Proposal for fate of "transcription" and corresponding regulation terms

From GO Wiki
Jump to: navigation, search

There are a couple problems with the term transcription (GO:0006350), and with its three associated regulation terms:

  • GO:0006350 transcription
  • GO:0045449 regulation of transcription
  • GO:0045941 positive regulation of transcription
  • GO:0016481 negative regulation of transcription

This page contains the 2 possible options for resolution followed by a detailed discussion of the issues and some supporting data.

Proposal

There are 2 possible ways to go with these terms:

  1. Merge the transcription terms into the 4 corresponding transcription, DNA-dependent terms (pairs shown below). Since we think that essentially all of the annotations should have been made to the more granular transcription, DNA-dependent terms, we feel this might be the conservative approach with respect to annotations.
  2. Obsolete the 4 transcription and suggest replacement terms. Since the vast majority of annotations are IEAs, which would be fixed by fixing the mappings rather than by having to manually evaluate each annotation, perhaps the group would prefer to go this way rather than risk inappropriately moving a small number of annotations which should actually be to reverse transcription or transcription, RNA-dependent to the transcription, DNA-dependent term.

To minimize reannotation work, we are leaning towards the MERGE option. We feel that the chance of creating bad annotations by transferring annotations from the "transcription" terms to the corresponding "transcription, DNA-dependent" terms is very small. If someone feels that there is a reason that these terms must be OBSOLETED instead of MERGED, please let us know.

Regardless of which option is chosen, we are not planning to create a replacement grouping term to group transcription, DNA-dependent and transcription, RNA-dependent. We feel that the existing term RNA biosynthetic process is sufficient, and unlikely to produce confusion in the way that having a grouping term named transcription has.

-Karen & David

Comment Period

Date mailed: 2/21/2011

Deadline for comments: 3/07/2011 - Unless objections are received by March 7, we will assume that you agree to this MERGE option.

Done: 3/18/2011 (merge option)

Problems

  1. Transcription (GO:0006350) is defined incorrectly.
    • Current definition: The cellular synthesis of either RNA on a template of DNA or DNA on a template of RNA.
    • As written, the definition is specifically grouping "normal" (DNA-dependent) transcription from DNA templates with reverse transcription, which is actually a type of DNA synthesis which should NOT be grouped with transcription at all. It is also excluding production of RNA transcripts from RNA templates, which is a kind of transcription and which occurs in some viruses.
  2. Confusing use in annotations
    • The term transcription (GO:0006350) is being used for annotations as if it were equivalent to transcription, DNA-dependent (GO:0006351), and similarly for the regulation of transcription terms compared with the regulation of transcription, DNA-dependent terms. This is occurring for thousands of annotations, about 20% of the annotations made to transcription or its child terms (numbers from AmiGO below). David and I have scanned a small subset of these annotations and strongly suspect that almost all of these annotations should have been made to the equivalent transcription, DNA-dependent terms, rather than just to transcription; many might be more appropriate going to the even more specific term for transcription from RNA polymerase II promoter.
    • In addition to thousands of annotations to these 4 top level transcription terms, there are over 500 mappings (numbers of dbxref mappings below). These mappings are probably the main source of annotations as the vast majority of annotations to these high level grouping terms are by IEA (annotation counts for "transcription" below). So we will want to consider the fate of the mappings in this decision as well.

Fate of direct child terms, and other terms with relationships to these terms

terms with relationships to transcription (GO:0006350)

  • already included in proposal
    - GO:0045449 regulation of transcription
    - GO:0045941 positive regulation of transcription
    - GO:0016481 negative regulation of transcription
    These terms should be handled in the same manner as transcription.
  • input requested
    - GO:0000988 protein binding transcription factor activity
    - GO:0001071 nucleic acid binding transcription factor activity
    These are both new terms that have been added recently as part of the transcription overhaul. I put these in thinking only of DNA-dependent transcription. However, at the moment, nothing about the names or definitions of these terms distinguishes between DNA-dependent or RNA-dependent processes. If anyone knowledgeable about the RNA-dependent process thinks these functions would be needed for the RNA-dependent process, we can make these general terms and create new terms that are subtypes. If no one speaks up though, I might be inclined to just make these terms specific to DNA-dependent transcription since I know almost nothing about RNA-dependent transcription.
    - removing part_of relationships for now, but think we NEED to make these terms specific to the DNA-dependent form of transcription and make new part_of's
    - see [protein binding counts] and [nucleic acid binding counts] for supporting info on this
  • cross product relationships to be changed to use "transcription, DNA-dependent" done
    - GO:0034401 regulation of transcription by chromatin organization
    This term has transcription as part of cross product definition, but you have to have DNA to have chromatin, so this relationship seems like it would be more accurately made to transcription, DNA-dependent
    Note: Parentage may be wrong as it seems unlikely that all regulation of transcription by chromatin organization is in response to stress. See the SF item.
  • new parentage needed
    - GO:0019083 viral transcription done
    Similarly to transcription, DNA-dependent, we think that RNA biosynthetic process would be a sufficient is_a parent for this term. It is not currently a parent, so it would need to be added when transcription is removed.
  • no change needed
    - GO:0006351 transcription, DNA-dependent
    This already has an additional is_a parent of RNA biosynthetic process. We feel this is sufficient.
  • to be dealt with separately
    - GO:0006410 transcription, RNA-dependent
    - GO:0032199 transcription involved in RNA-mediated transposition
    Note that cross product relationship from 32199 was changed from "transcription" to "reverse transcription"

terms with relationships to regulation of transcription (GO:0045449)

  1. is_a child terms of GO:0045449 ! regulation of transcription
    • This is the term it is being merged into
      • GO:0006355 - regulation of transcription, DNA-dependent
        giving "transcription, DNA-dependent direct is_a relationships to:
        GO:2000112 - regulation of cellular macromolecule biosynthetic process
        GO:0010468 - regulation of gene expression
        GO:0019219 - regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

    • These will be merged as well, so not an issue
      • GO:0016481 - negative regulation of transcription
      • GO:0045941 - positive regulation of transcription
    • These can be moved down to be is_a children of "regulation of transcription, DNA-dependent" done
      • GO:0031935 - regulation of chromatin silencing
      • GO:0043620 - regulation of transcription in response to stress
        Def indicates organism is under stress. Is there any organismal txn that is not DNA-dependent?
        Should we modify the name to be more specific?
      • GO:0044324 - regulation of transcription involved in anterior/posterior axis specification
    • will move to be a child of "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" (GO:0019219) for now have moved, will need to follow up on
      • GO:0046782 - regulation of viral transcription (see SF item)
      • GO:0010630 - regulation of transcription, start site selection (defined with "or clause", obsolete and replaced with specific terms?)
      • GO:0052312 - modulation of transcription in other organism involved in symbiotic interaction (check with PAMGO)
      • GO:0075180 - regulation of transcription in response to host (check with PAMGO)
  1. part_of relationship: to "regulation of transcription" (GO:0045449)
    • This term will be merged also, so not an issue.
      • GO:0030528 - transcription regulator activity
        have removed the part_of relationship without any replacement
  2. terms with intersection_of: GO:0045449 ! regulation of transcription
    • These all seem like they could use "regulation of transcription, DNA-dependent" instead GO:0000114 - regulation of transcription involved in G1 phase of mitotic cell cycle
      • GO:0000115 - regulation of transcription involved in S phase of mitotic cell cycle
      • GO:0045896 - regulation of transcription during mitosis
      • GO:0051037 - regulation of transcription during meiosis
      • GO:0060849 - regulation of transcription involved in lymphatic endothelial cell fate commitment
      • GO:0060850 - regulation of transcription involved in cell fate commitment
      • GO:0060852 - regulation of transcription involved in venous endothelial cell fate commitment
      • GO:0060899 - regulation of transcription involved in eye field cell fate commitment of camera-type eye
      • GO:0090019 - regulation of transcription involved in anterior neural plate formation
      • GO:0090020 - regulation of transcription involved in posterior neural plate formation
        done: David, you should look at these, some have RNAP II specific defs, but are using a more general term in cross product def. I have replaced "transcription" with "transcription, DNA-dependent" in the cross product relationship in all cases

of terms with relationships to positive regulation of transcription (GO:0045941)

  1. is_a children of positive regulation of transcription (GO:0045449)
    • move to is_a pos reg of txn, DNA-dependent (GO:0045892) done
      • GO:0045893 - positive regulation of transcription, DNA-dependent
      • GO:0060469 - positive regulation of transcription involved in egg activation
      • GO:0007072 - positive regulation of transcription on exit from mitosis
    • move to is_a GO:0045935 - positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
      • GO:0050434 - positive regulation of viral transcription check with Jane
      • GO:0075181 - positive regulation of symbiont transcription in response to host include in SF item for PamGO
  2. terms with part_of relationships to positive regulation of transcription (GO:0045941)
    done: for now, just removing without replacement
    • have kept this term, so probably need to make specific to "transcription, DNA-dependent"
      • GO:0003713 - transcription coactivator activity
    • terms slated for merging into process terms
      • GO:0016563 - transcription activator activity
      • GO:0016986 - transcription initiation factor activity
  3. terms with intersection_of relationships : positive regulation of transcription (GO:0045941)
    • These terms could use "regulation of transcription, DNA-dependent" instead done
      • GO:0045897 - positive regulation of transcription during mitosis
      • GO:0060469 - positive regulation of transcription involved in egg activation
      • GO:0007072 - positive regulation of transcription on exit from mitosis

of terms with relationships to negative regulation of transcription (GO:0016481)

