Proposal to obsolete children of "transcription factor binding": Difference between revisions
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[[Category:Transcription]] | |||
=Proposal= | =Proposal= | ||
<font color=red>'''Proposal'''</font>: <font color=red>obsoletions</font> | <font color=red>'''Proposal'''</font>: <font color=red>obsoletions</font> | ||
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=Comment Period= | =Comment Period= | ||
'''Date mailed:''' | '''Date mailed:''' 3/14/2011 | ||
'''Deadline for Comments:''' | '''Deadline for Comments:''' 4/4/2011 - <font color="red"> Unless objections are received by April 4th, we will assume that you agree to this change. </font> | ||
=Problems= | =Problems= | ||
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GO:0030374..ligand-dependent nuclear receptor transcription coactivator activity 105 57 162 | GO:0030374..ligand-dependent nuclear receptor transcription coactivator activity 105 57 162 | ||
GO:0030375.........................thyroid hormone receptor coactivator activity 13 10 23 | GO:0030375.........................thyroid hormone receptor coactivator activity 13 10 23 | ||
</pre> | |||
== Annotation Counts for "transcription factor binding" vs its child terms == | |||
<pre> | |||
term(s)..................................... non-IEA IEA Grand Total | |||
----------------------------------------------------------------------------- | |||
Child terms of transcription factor binding 532 287 819 | |||
...............transcription factor binding 1063 17092 18155 | |||
................................Grand Total 1595 17379 18974 | |||
</pre> | |||
== Annotation counts by source and evidence code type == | |||
<pre> | |||
...................... TAS, Exp Seq IEA Grand Total | |||
NAS | |||
IC | |||
----------------------------------------------------------------------------- | |||
Source | |||
.......FB 2 2 2 - 6 | |||
......MGI 1 29 105 - 135 | |||
......RGD 4 25 110 33 172 | |||
.....TAIR - 1 - - 1 | |||
UniProtKB 29 127 92 254 502 | |||
.......WB - - 1 - 1 | |||
.....ZFIN - 2 - - 2 | |||
Grand Total 36 186 310 287 819 | |||
</pre> | </pre> | ||
Latest revision as of 17:06, 10 July 2014
Proposal
Proposal: obsoletions
Specific terms proposed to obsolete:
terms under transcription factor binding (GO:0008134)
- aryl hydrocarbon receptor binding - GO:0017162
- bHLH transcription factor binding - GO:0043425
- MRF binding - GO:0043426
- Mrf4 binding - GO:0051578
- Myf5 binding - GO:0051576
- MyoD binding - GO:0051577
- myogenin binding - GO:0051579
- NF-kappaB binding - GO:0051059
- NFAT protein binding - GO:0051525
- NFAT1 protein binding - GO:0051526
- NFAT2 protein binding - GO:0051527
- NFAT3 protein binding - GO:0051528
- NFAT4 protein binding - GO:0051529
- NFAT5 protein binding - GO:0051530
- retinoic acid receptor binding - GO:0042974
- retinoid X receptor binding - GO:0046965
- Tat protein binding - GO:0030957
- thyroid hormone receptor binding - GO:0046966
- vitamin D receptor binding - GO:0042809
terms under transcription coactivator activity (GO:0003713)
- cAMP response element binding protein binding - GO:0008140
- ligand-dependent nuclear receptor transcription coactivator activity - GO:0030374
- thyroid hormone receptor coactivator activity - GO:0030375
This list of terms is identical to what we proposed in the [original proposal] except for the addition of vitamin D receptor binding (GO:0042809), which presumably I just missed previously.
Comment Period
Date mailed: 3/14/2011
Deadline for Comments: 4/4/2011 - Unless objections are received by April 4th, we will assume that you agree to this change.
Problems
Currently, most of the child terms of "transcription factor binding" of "transcription coactivator activity", with a few exceptions like "transcription cofactor activity" represent binding to specific proteins. We feel that this is too specific to represent with individual GO terms because there are thousands and thousands of specific transcription factors. Groups who wish to curate this level of detail should utilize column 16 to indicate what is being bound.
We would like to represent binding just to classes of transcription factors, such as basal or regulatory transcription factors. In the course of the transcription overhaul, we have decided that we do need to represent binding to classes of basal transcription factors, e.g. TFIIB, TFIID, etc., because the functions of some other transcription factors are best described in terms of what basal factor they act through, via binding. This is feasible because there are a relatively small number of basal factors. Thus, we have made binding terms for classes of basal factors, e.g. "TFIID-class transcription factor binding". However, considering the vast number of other (non-basal) transcription factors, we feel that GO should not have terms representing binding to each of these separately.
