Proposal to obsolete children of "transcription factor binding"

Proposal

Proposal: obsoletions

Specific terms proposed to obsolete:

terms under transcription factor binding

• 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

terms under transcription cofactor activity

• cAMP response element binding protein binding - GO:0008140
• ligand-dependent nuclear receptor transcription coactivator activity - GO:0030374
• thyroid hormone receptor coactivator activity - GO:0030375

Comment Period

Date mailed:

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

Problems

Currently, most of the child terms of "transcription factor binding" (except "transcription cofactor activity") and the children of "transcription coactivator 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.

Annotation Counts

Total for all terms by Source & by IEA vs non-IEA

	
__Source_	Non-IEA	IEA	Grand Total	
.......FB	6	-	6
......MGI	126	-	126
......RGD	131	29	160
.....TAIR	1	-	1
UniProtKB	233	226	459
.......WB	1	-	1
.....ZFIN	1	-	1
Grand Total	499	255	754