  1. is_a child terms of negative regulation of transcription (GO:0016481)
    • move to is_a neg reg of txn, DNA-dependent (GO:0045892) done
      • GO:0010678 - negative regulation of cellular carbohydrate metabolic process by repression of transcription
    • move to is_a GO:0045934 - negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
      • GO:0032897 - negative regulation of viral transcription check with Jane
      • GO:0075182 - negative regulation of symbiont transcription in response to host check with PAMGO
    • may need a new parent in regulation tree
      • GO:0045892 - negative regulation of transcription, DNA-dependent
  1. terms with part_of relationships to negative regulation of transcription (GO:0016481)
    removing part_of relationship for now, without replacement
    • GO:0003714 - transcription corepressor activity
    • GO:0016564 - transcription repressor activity
    • GO:0016988 - transcription initiation factor antagonist activity
  2. terms with intersection_of relationships to negative regulation of transcription (GO:0016481)
    • use "negative regulation of transcription, DNA-dependent" term instead done
      • GO:0060277 - negative regulation of transcription involved in G1 phase of mitotic cell cycle
        Note: This term is a child of the neg reg of txn from RNAP II promoter term, but is not defined as RNAP II specific. It's Intersection Genus term (neg reg of transcription) is also broader than the position in the tree suggests


Supporting Information

transcription & transcription, DNA-dependent term pairs

GO:0006350 transcription
 => GO:0006351 transcription, DNA-dependent

GO:0045449 regulation of transcription
 => GO:0006355 regulation of transcription, DNA-dependent

GO:0045941 positive regulation of transcription
 => GO:0045893 positive regulation of transcription, DNA-dependent

GO:0016481 negative regulation of transcription
 => GO:0045892 negative regulation of transcription, DNA-dependent


Gene product Annotation counts from AmiGO (Jan 2011)

GO:0006350 : transcription [28093 gene products]
- GO:0006351 : transcription, DNA-dependent [21637 gene products]
- GO:0006410 : transcription, RNA-dependent [79 gene products]
- GO:0019083 : viral transcription [265 gene products]

GO:0045449 : regulation of transcription [25298 gene products]
- GO:0006355 : regulation of transcription, DNA-dependent [19684 gene products]
- GO:0046782 : regulation of viral transcription [80 gene products]

GO:0045941 : positive regulation of transcription [3897 gene products]
- GO:0045893 : positive regulation of transcription, DNA-dependent [3099 gene products]
- GO:0050434 : positive regulation of viral transcription [58 gene products]

GO:0016481 : negative regulation of transcription [4008 gene products]
- GO:0075182 : negative regulation of symbiont transcription in response to host [1 gene product]
- GO:0045892 : negative regulation of transcription, DNA-dependent [2852 gene products]
- GO:0032897 : negative regulation of viral transcription [25 gene products]

Annotation counts for terms by Source and Evidence code (2-17-2011)

transcription

GO:0006350	transcription	AspGD	IEA	2
GO:0006350	transcription	AspGD	IMP	4
GO:0006350	transcription	AspGD	ISA	1
GO:0006350	transcription	CGD	IEA	6
GO:0006350	transcription	dictyBase	IC	1
GO:0006350	transcription	dictyBase	IEA	29
GO:0006350	transcription	dictyBase	ISS	1
GO:0006350	transcription	EcoCyc	IDA	11
GO:0006350	transcription	EcoCyc	IEA	470
GO:0006350	transcription	EcoCyc	IEP	17
GO:0006350	transcription	EcoCyc	IGI	3
GO:0006350	transcription	EcoCyc	IMP	11
GO:0006350	transcription	EcoCyc	ISS	53
GO:0006350	transcription	EcoCyc	RCA	1
GO:0006350	transcription	Ensembl	IEA	24
GO:0006350	transcription	FB	IDA	7
GO:0006350	transcription	FB	IEA	11
GO:0006350	transcription	FB	IEP	2
GO:0006350	transcription	FB	IMP	3
GO:0006350	transcription	FB	ISS	13
GO:0006350	transcription	FB	NAS	8
GO:0006350	transcription	FB	TAS	4
GO:0006350	transcription	GeneDB_Pfalciparum	ISS	1
GO:0006350	transcription	GeneDB_Spombe	IEA	3
GO:0006350	transcription	GeneDB_Spombe	ISS	5
GO:0006350	transcription	GeneDB_Spombe	NAS	1
GO:0006350	transcription	GeneDB_Tbrucei	IDA	1
GO:0006350	transcription	GeneDB_Tbrucei	ISS	13
GO:0006350	transcription	GR_protein	IC	1
GO:0006350	transcription	GR_protein	RCA	3
GO:0006350	transcription	JCVI_CMR	ISS	54
GO:0006350	transcription	MGI	IDA	4
GO:0006350	transcription	MGI	IEA	1594
GO:0006350	transcription	MGI	IGI	1
GO:0006350	transcription	MGI	IMP	3
GO:0006350	transcription	MGI	IPI	1
GO:0006350	transcription	MGI	ISA	1
GO:0006350	transcription	MGI	ISO	5
GO:0006350	transcription	MGI	ISS	1
GO:0006350	transcription	MGI	NAS	2
GO:0006350	transcription	MGI	TAS	6
GO:0006350	transcription	NCBI	ISS	2
GO:0006350	transcription	PDB	IEA	2653
GO:0006350	transcription	PseudoCAP	RCA	6
GO:0006350	transcription	RefSeq	IEA	22
GO:0006350	transcription	RGD	IEA	43
GO:0006350	transcription	RGD	ISO	13
GO:0006350	transcription	RGD	ISS	1
GO:0006350	transcription	SGD	IDA	6
GO:0006350	transcription	SGD	IEA	574
GO:0006350	transcription	SGD	IGI	6
GO:0006350	transcription	SGD	IMP	8
GO:0006350	transcription	SGD	IPI	8
GO:0006350	transcription	SGD	ISA	1
GO:0006350	transcription	SGD	ISS	3
GO:0006350	transcription	SGD	RCA	2
GO:0006350	transcription	SGD	TAS	4
GO:0006350	transcription	SGN	IEP	1
GO:0006350	transcription	TAIR	IEA	57
GO:0006350	transcription	TAIR	ISS	42
GO:0006350	transcription	TIGR_CMR	ISS	71
GO:0006350	transcription	UniProtKB	IDA	11
GO:0006350	transcription	UniProtKB	IEA	467041
GO:0006350	transcription	UniProtKB	ISS	7
GO:0006350	transcription	UniProtKB	NAS	7
GO:0006350	transcription	UniProtKB	TAS	204
GO:0006350	transcription	WB	IDA	1
GO:0006350	transcription	WB	IEA	30
GO:0006350	transcription	WB	IMP	1
GO:0006350	transcription	ZFIN	IEA	592