Reannotation suggestions
For reannotation of terms under transcription factor binding (GO:0008134)
For reannotation of these 19 terms:
- aryl hydrocarbon receptor binding - GO:0017162
- bHLH transcription factor binding - GO:0043425
- MRF binding - GO:0043426
- Mrf4 binding - GO:0051578
- Myf5 binding - GO:0051576
- MyoD binding - GO:0051577
- myogenin binding - GO:0051579
- NF-kappaB binding - GO:0051059
- NFAT protein binding - GO:0051525
- NFAT1 protein binding - GO:0051526
- NFAT2 protein binding - GO:0051527
- NFAT3 protein binding - GO:0051528
- NFAT4 protein binding - GO:0051529
- NFAT5 protein binding - GO:0051530
- retinoic acid receptor binding - GO:0042974
- retinoid X receptor binding - GO:0046965
- Tat protein binding - GO:0030957
- thyroid hormone receptor binding - GO:0046966
- vitamin D receptor binding - GO:0042809
under transcription factor binding (GO:0008134), please consider using transcription factor binding (GO:0008134) itself or its child terms, especially RNA polymerase II transcription factor binding (GO:0001085) as most of these terms to be obsoleted look specific to eukaryotes and most likely RNAP II.
For reannotation of 2 "____ coactivator activity" terms
For reannotation of these two terms:
- ligand-dependent nuclear receptor transcription coactivator activity - GO:0030374
- thyroid hormone receptor coactivator activity - GO:0030375
under transcription coactivator activity (GO:0003713), please consider the term transcription coactivator activity (GO:0003713) itself or its child terms, especially RNA polymerase II transcription coactivator activity (GO:0001105) as both of these to be obsoleted terms look specific to eukaryotes and most likely RNAP II.
For reannotation of "cAMP response element binding protein binding" (GO:0008140)
Though the term cAMP response element binding protein binding (GO:0008140) is placed under transcription coactivator activity (GO:0003713) it is defined more generally just in terms of binding to a specific protein. Thus, we suggest consideration of the term transcription factor binding (GO:0008134) or any of its child terms.
Note that at the moment, there are terms specifically for the RNAP II cofactor activities, but not for other varieties of RNAP. If you need cofactor terms for some other form of RNAP, please request them via [SourceForge].
- cAMP response element binding protein binding - GO:0008140
Annotation Counts
numbers from 3/10/2011 via GOOSE using the Berkeley BOP database
Total non-IEA and IEA annotation counts for each source (combined for all terms)
Source__ non-IEA IEA Grand Total .......FB 6 6 ......MGI 135 135 ......RGD 139 33 172 .....TAIR 1 1 UniProtKB 248 254 502 .......WB 1 1 .....ZFIN 2 2 Grand Total 532 287 819
Total number of annotations per term
Term_name_______________________________________________________________________ non-IEA IEA Total GO:0017162.....................................aryl hydrocarbon receptor binding 12 8 20 GO:0043425.....................................bHLH transcription factor binding 77 15 92 GO:0043426...........................................................MRF binding 0 0 0 GO:0051578..........................................................Mrf4 binding 0 0 0 GO:0051576..........................................................Myf5 binding 0 0 0 GO:0051577..........................................................MyoD binding 9 1 10 GO:0051579......................................................myogenin binding 0 0 0 GO:0051059.....................................................NF-kappaB binding 80 41 121 GO:0051525..................................................NFAT protein binding 14 2 16 GO:0051526.................................................NFAT1 protein binding 0 0 0 GO:0051527.................................................NFAT2 protein binding 0 0 0 GO:0051528.................................................NFAT3 protein binding 0 0 0 GO:0051529.................................................NFAT4 protein binding 0 0 0 GO:0051530.................................................NFAT5 protein binding 0 0 0 GO:0042974........................................retinoic acid receptor binding 29 7 36 GO:0046965...........................................retinoid X receptor binding 56 55 111 GO:0030957...................................................Tat protein binding 7 8 15 GO:0046966......................................thyroid hormone receptor binding 88 44 132 GO:0042809............................................vitamin D receptor binding 33 32 65 GO:0008140.........................cAMP response element binding protein binding 9 7 16 GO:0030374..ligand-dependent nuclear receptor transcription coactivator activity 105 57 162 GO:0030375.........................thyroid hormone receptor coactivator activity 13 10 23
