '''GO:0044213 - intronic transcription regulatory region DNA binding'''
* '''GO:0001161 - intronic transcription regulatory region sequence-specific DNA binding'''
* '''GO:0001162 - RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding'''

==For reannotation of remaining 8 terms==
These eight terms were likely all intended to be for annotation of
multicellular eukaryotes, but only 4 (the latter 4 terms) have
definitions specific enough to be sure of this. Therefore, for
reannotation, I have suggested a high level term and emphasized a
particular child term. 

* cAMP response element binding - GO:0035497
* carbohydrate response element binding - GO:0035538
* sterol response element binding - GO:0032810
* vitamin D response element binding - GO:0070644
* E-box binding - GO:0070888
* estrogen response element binding - GO:0034056
* juvenile hormone response element binding - GO:0070594
* serum response element binding - GO:0010736


<font color="red">Consider</font> this term:
* '''GO:0001159 - core promoter proximal region DNA binding'''

and its children, especially:
* '''GO:0000978 - RNA polymerase II core promoter proximal region sequence-specific DNA binding'''

= Annotation Counts =

Annotation counts are from [[http://www.berkeleybop.org/goose/ GOOSE]] using the Berkeley BOP mirror on 3/2/2011, except for the term '''juvenile hormone response element binding''' which produced 0 results via GOOSE, but has 2 via the AmiGO website.

==Total number of annotations per term==

<pre>
1371    promoter binding
  44    E-box binding
  21    estrogen response element binding
  19    vitamin D response element binding
  15    serum response element binding
  10    mitochondrial light strand promoter anti-sense binding
   9    sterol response element binding
   8    purine-rich negative regulatory element
   6    cAMP response element binding
   6    mitochondrial heavy strand promoter anti-sense binding
   4    mitochondrial heavy strand promoter sense binding
   4    mitochondrial light strand promoter sense binding
   3    carbohydrate response element binding
   2    juvenile hormone response element binding
</pre>

==Total for all terms by Source & by IEA vs non-IEA==
<pre>
.............	non-IEA IEA
........AspGD   29      4
..........CGD   4       4
.......EcoCyc   1
...........FB   5
......FlyBase   2
GeneDB_Spombe   3
..........MGI   231
..........RGD   199     47
..........SGD   9
.........TAIR   4
......UniProt   2
....UniProtKB   580     393
.........ZFIN   5
Grand Total     1074    448
</pre>

==Total for "promoter binding" only by Source & by IEA vs non-IEA==

<pre>
Source          non-IEA IEA
AspGD           29      4
CGD             4       4
EcoCyc          1
FB              5
GeneDB_Spombe   2
MGI             205
RGD             169     39
SGD             9
TAIR            4
UniProt         2
UniProtKB       545     344
ZFIN            5
Grand Total     980     391
</pre>



==Counts by source and evidence code for each term==

'''promoter binding'''
<pre>
GO:0010843    promoter binding  AspGD    IDA    27
GO:0010843    promoter binding  AspGD    IEA    4
GO:0010843    promoter binding  AspGD    IMP    1
GO:0010843    promoter binding  AspGD    IPI    1
GO:0010843    promoter binding  CGD      IDA    4
GO:0010843    promoter binding  CGD      IEA    4
GO:0010843    promoter binding  EcoCyc   IDA    1
GO:0010843    promoter binding  FB       IDA    5
GO:0010843    promoter binding  GeneDB_Spombe   IDA     2
GO:0010843    promoter binding  MGI             IDA     54
GO:0010843    promoter binding  MGI             IMP     3
GO:0010843    promoter binding  MGI             ISO     107
GO:0010843    promoter binding  MGI             ISS     41
GO:0010843    promoter binding  RGD             IDA     14
GO:0010843    promoter binding  RGD             IEA     39
GO:0010843    promoter binding  RGD             ISO     143
GO:0010843    promoter binding  RGD             ISS     12
GO:0010843    promoter binding  SGD             IDA     6
GO:0010843    promoter binding  SGD             NAS     3
GO:0010843    promoter binding  TAIR            IDA     4
GO:0010843    promoter binding  UniProt         IDA     2
GO:0010843    promoter binding  UniProtKB       IDA     160
GO:0010843    promoter binding  UniProtKB       IEA     344
GO:0010843    promoter binding  UniProtKB       IMP     8
GO:0010843    promoter binding  UniProtKB       ISS     376
GO:0010843    promoter binding  UniProtKB       TAS     1
GO:0010843    promoter binding  ZFIN            IDA     3
GO:0010843    promoter binding  ZFIN            IPI     2
</pre>

'''serum response element binding'''
<pre>
GO:0010736    serum response element binding    MGI     IDA     1
GO:0010736    serum response element binding    MGI     ISO     1
GO:0010736    serum response element binding    RGD     IEA     1
GO:0010736    serum response element binding    RGD     ISO     2
GO:0010736    serum response element binding    UniProtKB       IDA     1
GO:0010736    serum response element binding    UniProtKB       IEA     8
GO:0010736    serum response element binding    UniProtKB       ISS     1
</pre>