regulation of transcription

GO:0045449	regulation of transcription	ASAP	IMP	1
GO:0045449	regulation of transcription	AspGD	IEA	5
GO:0045449	regulation of transcription	AspGD	IMP	3
GO:0045449	regulation of transcription	AspGD	ISS	2
GO:0045449	regulation of transcription	CGD	IEA	9
GO:0045449	regulation of transcription	CGD	IMP	4
GO:0045449	regulation of transcription	CGD	ISS	1
GO:0045449	regulation of transcription	CGD	TAS	1
GO:0045449	regulation of transcription	dictyBase	IEA	25
GO:0045449	regulation of transcription	dictyBase	IMP	2
GO:0045449	regulation of transcription	dictyBase	ISS	7
GO:0045449	regulation of transcription	EcoCyc	IEA	174
GO:0045449	regulation of transcription	Ensembl	IEA	91
GO:0045449	regulation of transcription	FB	IDA	13
GO:0045449	regulation of transcription	FB	IEA	56
GO:0045449	regulation of transcription	FB	IGI	1
GO:0045449	regulation of transcription	FB	IMP	20
GO:0045449	regulation of transcription	FB	ISS	81
GO:0045449	regulation of transcription	FB	NAS	31
GO:0045449	regulation of transcription	FB	TAS	13
GO:0045449	regulation of transcription	GeneDB_Spombe	IDA	3
GO:0045449	regulation of transcription	GeneDB_Spombe	IEA	4
GO:0045449	regulation of transcription	GeneDB_Spombe	IMP	1
GO:0045449	regulation of transcription	GeneDB_Spombe	ISS	33
GO:0045449	regulation of transcription	GeneDB_Spombe	NAS	3
GO:0045449	regulation of transcription	GeneDB_Spombe	RCA	1
GO:0045449	regulation of transcription	GeneDB_Spombe	TAS	6
GO:0045449	regulation of transcription	GR_protein	IC	304
GO:0045449	regulation of transcription	GR_protein	IDA	1
GO:0045449	regulation of transcription	GR_protein	ISS	1
GO:0045449	regulation of transcription	GR_protein	RCA	18
GO:0045449	regulation of transcription	JCVI_CMR	IDA	2
GO:0045449	regulation of transcription	JCVI_CMR	IMP	2
GO:0045449	regulation of transcription	JCVI_CMR	ISS	57
GO:0045449	regulation of transcription	MGI	IDA	48
GO:0045449	regulation of transcription	MGI	IEA	1925
GO:0045449	regulation of transcription	MGI	IGI	6
GO:0045449	regulation of transcription	MGI	IMP	17
GO:0045449	regulation of transcription	MGI	IPI	1
GO:0045449	regulation of transcription	MGI	ISA	4
GO:0045449	regulation of transcription	MGI	ISO	39
GO:0045449	regulation of transcription	MGI	ISS	4
GO:0045449	regulation of transcription	MGI	NAS	3
GO:0045449	regulation of transcription	MGI	TAS	10
GO:0045449	regulation of transcription	PDB	IDA	12
GO:0045449	regulation of transcription	PDB	IEA	2737
GO:0045449	regulation of transcription	PDB	IGI	12
GO:0045449	regulation of transcription	PDB	IMP	21
GO:0045449	regulation of transcription	PseudoCAP	IDA	4
GO:0045449	regulation of transcription	PseudoCAP	ISS	2
GO:0045449	regulation of transcription	PseudoCAP	RCA	13
GO:0045449	regulation of transcription	RefSeq	IEA	61
GO:0045449	regulation of transcription	RGD	IDA	5
GO:0045449	regulation of transcription	RGD	IEA	332
GO:0045449	regulation of transcription	RGD	IMP	1
GO:0045449	regulation of transcription	RGD	ISO	90
GO:0045449	regulation of transcription	RGD	ISS	8
GO:0045449	regulation of transcription	RGD	NAS	2
GO:0045449	regulation of transcription	RGD	TAS	4
GO:0045449	regulation of transcription	SGD	IC	1
GO:0045449	regulation of transcription	SGD	IDA	2
GO:0045449	regulation of transcription	SGD	IEA	524
GO:0045449	regulation of transcription	SGD	IEP	1
GO:0045449	regulation of transcription	SGD	IGI	1
GO:0045449	regulation of transcription	SGD	IMP	15
GO:0045449	regulation of transcription	SGD	IPI	1
GO:0045449	regulation of transcription	SGD	TAS	2
GO:0045449	regulation of transcription	TAIR	IDA	6
GO:0045449	regulation of transcription	TAIR	IEA	224
GO:0045449	regulation of transcription	TAIR	IEP	3
GO:0045449	regulation of transcription	TAIR	IGI	3
GO:0045449	regulation of transcription	TAIR	IMP	9
GO:0045449	regulation of transcription	TAIR	ISS	2
GO:0045449	regulation of transcription	TAIR	TAS	529
GO:0045449	regulation of transcription	TIGR_CMR	ISS	41
GO:0045449	regulation of transcription	UniProt	IMP	2
GO:0045449	regulation of transcription	UniProtKB	IDA	52
GO:0045449	regulation of transcription	UniProtKB	IEA	471085
GO:0045449	regulation of transcription	UniProtKB	IGI	2
GO:0045449	regulation of transcription	UniProtKB	IMP	21
GO:0045449	regulation of transcription	UniProtKB	ISS	108
GO:0045449	regulation of transcription	UniProtKB	NAS	17
GO:0045449	regulation of transcription	UniProtKB	TAS	5
GO:0045449	regulation of transcription	WB	IC	1
GO:0045449	regulation of transcription	WB	IDA	2
GO:0045449	regulation of transcription	WB	IEA	193
GO:0045449	regulation of transcription	WB	IEP	2
GO:0045449	regulation of transcription	WB	ISS	5
GO:0045449	regulation of transcription	WB	TAS	7
GO:0045449	regulation of transcription	ZFIN	IDA	9
GO:0045449	regulation of transcription	ZFIN	IEA	1193
GO:0045449	regulation of transcription	ZFIN	IGI	2
GO:0045449	regulation of transcription	ZFIN	IMP	5
GO:0045449	regulation of transcription	ZFIN	ISS	2

positive regulation of transcription

GO:0045941	positive regulation of transcription	ASAP	IMP	2
GO:0045941	positive regulation of transcription	ASAP	ISA	2
GO:0045941	positive regulation of transcription	AspGD	IDA	1
GO:0045941	positive regulation of transcription	AspGD	IEA	1
GO:0045941	positive regulation of transcription	AspGD	IMP	2
GO:0045941	positive regulation of transcription	CGD	IDA	1
GO:0045941	positive regulation of transcription	CGD	IEA	1
GO:0045941	positive regulation of transcription	CGD	IMP	1
GO:0045941	positive regulation of transcription	CGD	ISS	1
GO:0045941	positive regulation of transcription	dictyBase	IEA	2
GO:0045941	positive regulation of transcription	dictyBase	IMP	2
GO:0045941	positive regulation of transcription	dictyBase	ISS	1
GO:0045941	positive regulation of transcription	EcoCyc	IEA	6
GO:0045941	positive regulation of transcription	EcoCyc	IMP	1
GO:0045941	positive regulation of transcription	FB	IDA	4
GO:0045941	positive regulation of transcription	FB	IEA	3
GO:0045941	positive regulation of transcription	FB	IGI	1
GO:0045941	positive regulation of transcription	FB	IMP	15
GO:0045941	positive regulation of transcription	FB	ISS	4
GO:0045941	positive regulation of transcription	FB	NAS	1
GO:0045941	positive regulation of transcription	FB	TAS	7
GO:0045941	positive regulation of transcription	GeneDB_Spombe	IDA	2
GO:0045941	positive regulation of transcription	GeneDB_Spombe	IEA	4
GO:0045941	positive regulation of transcription	GeneDB_Spombe	IGI	1
GO:0045941	positive regulation of transcription	GeneDB_Spombe	ISS	4
GO:0045941	positive regulation of transcription	JCVI_CMR	ISS	6
GO:0045941	positive regulation of transcription	MGI	IC	1
GO:0045941	positive regulation of transcription	MGI	IDA	128
GO:0045941	positive regulation of transcription	MGI	IEA	7
GO:0045941	positive regulation of transcription	MGI	IGI	6
GO:0045941	positive regulation of transcription	MGI	IMP	26
GO:0045941	positive regulation of transcription	MGI	IPI	3
GO:0045941	positive regulation of transcription	MGI	ISA	6
GO:0045941	positive regulation of transcription	MGI	ISO	137
GO:0045941	positive regulation of transcription	MGI	ISS	25
GO:0045941	positive regulation of transcription	MGI	TAS	14
GO:0045941	positive regulation of transcription	PDB	IDA	17
GO:0045941	positive regulation of transcription	PDB	IEA	60
GO:0045941	positive regulation of transcription	PDB	IGI	2
GO:0045941	positive regulation of transcription	RefSeq	IEA	1
GO:0045941	positive regulation of transcription	RGD	IDA	20
GO:0045941	positive regulation of transcription	RGD	IEA	21
GO:0045941	positive regulation of transcription	RGD	IEP	2
GO:0045941	positive regulation of transcription	RGD	IMP	14
GO:0045941	positive regulation of transcription	RGD	ISO	209
GO:0045941	positive regulation of transcription	RGD	ISS	17
GO:0045941	positive regulation of transcription	RGD	TAS	1
GO:0045941	positive regulation of transcription	SGD	IDA	3
GO:0045941	positive regulation of transcription	SGD	IEA	3
GO:0045941	positive regulation of transcription	SGD	IGI	1
GO:0045941	positive regulation of transcription	SGD	IMP	4
GO:0045941	positive regulation of transcription	SGD	IPI	2
GO:0045941	positive regulation of transcription	SGD	RCA	37
GO:0045941	positive regulation of transcription	TAIR	IDA	19
GO:0045941	positive regulation of transcription	TAIR	IEA	6
GO:0045941	positive regulation of transcription	TAIR	IEP	6
GO:0045941	positive regulation of transcription	TAIR	IGI	3
GO:0045941	positive regulation of transcription	TAIR	IMP	4
GO:0045941	positive regulation of transcription	TAIR	IPI	1
GO:0045941	positive regulation of transcription	TAIR	ISS	1
GO:0045941	positive regulation of transcription	TAIR	TAS	6
GO:0045941	positive regulation of transcription	TIGR_CMR	ISS	1
GO:0045941	positive regulation of transcription	UniProt	IDA	1
GO:0045941	positive regulation of transcription	UniProt	IMP	3
GO:0045941	positive regulation of transcription	UniProtKB	IDA	138
GO:0045941	positive regulation of transcription	UniProtKB	IEA	5256
GO:0045941	positive regulation of transcription	UniProtKB	IGI	3
GO:0045941	positive regulation of transcription	UniProtKB	IMP	27
GO:0045941	positive regulation of transcription	UniProtKB	ISS	202
GO:0045941	positive regulation of transcription	UniProtKB	NAS	7
GO:0045941	positive regulation of transcription	UniProtKB	TAS	10
GO:0045941	positive regulation of transcription	WB	IDA	1
GO:0045941	positive regulation of transcription	WB	IEA	1
GO:0045941	positive regulation of transcription	WB	IMP	1
GO:0045941	positive regulation of transcription	ZFIN	IDA	4
GO:0045941	positive regulation of transcription	ZFIN	IEA	17
GO:0045941	positive regulation of transcription	ZFIN	IGI	4
GO:0045941	positive regulation of transcription	ZFIN	IMP	8
GO:0045941	positive regulation of transcription	ZFIN	IPI	5
GO:0045941	positive regulation of transcription	ZFIN	NAS	1