Annotation Counts for "transcription factor binding" vs its child terms
term(s)..................................... non-IEA IEA Grand Total ----------------------------------------------------------------------------- Child terms of transcription factor binding 532 287 819 ...............transcription factor binding 1063 17092 18155 ................................Grand Total 1595 17379 18974
Annotation counts by source and evidence code type
...................... TAS, Exp Seq IEA Grand Total NAS IC ----------------------------------------------------------------------------- Source .......FB 2 2 2 - 6 ......MGI 1 29 105 - 135 ......RGD 4 25 110 33 172 .....TAIR - 1 - - 1 UniProtKB 29 127 92 254 502 .......WB - - 1 - 1 .....ZFIN - 2 - - 2 Grand Total 36 186 310 287 819
Annotation counts by source and evidence code for each term
cAMP response element binding protein binding
GO:0008140 cAMP response element binding protein binding FB TAS 1 GO:0008140 cAMP response element binding protein binding MGI IMP 1 GO:0008140 cAMP response element binding protein binding MGI ISO 2 GO:0008140 cAMP response element binding protein binding RGD IEA 1 GO:0008140 cAMP response element binding protein binding RGD ISO 2 GO:0008140 cAMP response element binding protein binding UniProtKB IDA 2 GO:0008140 cAMP response element binding protein binding UniProtKB IEA 6 GO:0008140 cAMP response element binding protein binding UniProtKB NAS 1
aryl hydrocarbon receptor binding
GO:0017162 aryl hydrocarbon receptor binding FB ISS 1 GO:0017162 aryl hydrocarbon receptor binding MGI IPI 1 GO:0017162 aryl hydrocarbon receptor binding MGI ISO 2 GO:0017162 aryl hydrocarbon receptor binding RGD IEA 2 GO:0017162 aryl hydrocarbon receptor binding RGD ISO 3 GO:0017162 aryl hydrocarbon receptor binding UniProtKB IDA 2 GO:0017162 aryl hydrocarbon receptor binding UniProtKB IEA 6 GO:0017162 aryl hydrocarbon receptor binding UniProtKB IPI 2 GO:0017162 aryl hydrocarbon receptor binding UniProtKB ISS 1
ligand-dependent nuclear receptor transcription coactivator activity
GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity FB IDA 1 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity FB NAS 1 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity MGI IDA 6 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity MGI ISO 21 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity RGD IDA 4 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity RGD IEA 6 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity RGD ISO 19 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity RGD ISS 5 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity UniProtKB IDA 11 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity UniProtKB IEA 51 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity UniProtKB IGI 1 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity UniProtKB IMP 5 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity UniProtKB IPI 2 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity UniProtKB ISS 19 GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity UniProtKB NAS 10
thyroid hormone receptor coactivator activity
GO:0030375 thyroid hormone receptor coactivator activity MGI IDA 2 GO:0030375 thyroid hormone receptor coactivator activity MGI ISO 2 GO:0030375 thyroid hormone receptor coactivator activity RGD IDA 1 GO:0030375 thyroid hormone receptor coactivator activity RGD IEA 1 GO:0030375 thyroid hormone receptor coactivator activity RGD ISO 3 GO:0030375 thyroid hormone receptor coactivator activity UniProtKB IDA 1 GO:0030375 thyroid hormone receptor coactivator activity UniProtKB IEA 9 GO:0030375 thyroid hormone receptor coactivator activity UniProtKB ISS 4
Tat protein binding
GO:0030957 Tat protein binding MGI ISO 2 GO:0030957 Tat protein binding RGD ISO 2 GO:0030957 Tat protein binding UniProtKB IDA 3 GO:0030957 Tat protein binding UniProtKB IEA 8
retinoic acid receptor binding