'''sterol response element binding'''
<pre>
GO:0032810    sterol response element binding   GeneDB_Spombe   IDA     1
GO:0032810    sterol response element binding   MGI             ISO     2
GO:0032810    sterol response element binding   MGI             ISS     1
GO:0032810    sterol response element binding   RGD             ISO     2
GO:0032810    sterol response element binding   RGD             ISS     1
GO:0032810    sterol response element binding   UniProtKB       IDA     2
</pre>

'''estrogen response element binding'''
<pre>
GO:0034056    estrogen response element binding MGI             ISO     1
GO:0034056    estrogen response element binding RGD             IEA     1
GO:0034056    estrogen response element binding RGD             ISO     1
GO:0034056    estrogen response element binding UniProtKB       IDA     1
GO:0034056    estrogen response element binding UniProtKB       IEA     17
</pre>

'''cAMP response element binding'''
<pre>
GO:0035497    cAMP response element binding     MGI             ISO     1
GO:0035497    cAMP response element binding     RGD             IEA     1
GO:0035497    cAMP response element binding     RGD             ISO     1
GO:0035497    cAMP response element binding     UniProtKB       IEA     2
GO:0035497    cAMP response element binding     UniProtKB       IMP     1
</pre>

'''carbohydrate response element binding'''
<pre>
GO:0035538    carbohydrate response element binding             MGI     TAS     1
GO:0035538    carbohydrate response element binding             RGD     NAS     1
GO:0035538    carbohydrate response element binding             UniProtKB       TAS     1
</pre>

'''mitochondrial light strand promoter anti-sense binding'''
<pre>
GO:0070361    mitochondrial light strand promoter anti-sense binding            MGI     IDA     1
GO:0070361    mitochondrial light strand promoter anti-sense binding            MGI     ISO     1
GO:0070361    mitochondrial light strand promoter anti-sense binding            RGD     ISO     2
GO:0070361    mitochondrial light strand promoter anti-sense binding            UniProtKB       IDA     1
GO:0070361    mitochondrial light strand promoter anti-sense binding            UniProtKB       ISS     5
</pre>

'''mitochondrial heavy strand promoter anti-sense binding'''
<pre>
GO:0070362    mitochondrial heavy strand promoter anti-sense binding            MGI             IDA     1
GO:0070362    mitochondrial heavy strand promoter anti-sense binding            MGI             ISO     1
GO:0070362    mitochondrial heavy strand promoter anti-sense binding            RGD             ISO     2
GO:0070362    mitochondrial heavy strand promoter anti-sense binding            UniProtKB       IDA     1
GO:0070362    mitochondrial heavy strand promoter anti-sense binding            UniProtKB       IEA     1
</pre>

'''mitochondrial heavy strand promoter anti-sense binding'''
<pre>
GO:0070363    mitochondrial light strand promoter sense binding                 MGI             IDA     1
GO:0070363    mitochondrial light strand promoter sense binding                 RGD             ISO     2
GO:0070363    mitochondrial light strand promoter sense binding                 UniProtKB       IDA     1
</pre>

'''mitochondrial heavy strand promoter sense binding'''
<pre>
GO:0070364    mitochondrial heavy strand promoter sense binding                 MGI             IDA     1
GO:0070364    mitochondrial heavy strand promoter sense binding                 RGD             ISO     2
GO:0070364    mitochondrial heavy strand promoter sense binding                 UniProtKB       IDA     1
</pre>

'''juvenile hormone response element binding'''
<pre>
GO:0070594    juvenile hormone response element binding         FlyBase         IDA     2
</pre>

'''vitamin D response element binding'''
<pre>
GO:0070644    vitamin D response element binding  MGI   ISO                     1
GO:0070644    vitamin D response element binding  RGD   IEA                     2
GO:0070644    vitamin D response element binding  RGD   ISO                     3
GO:0070644    vitamin D response element binding  UniProtKB                     IDA     3
GO:0070644    vitamin D response element binding  UniProtKB                     IEA     10
</pre>

'''E-box binding'''
<pre>
GO:0070888    E-box binding      MGI     IDA      4
GO:0070888    E-box binding      MGI     ISO      5
GO:0070888    E-box binding      RGD     IEA      3
GO:0070888    E-box binding      RGD     ISO      9
GO:0070888    E-box binding      UniProtKB        IDA   12
GO:0070888    E-box binding      UniProtKB        IEA   8
GO:0070888    E-box binding      UniProtKB        ISS   3
</pre>

'''purine-rich negative regulatory element binding'''
<pre>
GO:0032422    purine-rich negative regulatory element binding   MGI     ISO     2
GO:0032422    purine-rich negative regulatory element binding   RGD     IDA     1
GO:0032422    purine-rich negative regulatory element binding   RGD     ISO     1
GO:0032422    purine-rich negative regulatory element binding   UniProtKB       IDA     1
GO:0032422    purine-rich negative regulatory element binding   UniProtKB       IEA     3
</pre>

= Subsets and non-definition dbxrefs =
None of these terms are present in any subsets.

None of these terms is linked to any non-definition dbxrefs.