negative regulation of transcription

GO:0016481	negative regulation of transcription	ASAP	IDA	1
GO:0016481	negative regulation of transcription	ASAP	IMP	1
GO:0016481	negative regulation of transcription	ASAP	ISA	1
GO:0016481	negative regulation of transcription	AspGD	IEA	1
GO:0016481	negative regulation of transcription	AspGD	IMP	3
GO:0016481	negative regulation of transcription	CGD	IDA	1
GO:0016481	negative regulation of transcription	CGD	IGI	1
GO:0016481	negative regulation of transcription	CGD	IMP	9
GO:0016481	negative regulation of transcription	CGD	ISS	1
GO:0016481	negative regulation of transcription	dictyBase	IEA	1
GO:0016481	negative regulation of transcription	dictyBase	ISS	1
GO:0016481	negative regulation of transcription	EcoCyc	IDA	2
GO:0016481	negative regulation of transcription	EcoCyc	IEA	2
GO:0016481	negative regulation of transcription	EcoCyc	IMP	1
GO:0016481	negative regulation of transcription	Ensembl	IEA	3
GO:0016481	negative regulation of transcription	FB	IDA	18
GO:0016481	negative regulation of transcription	FB	IEA	2
GO:0016481	negative regulation of transcription	FB	IEP	2
GO:0016481	negative regulation of transcription	FB	IGI	4
GO:0016481	negative regulation of transcription	FB	IMP	10
GO:0016481	negative regulation of transcription	FB	ISS	3
GO:0016481	negative regulation of transcription	FB	NAS	14
GO:0016481	negative regulation of transcription	FB	TAS	8
GO:0016481	negative regulation of transcription	GeneDB_Spombe	IMP	1
GO:0016481	negative regulation of transcription	GeneDB_Spombe	ISS	5
GO:0016481	negative regulation of transcription	GeneDB_Tbrucei	ISS	3
GO:0016481	negative regulation of transcription	JCVI_CMR	ISS	8
GO:0016481	negative regulation of transcription	MGI	IC	2
GO:0016481	negative regulation of transcription	MGI	IDA	75
GO:0016481	negative regulation of transcription	MGI	IEA	6
GO:0016481	negative regulation of transcription	MGI	IGI	4
GO:0016481	negative regulation of transcription	MGI	IMP	16
GO:0016481	negative regulation of transcription	MGI	IPI	1
GO:0016481	negative regulation of transcription	MGI	ISA	3
GO:0016481	negative regulation of transcription	MGI	ISO	119
GO:0016481	negative regulation of transcription	MGI	ISS	42
GO:0016481	negative regulation of transcription	MGI	NAS	2
GO:0016481	negative regulation of transcription	MGI	RCA	1
GO:0016481	negative regulation of transcription	MGI	TAS	6
GO:0016481	negative regulation of transcription	PDB	IDA	37
GO:0016481	negative regulation of transcription	PDB	IEA	478
GO:0016481	negative regulation of transcription	RefSeq	IEA	2
GO:0016481	negative regulation of transcription	RGD	IDA	14
GO:0016481	negative regulation of transcription	RGD	IEA	18
GO:0016481	negative regulation of transcription	RGD	IEP	1
GO:0016481	negative regulation of transcription	RGD	IMP	13
GO:0016481	negative regulation of transcription	RGD	ISO	174
GO:0016481	negative regulation of transcription	RGD	ISS	20
GO:0016481	negative regulation of transcription	RGD	NAS	1
GO:0016481	negative regulation of transcription	RGD	TAS	2
GO:0016481	negative regulation of transcription	SGD	IDA	4
GO:0016481	negative regulation of transcription	SGD	IEA	2
GO:0016481	negative regulation of transcription	SGD	IMP	6
GO:0016481	negative regulation of transcription	SGD	IPI	2
GO:0016481	negative regulation of transcription	SGD	RCA	31
GO:0016481	negative regulation of transcription	TAIR	IDA	8
GO:0016481	negative regulation of transcription	TAIR	IEA	4
GO:0016481	negative regulation of transcription	TAIR	IEP	8
GO:0016481	negative regulation of transcription	TAIR	IGI	1
GO:0016481	negative regulation of transcription	TAIR	IMP	14
GO:0016481	negative regulation of transcription	TAIR	IPI	2
GO:0016481	negative regulation of transcription	TAIR	ISS	2
GO:0016481	negative regulation of transcription	TAIR	TAS	1
GO:0016481	negative regulation of transcription	TIGR_CMR	ISS	16
GO:0016481	negative regulation of transcription	UniProt	IDA	1
GO:0016481	negative regulation of transcription	UniProt	IGI	2
GO:0016481	negative regulation of transcription	UniProtKB	IC	1
GO:0016481	negative regulation of transcription	UniProtKB	IDA	116
GO:0016481	negative regulation of transcription	UniProtKB	IEA	42674
GO:0016481	negative regulation of transcription	UniProtKB	IMP	27
GO:0016481	negative regulation of transcription	UniProtKB	ISS	123
GO:0016481	negative regulation of transcription	UniProtKB	NAS	17
GO:0016481	negative regulation of transcription	UniProtKB	TAS	1
GO:0016481	negative regulation of transcription	WB	IDA	2
GO:0016481	negative regulation of transcription	WB	IEA	2
GO:0016481	negative regulation of transcription	WB	IMP	2
GO:0016481	negative regulation of transcription	WB	ISS	1
GO:0016481	negative regulation of transcription	WB	TAS	3
GO:0016481	negative regulation of transcription	ZFIN	IDA	5
GO:0016481	negative regulation of transcription	ZFIN	IEA	8
GO:0016481	negative regulation of transcription	ZFIN	IGI	2
GO:0016481	negative regulation of transcription	ZFIN	IMP	2

Subsets that terms are included in (2-17-2011)

GO:0006350	transcription	Candida GO slim
GO:0006350	transcription	Fission yeast GO slim
GO:0006350	transcription	Generic GO slim
GO:0006350	transcription	PIR GO slim
GO:0006350	transcription	Plant GO slim
GO:0006350	transcription	Prokaryotic GO subset
GO:0006350	transcription	Yeast GO slim

GO:0016481	negative regulation of transcription	Prokaryotic GO subset

GO:0045449	regulation of transcription	Prokaryotic GO subset

GO:0045941	positive regulation of transcription	Prokaryotic GO subset

Non-definition dbxrefs for terms (2-17-2011)

