Proposal to obsolete children of "transcription factor binding"

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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.