GO:0042974 retinoic acid receptor binding MGI IDA 1 GO:0042974 retinoic acid receptor binding MGI IPI 2 GO:0042974 retinoic acid receptor binding MGI ISO 5 GO:0042974 retinoic acid receptor binding RGD IDA 1 GO:0042974 retinoic acid receptor binding RGD IPI 1 GO:0042974 retinoic acid receptor binding RGD ISO 6 GO:0042974 retinoic acid receptor binding RGD ISS 1 GO:0042974 retinoic acid receptor binding UniProtKB IDA 2 GO:0042974 retinoic acid receptor binding UniProtKB IEA 7 GO:0042974 retinoic acid receptor binding UniProtKB IPI 2 GO:0042974 retinoic acid receptor binding UniProtKB ISS 8
bHLH transcription factor binding
GO:0043425 bHLH transcription factor binding FB IDA 1 GO:0043425 bHLH transcription factor binding MGI IPI 1 GO:0043425 bHLH transcription factor binding MGI ISO 9 GO:0043425 bHLH transcription factor binding MGI ISS 1 GO:0043425 bHLH transcription factor binding RGD IDA 1 GO:0043425 bHLH transcription factor binding RGD IEA 4 GO:0043425 bHLH transcription factor binding RGD IPI 2 GO:0043425 bHLH transcription factor binding RGD ISO 7 GO:0043425 bHLH transcription factor binding RGD TAS 1 GO:0043425 bHLH transcription factor binding TAIR IPI 1 GO:0043425 bHLH transcription factor binding UniProtKB IEA 11 GO:0043425 bHLH transcription factor binding UniProtKB IPI 33 GO:0043425 bHLH transcription factor binding UniProtKB ISS 19 GO:0043425 bHLH transcription factor binding WB ISS 1
retinoid X receptor binding
GO:0046965 retinoid X receptor binding MGI IDA 5 GO:0046965 retinoid X receptor binding MGI IMP 1 GO:0046965 retinoid X receptor binding MGI IPI 2 GO:0046965 retinoid X receptor binding MGI ISO 6 GO:0046965 retinoid X receptor binding MGI TAS 1 GO:0046965 retinoid X receptor binding RGD IDA 1 GO:0046965 retinoid X receptor binding RGD IEA 6 GO:0046965 retinoid X receptor binding RGD IPI 3 GO:0046965 retinoid X receptor binding RGD ISO 10 GO:0046965 retinoid X receptor binding RGD ISS 1 GO:0046965 retinoid X receptor binding UniProtKB IDA 2 GO:0046965 retinoid X receptor binding UniProtKB IEA 49 GO:0046965 retinoid X receptor binding UniProtKB IPI 7 GO:0046965 retinoid X receptor binding UniProtKB ISS 16 GO:0046965 retinoid X receptor binding UniProtKB TAS 1
thyroid hormone receptor binding
GO:0046966 thyroid hormone receptor binding FB ISS 1 GO:0046966 thyroid hormone receptor binding MGI IDA 1 GO:0046966 thyroid hormone receptor binding MGI IPI 2 GO:0046966 thyroid hormone receptor binding MGI ISO 21 GO:0046966 thyroid hormone receptor binding RGD IDA 2 GO:0046966 thyroid hormone receptor binding RGD IEA 5 GO:0046966 thyroid hormone receptor binding RGD IPI 2 GO:0046966 thyroid hormone receptor binding RGD ISO 19 GO:0046966 thyroid hormone receptor binding RGD ISS 2 GO:0046966 thyroid hormone receptor binding UniProtKB IDA 12 GO:0046966 thyroid hormone receptor binding UniProtKB IEA 39 GO:0046966 thyroid hormone receptor binding UniProtKB IPI 12 GO:0046966 thyroid hormone receptor binding UniProtKB ISS 8 GO:0046966 thyroid hormone receptor binding UniProtKB NAS 3 GO:0046966 thyroid hormone receptor binding UniProtKB TAS 3
NF-kappaB binding
GO:0051059 NF-kappaB binding MGI IPI 1 GO:0051059 NF-kappaB binding MGI ISO 22 GO:0051059 NF-kappaB binding RGD IC 3 GO:0051059 NF-kappaB binding RGD IDA 1 GO:0051059 NF-kappaB binding RGD IEA 4 GO:0051059 NF-kappaB binding RGD IPI 4 GO:0051059 NF-kappaB binding RGD ISO 18 GO:0051059 NF-kappaB binding RGD ISS 3 GO:0051059 NF-kappaB binding UniProtKB IDA 6 GO:0051059 NF-kappaB binding UniProtKB IEA 37 GO:0051059 NF-kappaB binding UniProtKB IPI 14 GO:0051059 NF-kappaB binding UniProtKB ISS 6 GO:0051059 NF-kappaB binding UniProtKB NAS 1 GO:0051059 NF-kappaB binding ZFIN IPI 1
NFAT protein binding
GO:0051525 NFAT protein binding MGI ISO 1 GO:0051525 NFAT protein binding MGI ISS 1 GO:0051525 NFAT protein binding RGD ISO 1 GO:0051525 NFAT protein binding UniProtKB IEA 2 GO:0051525 NFAT protein binding UniProtKB IPI 1 GO:0051525 NFAT protein binding UniProtKB ISS 10
MyoD binding
GO:0051577 MyoD binding MGI IPI 2 GO:0051577 MyoD binding MGI ISO 2 GO:0051577 MyoD binding RGD ISO 2 GO:0051577 MyoD binding UniProtKB IDA 2 GO:0051577 MyoD binding UniProtKB IEA 1 GO:0051577 MyoD binding UniProtKB ISS 1
Total for all terms by Source & by IEA vs non-IEA
Subsets and non-definition dbxrefs
None of these terms are included in subsets.
None of these terms have non-definition dbxrefs.