transcription

GO:0006350	transcription	COG:K
GO:0006350	transcription	InterPro:IPR000722
GO:0006350	transcription	InterPro:IPR000783
GO:0006350	transcription	InterPro:IPR001009
GO:0006350	transcription	InterPro:IPR001016
GO:0006350	transcription	InterPro:IPR001205
GO:0006350	transcription	InterPro:IPR001407
GO:0006350	transcription	InterPro:IPR001514
GO:0006350	transcription	InterPro:IPR001529
GO:0006350	transcription	InterPro:IPR001591
GO:0006350	transcription	InterPro:IPR001788
GO:0006350	transcription	InterPro:IPR001795
GO:0006350	transcription	InterPro:IPR002092
GO:0006350	transcription	InterPro:IPR002166
GO:0006350	transcription	InterPro:IPR002693
GO:0006350	transcription	InterPro:IPR003176
GO:0006350	transcription	InterPro:IPR003617
GO:0006350	transcription	InterPro:IPR003618
GO:0006350	transcription	InterPro:IPR004519
GO:0006350	transcription	InterPro:IPR005570
GO:0006350	transcription	InterPro:IPR005571
GO:0006350	transcription	InterPro:IPR005574
GO:0006350	transcription	InterPro:IPR005576
GO:0006350	transcription	InterPro:IPR006288
GO:0006350	transcription	InterPro:IPR006591
GO:0006350	transcription	InterPro:IPR006592
GO:0006350	transcription	InterPro:IPR006711
GO:0006350	transcription	InterPro:IPR006712
GO:0006350	transcription	InterPro:IPR006886
GO:0006350	transcription	InterPro:IPR007012
GO:0006350	transcription	InterPro:IPR007015
GO:0006350	transcription	InterPro:IPR007025
GO:0006350	transcription	InterPro:IPR007066
GO:0006350	transcription	InterPro:IPR007073
GO:0006350	transcription	InterPro:IPR007075
GO:0006350	transcription	InterPro:IPR007080
GO:0006350	transcription	InterPro:IPR007081
GO:0006350	transcription	InterPro:IPR007083
GO:0006350	transcription	InterPro:IPR007120
GO:0006350	transcription	InterPro:IPR007121
GO:0006350	transcription	InterPro:IPR007219
GO:0006350	transcription	InterPro:IPR007322
GO:0006350	transcription	InterPro:IPR007610
GO:0006350	transcription	InterPro:IPR007641
GO:0006350	transcription	InterPro:IPR007642
GO:0006350	transcription	InterPro:IPR007644
GO:0006350	transcription	InterPro:IPR007645
GO:0006350	transcription	InterPro:IPR007646
GO:0006350	transcription	InterPro:IPR007647
GO:0006350	transcription	InterPro:IPR007759
GO:0006350	transcription	InterPro:IPR007832
GO:0006350	transcription	InterPro:IPR008193
GO:0006350	transcription	InterPro:IPR008448
GO:0006350	transcription	InterPro:IPR008723
GO:0006350	transcription	InterPro:IPR008806
GO:0006350	transcription	InterPro:IPR009025
GO:0006350	transcription	InterPro:IPR009162
GO:0006350	transcription	InterPro:IPR009469
GO:0006350	transcription	InterPro:IPR009668
GO:0006350	transcription	InterPro:IPR009674
GO:0006350	transcription	InterPro:IPR010243
GO:0006350	transcription	InterPro:IPR010533
GO:0006350	transcription	InterPro:IPR011260
GO:0006350	transcription	InterPro:IPR011261
GO:0006350	transcription	InterPro:IPR011262
GO:0006350	transcription	InterPro:IPR011263
GO:0006350	transcription	InterPro:IPR012164
GO:0006350	transcription	InterPro:IPR012754
GO:0006350	transcription	InterPro:IPR012755
GO:0006350	transcription	InterPro:IPR012756
GO:0006350	transcription	InterPro:IPR012757
GO:0006350	transcription	InterPro:IPR012758
GO:0006350	transcription	InterPro:IPR013676
GO:0006350	transcription	InterPro:IPR015699
GO:0006350	transcription	InterPro:IPR015700
GO:0006350	transcription	InterPro:IPR015712
GO:0006350	transcription	InterPro:IPR016075
GO:0006350	transcription	InterPro:IPR016263
GO:0006350	transcription	InterPro:IPR016371
GO:0006350	transcription	InterPro:IPR017890
GO:0006350	transcription	InterPro:IPR017923
GO:0006350	transcription	InterPro:IPR019969
GO:0006350	transcription	InterPro:IPR020357
GO:0006350	transcription	JCVI_TIGRFAMS:TIGR00448
GO:0006350	transcription	JCVI_TIGRFAMS:TIGR00621
GO:0006350	transcription	JCVI_TIGRFAMS:TIGR00690
GO:0006350	transcription	JCVI_TIGRFAMS:TIGR01384
GO:0006350	transcription	JCVI_TIGRFAMS:TIGR01385
GO:0006350	transcription	JCVI_TIGRFAMS:TIGR02013
GO:0006350	transcription	JCVI_TIGRFAMS:TIGR02027
GO:0006350	transcription	JCVI_TIGRFAMS:TIGR02386
GO:0006350	transcription	JCVI_TIGRFAMS:TIGR03298
GO:0006350	transcription	MIPS_funcat:11
GO:0006350	transcription	MIPS_funcat:11.02.03.01
GO:0006350	transcription	MultiFun:2.2.2
GO:0006350	transcription	Pfam:PF00562
GO:0006350	transcription	Pfam:PF00602
GO:0006350	transcription	Pfam:PF00603
GO:0006350	transcription	Pfam:PF00604
GO:0006350	transcription	Pfam:PF00623
GO:0006350	transcription	Pfam:PF00680
GO:0006350	transcription	Pfam:PF00940
GO:0006350	transcription	Pfam:PF00946
GO:0006350	transcription	Pfam:PF00978
GO:0006350	transcription	Pfam:PF00998
GO:0006350	transcription	Pfam:PF01000
GO:0006350	transcription	Pfam:PF01191
GO:0006350	transcription	Pfam:PF01193
GO:0006350	transcription	Pfam:PF01806
GO:0006350	transcription	Pfam:PF02123
GO:0006350	transcription	Pfam:PF02150
GO:0006350	transcription	Pfam:PF02236
GO:0006350	transcription	Pfam:PF03118
GO:0006350	transcription	Pfam:PF03604
GO:0006350	transcription	Pfam:PF03870
GO:0006350	transcription	Pfam:PF03871
GO:0006350	transcription	Pfam:PF03874
GO:0006350	transcription	Pfam:PF03876
GO:0006350	transcription	Pfam:PF04082
GO:0006350	transcription	Pfam:PF04196
GO:0006350	transcription	Pfam:PF04522
GO:0006350	transcription	Pfam:PF04560
GO:0006350	transcription	Pfam:PF04561
GO:0006350	transcription	Pfam:PF04563
GO:0006350	transcription	Pfam:PF04565
GO:0006350	transcription	Pfam:PF04566
GO:0006350	transcription	Pfam:PF04567
GO:0006350	transcription	Pfam:PF04617
GO:0006350	transcription	Pfam:PF04618
GO:0006350	transcription	Pfam:PF04801
GO:0006350	transcription	Pfam:PF04928
GO:0006350	transcription	Pfam:PF04931
GO:0006350	transcription	Pfam:PF04941
GO:0006350	transcription	Pfam:PF04983
GO:0006350	transcription	Pfam:PF04990
GO:0006350	transcription	Pfam:PF04992
GO:0006350	transcription	Pfam:PF04997
GO:0006350	transcription	Pfam:PF04998
GO:0006350	transcription	Pfam:PF05000
GO:0006350	transcription	Pfam:PF05066
GO:0006350	transcription	Pfam:PF05158
GO:0006350	transcription	Pfam:PF05645
GO:0006350	transcription	Pfam:PF05788
GO:0006350	transcription	Pfam:PF05864
GO:0006350	transcription	Pfam:PF06478
GO:0006350	transcription	Pfam:PF06529
GO:0006350	transcription	Pfam:PF06870
GO:0006350	transcription	Pfam:PF06883
GO:0006350	transcription	Pfam:PF07180
GO:0006350	transcription	Pfam:PF07500
GO:0006350	transcription	Pfam:PF08469
GO:0006350	transcription	Pfam:PF08711
GO:0006350	transcription	PIRSF:PIRSF000745
GO:0006350	transcription	PIRSF:PIRSF000770
GO:0006350	transcription	PIRSF:PIRSF000779
GO:0006350	transcription	PIRSF:PIRSF000821
GO:0006350	transcription	PIRSF:PIRSF000827
GO:0006350	transcription	PIRSF:PIRSF002939
GO:0006350	transcription	PIRSF:PIRSF005586
GO:0006350	transcription	PIRSF:PIRSF028763
GO:0006350	transcription	PRINTS:PR00914
GO:0006350	transcription	ProDom:PD001179
GO:0006350	transcription	ProDom:PD001667
GO:0006350	transcription	ProDom:PD005155
GO:0006350	transcription	ProDom:PD019250
GO:0006350	transcription	ProDom:PD081346
GO:0006350	transcription	PROSITE:MF_00357
GO:0006350	transcription	PROSITE:MF_00411
GO:0006350	transcription	PROSITE:MF_01321
GO:0006350	transcription	PROSITE:MF_01322
GO:0006350	transcription	PROSITE:MF_01324
GO:0006350	transcription	PROSITE:PS00446
GO:0006350	transcription	PROSITE:PS00489
GO:0006350	transcription	PROSITE:PS00900
GO:0006350	transcription	PROSITE:PS01154
GO:0006350	transcription	PROSITE:PS01166
GO:0006350	transcription	PROSITE:PS51319
GO:0006350	transcription	PROSITE:PS51321
GO:0006350	transcription	Reactome:1006454
GO:0006350	transcription	Reactome:1006472
GO:0006350	transcription	Reactome:1024797
GO:0006350	transcription	Reactome:1024798
GO:0006350	transcription	Reactome:1051758
GO:0006350	transcription	Reactome:1051777
GO:0006350	transcription	Reactome:1076727
GO:0006350	transcription	Reactome:1076728
GO:0006350	transcription	Reactome:1097242
GO:0006350	transcription	Reactome:1097243
GO:0006350	transcription	Reactome:1116518
GO:0006350	transcription	Reactome:1116536
GO:0006350	transcription	Reactome:1140334
GO:0006350	transcription	Reactome:1140353
GO:0006350	transcription	Reactome:1170595
GO:0006350	transcription	Reactome:1170596
GO:0006350	transcription	Reactome:1192400
GO:0006350	transcription	Reactome:1192418
GO:0006350	transcription	Reactome:1206594
GO:0006350	transcription	Reactome:1206613
GO:0006350	transcription	Reactome:1221238
GO:0006350	transcription	Reactome:1221239
GO:0006350	transcription	Reactome:1239222
GO:0006350	transcription	Reactome:1239223
GO:0006350	transcription	Reactome:1246798
GO:0006350	transcription	Reactome:1246799
GO:0006350	transcription	Reactome:1252555
GO:0006350	transcription	Reactome:1252556
GO:0006350	transcription	Reactome:1258342
GO:0006350	transcription	Reactome:1258343
GO:0006350	transcription	Reactome:1262041
GO:0006350	transcription	Reactome:1262042
GO:0006350	transcription	Reactome:504046
GO:0006350	transcription	Reactome:74159
GO:0006350	transcription	Reactome:979861
GO:0006350	transcription	Reactome:979877
GO:0006350	transcription	SMART:SM00509
GO:0006350	transcription	SMART:SM00510
GO:0006350	transcription	SMART:SM00658
GO:0006350	transcription	SMART:SM00659
GO:0006350	transcription	SMART:SM00661
GO:0006350	transcription	SMART:SM00662
GO:0006350	transcription	SMART:SM00663
GO:0006350	transcription	SMART:SM00906
GO:0006350	transcription	SP_KW:KW-0804
GO:0006350	transcription	TIGR_role:20050
GO:0006350	transcription	Wikipedia:Transcription_(genetics)

