Proposal to obsolete "promoter binding" and child terms: Difference between revisions
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= Annotation Counts = | = 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 for each Source by IEA vs non-IEA== | ==Total for each Source by IEA vs non-IEA== |
Revision as of 20:01, 2 March 2011
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)
- all current children of promoter binding:
These obsolations were all proposed in the [original proposal].
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
consider 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 a specific region 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.
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
consider 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)
consider 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. consider:
- 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
consider 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 [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 for each Source by IEA vs non-IEA
............. 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
Total number of annotations per term
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
Counts by source and evidence code for each term
promoter binding
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
serum response element binding
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
sterol response element binding
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
estrogen response element binding
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
cAMP response element binding
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
carbohydrate response element binding
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
mitochondrial light strand promoter anti-sense binding
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
mitochondrial heavy strand promoter anti-sense binding
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
mitochondrial heavy strand promoter anti-sense binding
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
mitochondrial heavy strand promoter sense binding
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
juvenile hormone response element binding
GO:0070594 juvenile hormone response element binding FlyBase IDA 2
vitamin D response element binding
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
E-box binding
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
purine-rich negative regulatory element binding
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
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.