negative regulation of transcription

GO:0016481	negative regulation of transcription	HAMAP:MF_01140
GO:0016481	negative regulation of transcription	HAMAP:MF_01814
GO:0016481	negative regulation of transcription	InterPro:IPR003012
GO:0016481	negative regulation of transcription	InterPro:IPR003796
GO:0016481	negative regulation of transcription	InterPro:IPR004111
GO:0016481	negative regulation of transcription	InterPro:IPR005650
GO:0016481	negative regulation of transcription	InterPro:IPR006942
GO:0016481	negative regulation of transcription	InterPro:IPR006986
GO:0016481	negative regulation of transcription	InterPro:IPR006988
GO:0016481	negative regulation of transcription	InterPro:IPR006989
GO:0016481	negative regulation of transcription	InterPro:IPR007412
GO:0016481	negative regulation of transcription	InterPro:IPR008468
GO:0016481	negative regulation of transcription	InterPro:IPR009718
GO:0016481	negative regulation of transcription	InterPro:IPR010078
GO:0016481	negative regulation of transcription	InterPro:IPR010089
GO:0016481	negative regulation of transcription	InterPro:IPR010405
GO:0016481	negative regulation of transcription	InterPro:IPR010575
GO:0016481	negative regulation of transcription	InterPro:IPR010712
GO:0016481	negative regulation of transcription	InterPro:IPR010744
GO:0016481	negative regulation of transcription	InterPro:IPR011350
GO:0016481	negative regulation of transcription	InterPro:IPR012712
GO:0016481	negative regulation of transcription	InterPro:IPR012771
GO:0016481	negative regulation of transcription	InterPro:IPR012925
GO:0016481	negative regulation of transcription	InterPro:IPR013571
GO:0016481	negative regulation of transcription	InterPro:IPR013573
GO:0016481	negative regulation of transcription	InterPro:IPR015309
GO:0016481	negative regulation of transcription	InterPro:IPR015893
GO:0016481	negative regulation of transcription	InterPro:IPR016429
GO:0016481	negative regulation of transcription	InterPro:IPR017275
GO:0016481	negative regulation of transcription	JCVI_TIGRFAMS:TIGR02451
GO:0016481	negative regulation of transcription	Pfam:PF02909
GO:0016481	negative regulation of transcription	Pfam:PF03965
GO:0016481	negative regulation of transcription	Pfam:PF04316
GO:0016481	negative regulation of transcription	Pfam:PF04858
GO:0016481	negative regulation of transcription	Pfam:PF04902
GO:0016481	negative regulation of transcription	Pfam:PF04904
GO:0016481	negative regulation of transcription	Pfam:PF04905
GO:0016481	negative regulation of transcription	Pfam:PF05499
GO:0016481	negative regulation of transcription	Pfam:PF06209
GO:0016481	negative regulation of transcription	Pfam:PF06613
GO:0016481	negative regulation of transcription	Pfam:PF06953
GO:0016481	negative regulation of transcription	Pfam:PF06971
GO:0016481	negative regulation of transcription	Pfam:PF07022
GO:0016481	negative regulation of transcription	Pfam:PF07739
GO:0016481	negative regulation of transcription	Pfam:PF08360
GO:0016481	negative regulation of transcription	Pfam:PF08362
GO:0016481	negative regulation of transcription	Pfam:PF09228
GO:0016481	negative regulation of transcription	PIRSF:PIRSF000197
GO:0016481	negative regulation of transcription	PIRSF:PIRSF004776
GO:0016481	negative regulation of transcription	PIRSF:PIRSF017930
GO:0016481	negative regulation of transcription	PIRSF:PIRSF037733
GO:0016481	negative regulation of transcription	PRINTS:PR00400
GO:0016481	negative regulation of transcription	ProDom:PD342192
GO:0016481	negative regulation of transcription	ProDom:PD492828
GO:0016481	negative regulation of transcription	PROSITE:MF_00440
GO:0016481	negative regulation of transcription	PROSITE:MF_01017
GO:0016481	negative regulation of transcription	PROSITE:MF_01814

regulation of transcription

GO:0045449	regulation of transcription	HAMAP:MF_00637
GO:0045449	regulation of transcription	HAMAP:MF_00638
GO:0045449	regulation of transcription	HAMAP:MF_00696
GO:0045449	regulation of transcription	HAMAP:MF_01181
GO:0045449	regulation of transcription	HAMAP:MF_01449
GO:0045449	regulation of transcription	HAMAP:MF_01607
GO:0045449	regulation of transcription	InterPro:IPR001092
GO:0045449	regulation of transcription	InterPro:IPR001222
GO:0045449	regulation of transcription	InterPro:IPR001523
GO:0045449	regulation of transcription	InterPro:IPR002717
GO:0045449	regulation of transcription	InterPro:IPR002910
GO:0045449	regulation of transcription	InterPro:IPR003000
GO:0045449	regulation of transcription	InterPro:IPR003311
GO:0045449	regulation of transcription	InterPro:IPR003441
GO:0045449	regulation of transcription	InterPro:IPR003657
GO:0045449	regulation of transcription	InterPro:IPR003851
GO:0045449	regulation of transcription	InterPro:IPR004092
GO:0045449	regulation of transcription	InterPro:IPR005559
GO:0045449	regulation of transcription	InterPro:IPR006197
GO:0045449	regulation of transcription	InterPro:IPR006377
GO:0045449	regulation of transcription	InterPro:IPR006417
GO:0045449	regulation of transcription	InterPro:IPR006699
GO:0045449	regulation of transcription	InterPro:IPR006779
GO:0045449	regulation of transcription	InterPro:IPR006793
GO:0045449	regulation of transcription	InterPro:IPR006794
GO:0045449	regulation of transcription	InterPro:IPR006820
GO:0045449	regulation of transcription	InterPro:IPR006923
GO:0045449	regulation of transcription	InterPro:IPR007127
GO:0045449	regulation of transcription	InterPro:IPR007198
GO:0045449	regulation of transcription	InterPro:IPR007207
GO:0045449	regulation of transcription	InterPro:IPR007282
GO:0045449	regulation of transcription	InterPro:IPR007448
GO:0045449	regulation of transcription	InterPro:IPR007576
GO:0045449	regulation of transcription	InterPro:IPR007582
GO:0045449	regulation of transcription	InterPro:IPR007654
GO:0045449	regulation of transcription	InterPro:IPR007668
GO:0045449	regulation of transcription	InterPro:IPR007684
GO:0045449	regulation of transcription	InterPro:IPR007689
GO:0045449	regulation of transcription	InterPro:IPR007738
GO:0045449	regulation of transcription	InterPro:IPR007790
GO:0045449	regulation of transcription	InterPro:IPR007933
GO:0045449	regulation of transcription	InterPro:IPR008095
GO:0045449	regulation of transcription	InterPro:IPR008246
GO:0045449	regulation of transcription	InterPro:IPR008247
GO:0045449	regulation of transcription	InterPro:IPR008329
GO:0045449	regulation of transcription	InterPro:IPR008415
GO:0045449	regulation of transcription	InterPro:IPR008422
GO:0045449	regulation of transcription	InterPro:IPR008648
GO:0045449	regulation of transcription	InterPro:IPR008807
GO:0045449	regulation of transcription	InterPro:IPR008831
GO:0045449	regulation of transcription	InterPro:IPR008895
GO:0045449	regulation of transcription	InterPro:IPR008917
GO:0045449	regulation of transcription	InterPro:IPR008967
GO:0045449	regulation of transcription	InterPro:IPR009110
GO:0045449	regulation of transcription	InterPro:IPR009146
GO:0045449	regulation of transcription	InterPro:IPR009170
GO:0045449	regulation of transcription	InterPro:IPR009184
GO:0045449	regulation of transcription	InterPro:IPR009210
GO:0045449	regulation of transcription	InterPro:IPR009349
GO:0045449	regulation of transcription	InterPro:IPR009429
GO:0045449	regulation of transcription	InterPro:IPR009554
GO:0045449	regulation of transcription	InterPro:IPR010525
GO:0045449	regulation of transcription	InterPro:IPR010534
GO:0045449	regulation of transcription	InterPro:IPR010684
GO:0045449	regulation of transcription	InterPro:IPR010912
GO:0045449	regulation of transcription	InterPro:IPR010981
GO:0045449	regulation of transcription	InterPro:IPR010985
GO:0045449	regulation of transcription	InterPro:IPR011075
GO:0045449	regulation of transcription	InterPro:IPR011494
GO:0045449	regulation of transcription	InterPro:IPR011520
GO:0045449	regulation of transcription	InterPro:IPR011539
GO:0045449	regulation of transcription	InterPro:IPR011598
GO:0045449	regulation of transcription	InterPro:IPR011663
GO:0045449	regulation of transcription	InterPro:IPR011794
GO:0045449	regulation of transcription	InterPro:IPR012052
GO:0045449	regulation of transcription	InterPro:IPR012113
GO:0045449	regulation of transcription	InterPro:IPR012129
GO:0045449	regulation of transcription	InterPro:IPR012170
GO:0045449	regulation of transcription	InterPro:IPR012270
GO:0045449	regulation of transcription	InterPro:IPR012287
GO:0045449	regulation of transcription	InterPro:IPR012288
GO:0045449	regulation of transcription	InterPro:IPR012318
GO:0045449	regulation of transcription	InterPro:IPR012423
GO:0045449	regulation of transcription	InterPro:IPR012642
GO:0045449	regulation of transcription	InterPro:IPR012781
GO:0045449	regulation of transcription	InterPro:IPR012845
GO:0045449	regulation of transcription	InterPro:IPR012890
GO:0045449	regulation of transcription	InterPro:IPR012900
GO:0045449	regulation of transcription	InterPro:IPR012957
GO:0045449	regulation of transcription	InterPro:IPR012958
GO:0045449	regulation of transcription	InterPro:IPR013137
GO:0045449	regulation of transcription	InterPro:IPR013192
GO:0045449	regulation of transcription	InterPro:IPR013193
GO:0045449	regulation of transcription	InterPro:IPR013321
GO:0045449	regulation of transcription	InterPro:IPR013503
GO:0045449	regulation of transcription	InterPro:IPR013516
GO:0045449	regulation of transcription	InterPro:IPR013654
GO:0045449	regulation of transcription	InterPro:IPR013700
GO:0045449	regulation of transcription	InterPro:IPR014410
GO:0045449	regulation of transcription	InterPro:IPR014744
GO:0045449	regulation of transcription	InterPro:IPR014920
GO:0045449	regulation of transcription	InterPro:IPR014978
GO:0045449	regulation of transcription	InterPro:IPR015115
GO:0045449	regulation of transcription	InterPro:IPR015265
GO:0045449	regulation of transcription	InterPro:IPR015350
GO:0045449	regulation of transcription	InterPro:IPR016132
GO:0045449	regulation of transcription	InterPro:IPR017366
GO:0045449	regulation of transcription	InterPro:IPR022783
GO:0045449	regulation of transcription	JCVI_TIGRFAMS:TIGR00244
GO:0045449	regulation of transcription	JCVI_TIGRFAMS:TIGR01636
GO:0045449	regulation of transcription	JCVI_TIGRFAMS:TIGR01637
GO:0045449	regulation of transcription	JCVI_TIGRFAMS:TIGR01955
GO:0045449	regulation of transcription	JCVI_TIGRFAMS:TIGR02420
GO:0045449	regulation of transcription	JCVI_TIGRFAMS:TIGR02702
GO:0045449	regulation of transcription	JCVI_TIGRFAMS:TIGR02886
GO:0045449	regulation of transcription	MIPS_funcat:11.02.03.04
GO:0045449	regulation of transcription	Pfam:PF00010
GO:0045449	regulation of transcription	Pfam:PF00292
GO:0045449	regulation of transcription	Pfam:PF00554
GO:0045449	regulation of transcription	Pfam:PF01096
GO:0045449	regulation of transcription	Pfam:PF01698
GO:0045449	regulation of transcription	Pfam:PF01853
GO:0045449	regulation of transcription	Pfam:PF02146
GO:0045449	regulation of transcription	Pfam:PF02309
GO:0045449	regulation of transcription	Pfam:PF02365
GO:0045449	regulation of transcription	Pfam:PF02701
GO:0045449	regulation of transcription	Pfam:PF02820
GO:0045449	regulation of transcription	Pfam:PF03106
GO:0045449	regulation of transcription	Pfam:PF03859
GO:0045449	regulation of transcription	Pfam:PF03979
GO:0045449	regulation of transcription	Pfam:PF04056
GO:0045449	regulation of transcription	Pfam:PF04065
GO:0045449	regulation of transcription	Pfam:PF04153
GO:0045449	regulation of transcription	Pfam:PF04309
GO:0045449	regulation of transcription	Pfam:PF04353
GO:0045449	regulation of transcription	Pfam:PF04487
GO:0045449	regulation of transcription	Pfam:PF04494
GO:0045449	regulation of transcription	Pfam:PF04574
GO:0045449	regulation of transcription	Pfam:PF04589
GO:0045449	regulation of transcription	Pfam:PF04606
GO:0045449	regulation of transcription	Pfam:PF04611
GO:0045449	regulation of transcription	Pfam:PF04689
GO:0045449	regulation of transcription	Pfam:PF04704
GO:0045449	regulation of transcription	Pfam:PF04731
GO:0045449	regulation of transcription	Pfam:PF04838
GO:0045449	regulation of transcription	Pfam:PF05044
GO:0045449	regulation of transcription	Pfam:PF05098
GO:0045449	regulation of transcription	Pfam:PF05269
GO:0045449	regulation of transcription	Pfam:PF05443
GO:0045449	regulation of transcription	Pfam:PF05459
GO:0045449	regulation of transcription	Pfam:PF05669
GO:0045449	regulation of transcription	Pfam:PF05764
GO:0045449	regulation of transcription	Pfam:PF05847
GO:0045449	regulation of transcription	Pfam:PF05920
GO:0045449	regulation of transcription	Pfam:PF06221
GO:0045449	regulation of transcription	Pfam:PF06385
GO:0045449	regulation of transcription	Pfam:PF06507
GO:0045449	regulation of transcription	Pfam:PF06530
GO:0045449	regulation of transcription	Pfam:PF06667
GO:0045449	regulation of transcription	Pfam:PF06881
GO:0045449	regulation of transcription	Pfam:PF07545
GO:0045449	regulation of transcription	Pfam:PF07569
GO:0045449	regulation of transcription	Pfam:PF07702
GO:0045449	regulation of transcription	Pfam:PF07777
GO:0045449	regulation of transcription	Pfam:PF07842
GO:0045449	regulation of transcription	Pfam:PF07904
GO:0045449	regulation of transcription	Pfam:PF07988
GO:0045449	regulation of transcription	Pfam:PF08073
GO:0045449	regulation of transcription	Pfam:PF08074
GO:0045449	regulation of transcription	Pfam:PF08271
GO:0045449	regulation of transcription	Pfam:PF08300
GO:0045449	regulation of transcription	Pfam:PF08301
GO:0045449	regulation of transcription	Pfam:PF08446
GO:0045449	regulation of transcription	Pfam:PF08493
GO:0045449	regulation of transcription	Pfam:PF08671
GO:0045449	regulation of transcription	Pfam:PF08815
GO:0045449	regulation of transcription	Pfam:PF08880
GO:0045449	regulation of transcription	Pfam:PF09026
GO:0045449	regulation of transcription	Pfam:PF09030
GO:0045449	regulation of transcription	Pfam:PF09182
GO:0045449	regulation of transcription	Pfam:PF09270
GO:0045449	regulation of transcription	PIRSF:PIRSF000084
GO:0045449	regulation of transcription	PIRSF:PIRSF002395
GO:0045449	regulation of transcription	PIRSF:PIRSF002937
GO:0045449	regulation of transcription	PIRSF:PIRSF003669
GO:0045449	regulation of transcription	PIRSF:PIRSF005259
GO:0045449	regulation of transcription	PIRSF:PIRSF005290
GO:0045449	regulation of transcription	PIRSF:PIRSF006171
GO:0045449	regulation of transcription	PIRSF:PIRSF006198
GO:0045449	regulation of transcription	PIRSF:PIRSF015919
GO:0045449	regulation of transcription	PIRSF:PIRSF016548
GO:0045449	regulation of transcription	PIRSF:PIRSF027019
GO:0045449	regulation of transcription	PIRSF:PIRSF036385
GO:0045449	regulation of transcription	PIRSF:PIRSF036579
GO:0045449	regulation of transcription	PIRSF:PIRSF038051
GO:0045449	regulation of transcription	PRINTS:PR00027
GO:0045449	regulation of transcription	PRINTS:PR00726
GO:0045449	regulation of transcription	PRINTS:PR01719
GO:0045449	regulation of transcription	PRINTS:PR01850
GO:0045449	regulation of transcription	ProDom:PD007170
GO:0045449	regulation of transcription	ProDom:PD007478
GO:0045449	regulation of transcription	ProDom:PD016258
GO:0045449	regulation of transcription	ProDom:PD029816
GO:0045449	regulation of transcription	ProDom:PD407430
GO:0045449	regulation of transcription	PROSITE:MF_01121
GO:0045449	regulation of transcription	PROSITE:PS00034
GO:0045449	regulation of transcription	PROSITE:PS00245
GO:0045449	regulation of transcription	PROSITE:PS00466
GO:0045449	regulation of transcription	PROSITE:PS01361
GO:0045449	regulation of transcription	PROSITE:PS50046
GO:0045449	regulation of transcription	PROSITE:PS50254
GO:0045449	regulation of transcription	PROSITE:PS50305
GO:0045449	regulation of transcription	PROSITE:PS50811
GO:0045449	regulation of transcription	PROSITE:PS50884
GO:0045449	regulation of transcription	PROSITE:PS50888
GO:0045449	regulation of transcription	PROSITE:PS50917
GO:0045449	regulation of transcription	PROSITE:PS51005
GO:0045449	regulation of transcription	PROSITE:PS51057
GO:0045449	regulation of transcription	PROSITE:PS51063
GO:0045449	regulation of transcription	PROSITE:PS51079
GO:0045449	regulation of transcription	PROSITE:PS51133
GO:0045449	regulation of transcription	PROSITE:PS51134
GO:0045449	regulation of transcription	PROSITE:PS51437
GO:0045449	regulation of transcription	PROSITE:PS51500
GO:0045449	regulation of transcription	SMART:SM00351
GO:0045449	regulation of transcription	SMART:SM00353
GO:0045449	regulation of transcription	SMART:SM00440
GO:0045449	regulation of transcription	SMART:SM00561
GO:0045449	regulation of transcription	SMART:SM00774
GO:0045449	regulation of transcription	SMART:SM00866
GO:0045449	regulation of transcription	SMART:SM00951
GO:0045449	regulation of transcription	SP_KW:KW-0805

positive regulation of transcription

GO:0045941	positive regulation of transcription	HAMAP:MF_00779
GO:0045941	positive regulation of transcription	HAMAP:MF_01178
GO:0045941	positive regulation of transcription	InterPro:IPR004120
GO:0045941	positive regulation of transcription	InterPro:IPR004247
GO:0045941	positive regulation of transcription	InterPro:IPR004619
GO:0045941	positive regulation of transcription	InterPro:IPR004956
GO:0045941	positive regulation of transcription	InterPro:IPR005205
GO:0045941	positive regulation of transcription	InterPro:IPR005206
GO:0045941	positive regulation of transcription	InterPro:IPR006897
GO:0045941	positive regulation of transcription	InterPro:IPR006898
GO:0045941	positive regulation of transcription	InterPro:IPR006899
GO:0045941	positive regulation of transcription	InterPro:IPR007532
GO:0045941	positive regulation of transcription	InterPro:IPR007911
GO:0045941	positive regulation of transcription	InterPro:IPR007944
GO:0045941	positive regulation of transcription	InterPro:IPR008013
GO:0045941	positive regulation of transcription	InterPro:IPR008851
GO:0045941	positive regulation of transcription	InterPro:IPR009287
GO:0045941	positive regulation of transcription	InterPro:IPR009508
GO:0045941	positive regulation of transcription	InterPro:IPR011399
GO:0045941	positive regulation of transcription	InterPro:IPR011665
GO:0045941	positive regulation of transcription	InterPro:IPR011789
GO:0045941	positive regulation of transcription	InterPro:IPR012787
GO:0045941	positive regulation of transcription	InterPro:IPR012794
GO:0045941	positive regulation of transcription	InterPro:IPR016679
GO:0045941	positive regulation of transcription	JCVI_TIGRFAMS:TIGR01716
GO:0045941	positive regulation of transcription	JCVI_TIGRFAMS:TIGR02915
GO:0045941	positive regulation of transcription	Pfam:PF02959
GO:0045941	positive regulation of transcription	Pfam:PF02998
GO:0045941	positive regulation of transcription	Pfam:PF03274
GO:0045941	positive regulation of transcription	Pfam:PF03309
GO:0045941	positive regulation of transcription	Pfam:PF03584
GO:0045941	positive regulation of transcription	Pfam:PF03585
GO:0045941	positive regulation of transcription	Pfam:PF04441
GO:0045941	positive regulation of transcription	Pfam:PF04812
GO:0045941	positive regulation of transcription	Pfam:PF04813
GO:0045941	positive regulation of transcription	Pfam:PF04814
GO:0045941	positive regulation of transcription	Pfam:PF05247
GO:0045941	positive regulation of transcription	Pfam:PF05280
GO:0045941	positive regulation of transcription	Pfam:PF05349
GO:0045941	positive regulation of transcription	Pfam:PF05793
GO:0045941	positive regulation of transcription	Pfam:PF06573
GO:0045941	positive regulation of transcription	Pfam:PF07741
GO:0045941	positive regulation of transcription	PIRSF:PIRSF016992
GO:0045941	positive regulation of transcription	PIRSF:PIRSF025023
GO:0045941	positive regulation of transcription	PIRSF:PIRSF036354
GO:0045941	positive regulation of transcription	ProDom:PD007233
GO:0045941	positive regulation of transcription	ProDom:PD015582
GO:0045941	positive regulation of transcription	ProDom:PD016592
GO:0045941	positive regulation of transcription	ProDom:PD355092
GO:0045941	positive regulation of transcription	PROSITE:MF_01274
GO:0045941	positive regulation of transcription	Reactome:1006808
GO:0045941	positive regulation of transcription	Reactome:1025094
GO:0045941	positive regulation of transcription	Reactome:1052118
GO:0045941	positive regulation of transcription	Reactome:1077051
GO:0045941	positive regulation of transcription	Reactome:1097542
GO:0045941	positive regulation of transcription	Reactome:1116833
GO:0045941	positive regulation of transcription	Reactome:1140675
GO:0045941	positive regulation of transcription	Reactome:1170921
GO:0045941	positive regulation of transcription	Reactome:1192674
GO:0045941	positive regulation of transcription	Reactome:1206838
GO:0045941	positive regulation of transcription	Reactome:1221380
GO:0045941	positive regulation of transcription	Reactome:1239363
GO:0045941	positive regulation of transcription	Reactome:1247032
GO:0045941	positive regulation of transcription	Reactome:1252712
GO:0045941	positive regulation of transcription	Reactome:1258516
GO:0045941	positive regulation of transcription	Reactome:1262144
GO:0045941	positive regulation of transcription	Reactome:1264256
GO:0045941	positive regulation of transcription	Reactome:1265693
GO:0045941	positive regulation of transcription	Reactome:1266788
GO:0045941	positive regulation of transcription	Reactome:163765
GO:0045941	positive regulation of transcription	Reactome:980204


Annotation counts for protein binding transcription factor binding and child terms (3-22-2011)

GOID                    other*  Exp     Seq     IEA     Total   Term Name
(new terms)
GO:0000988                      3       3               6       protein binding transcription factor activity
GO:0000989                      4       2               6       transcription factor binding transcription factor activity
GO:0001010                      1       2               3       sequence-specific DNA binding transcription factor recruiting transcription factor activity
GO:0001087                      1       2               3       TFIIB-class binding transcription factor activity
(previously existing terms)
GO:0003712              30      44      73      65      212     transcription cofactor activity
GO:0003713              127     235     320     195     877     transcription coactivator activity
GO:0003714              104     171     185     128     588     transcription corepressor activity
GO:0008140              2       3       4       4       13      cAMP response element binding protein binding
GO:0016987              6       11      185     131     333     sigma factor activity
GO:0016989              2       5       18      13      38      sigma factor antagonist activity
GO:0030374              11      31      59      28      129     ligand-dependent nuclear receptor transcription coactivator activity
GO:0030375                      4       7       8       19      thyroid hormone receptor coactivator activity
GO:0034246                      2               1       3       mitochondrial RNA polymerase binding promoter specificity activity
GO:0043856                      5                       5       anti-sigma factor antagonist activity
Grand Total             282     520     860     573     2235

*other = TAS, NAS, IC, RCA

Annotation counts for nucleic acid binding transcription factor binding and child terms (3-22-2011)

These counts were obtained to determine if we can change nucleic acid binding transcription factor binding to be specific to transcription, DNA-dependent.

GOID            other*  Exp     Seq     IEA     Total   Term Name
(new terms)
GO:0000981      1       9       13              23      sequence-specific DNA binding RNA polymerase II transcription factor activity
GO:0001010              1       2               3       sequence-specific DNA binding transcription factor recruiting transcription factor activity
GO:0001011              1       2               3       sequence-specific DNA binding RNA polymerase recruiting transcription factor activity
GO:0001071              1       7               8       nucleic acid binding transcription factor activity
GO:0001077              11      9               20      RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription
GO:0001078              2                       2       RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription
(previously existing terms)
GO:0003700      814     1030    6069    7386    15299   sequence-specific DNA binding transcription factor activity
GO:0003705      17      71      225     59      372     sequence-specific enhancer binding RNA polymerase II transcription factor activity
Grand Total     832     1126    6327    7445    15730

*other = TAS, NAS, IC, RCA, NR



- Why is this Exp annotation made to a term this high up? (have requested paper)
GO:0001071      nucleic acid binding transcription factor activity

- These 7 terms are explicitly DNA binding already
GO:0000981      sequence-specific DNA binding RNA polymerase II transcription factor activity
GO:0001010      sequence-specific DNA binding transcription factor recruiting transcription factor activity
GO:0001011      sequence-specific DNA binding RNA polymerase recruiting transcription factor activity
GO:0001077      RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription
GO:0001078      RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription
GO:0003700      sequence-specific DNA binding transcription factor activity
GO:0003705      sequence-specific enhancer binding RNA polymerase II transcription factor activity

Summary: I think we can go ahead and alter the name and position of this term to be explicitly specific to DNA-dependent transcription, as its definition already implies.