View source for Fate of terms referring to general/nonspecific/basal versus specific transcription

[[Category:Transcription]] [[Category:Ontology]]
= Proposal =

This is a group of 12 Biological Process (BP) and 7 Molecular
Function (MF) terms that represent general/nonspecific/basal
transcription versus specific transcription.

# <font color="red">MERGE 6 MF terms into equivalent BP terms</font>: In MF, there are three terms for general/nonspecific/basal vs specific transcription repressor activities and there are three RNAP II specific terms for general/nonspecific/basal vs specific "transcription factor activity". We propose to MERGE these 6 MF terms into the BP terms with the same meanings because they are defined only in terms of affect on a process and not in terms of how they act, which is how we are now defining MF terms. 
#: - <font color="red">There was a counterproposal to the original proposal to MERGE; thus instead, these will be OBSOLETED</font>.
#* GO:0003704  specific RNA polymerase II transcription factor activity
#* GO:0016252  nonspecific RNA polymerase II transcription factor activity
#* GO:0016251  general RNA polymerase II transcription factor activity
#* GO:0016566  specific transcriptional repressor activity
#* GO:0017163  basal transcription repressor activity
#* GO:0016565  general transcriptional repressor activity
# <font color="red">MERGE 1 MF term into a more general MF term</font>: The mediator activity MF term is included here because it is a child of one of the above terms. We propose to merge it into a more general MF term that is defined in terms of how this class of factors act.
#* GO:0016455  RNA polymerase II transcription mediator activity
# <font color="red">MERGE 11 BP terms into parent BP terms</font>: In BP, there are two terms for RNAP II processes. The rest are all regulation terms; most of these are specific to RNAP II, but three are general to any "gene-specific transcription". We propose to MERGE these 11 BP terms into parent BP terms. 
#* GO:0032569  gene-specific transcription from RNA polymerase II promoter
#* GO:0032568  general transcription from RNA polymerase II promoter
#* GO:0032583  regulation of gene-specific transcription
#* GO:0043193  positive regulation of gene-specific transcription
#* GO:0032582  negative regulation of gene-specific transcription
#* GO:0010551  regulation of gene-specific transcription from RNA polymerase II promoter
#* GO:0010552  positive regulation of gene-specific transcription from RNA polymerase II promoter
#* GO:0010553  negative regulation of gene-specific transcription from RNA polymerase II promoter
#* GO:0090039  regulation of gene-specific transcription elongation from RNA polymerase II promoter
#* GO:0090040  positive regulation of gene-specific transcription elongation from RNA polymerase II promoter
#* GO:0090041  negative regulation of gene-specific transcription elongation from RNA polymerase II promoter
# <font color="red">RENAME 1 BP term</font> One of these BP terms merely needs to be renamed to be consistent with its existing definition and placement in the structure.
#* GO:0006990  positive regulation of gene-specific transcription involved in unfolded protein response

= Comment Period =

'''Date mailed:''' 3/30/2011

'''Deadline for Comments:''' 4/19/2011 - <font color="red"> Unless objections are received by April 19th, we will assume that you agree to this change. </font>

= Summary of Actions Taken =

* As proposed, merged '''RNA polymerase II transcription mediator activity''' (GO:0016455) into MF term '''RNA polymerase II transcription cofactor activity''' (GO:0001104) [done 5/11/2011]
* As proposed, MERGED 11 BP terms into parent BP terms. [done 5/12/2011]
* As proposed, RENAMED 1 BP term (originally '''positive regulation of gene-specific transcription involved in unfolded protein response'''; GO:0006990) to remove "gene-specific" phrase and be consistent with its existing definition and placement in the structure  [done 5/12/2011]

= Problems with "general/non-specific/basal" vs "specific" transcription =

<font color=red>'''Issues'''</font>

In the [[http://wiki.geneontology.org/index.php/Proposals_to_overhaul_transcription_in_GO_-_2010#Clarification_of_.22general.2Fnon-specific.2Fbasal.22_vs_.22specific.22_transcription original proposal for the "general/non-specific/basal" vs "specific" terms]], we proposed to try to rework these terms to be types of preinitiation complex (PIC) formation. However, we have been unable to come up with any clear distinction or separation between these terms, either in terms of function or process. Basically, these terms reflect outdating thinking, probably based in part on the use of a very limited set of promoters for in vitro experiments. 

* Early on it was thought that the RNAP II "general transcription factors", or GTFs were involved in preinitation complex (PIC) formation at ALL RNAP II promoters. However, it is now clear that there is no single type of RNAP II promoter. Thus there are probably many types of PICs and the "general" factors may not be general. Thus [http://www.ncbi.nlm.nih.gov/pubmed/19411170 Sikorsky & Buratowski (2009)] use the term '''basal''' rather than '''general'''.
* The current definition for '''general''' says "non-specifically regulated". This is probably not really the case. Transcription of the set of genes that requires only basal transcription factors is regulated, they just don't require additional non-basal factors to recognize the promoter. It is also a quite large set of genes, larger than the typical number of genes that is responsive to a typical "gene-specific" activator, and they are active in "standard" growth conditions. It is now known that there are some large scale changes in the transcriptome of a cell, for example during differentiation, that are regulated by changing the set of basal transcription factors that are expressed.
* It is not the case that there is one set of genes involved in basal transcription and another set involved in specific transcription. Basal refers to transcription that can occur only with basal transcription (initiation) factors. "Gene-specific" refers to cases where the promoter sequence is not recognized directly by the basal factors, but instead by a "gene-specific" regulatory transcription factor, which then initiates the process to recruit basal transcription factors and RNAP II. Everything involved in basal transcription is also involved in gene-specific transcription. Thus "gene-specific transcription" does not represent a completely separate process from "general/non-specific/basal transcription", but rather an additional level of regulation where additional factors are required for promoter recognition or some subsequent step, but which still requires basal factors. In a comprehensive review of eukaryotic general transcription machinery, [http://www.ncbi.nlm.nih.gov/pubmed/16858867 Thomas and Chiang (2006)] use the phrase '''activator-dependent''' for this situation, consistent with the phrase that is used in E. coli for these cases where an "activator" is required in addition to basal machinery.

'''Useful reviews'''
* [http://www.ncbi.nlm.nih.gov/pubmed/19411170 Sikorski TW, Buratowski S. The basal initiation machinery: beyond the general transcription factors. Curr Opin Cell Biol. 2009 Jun;21(3):344-51. PMID: 19411170]
* [http://www.ncbi.nlm.nih.gov/pubmed/16858867 Thomas MC, Chiang CM. The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol. 2006 May-Jun;41(3):105-78. PMID: 16858867]
* [http://www.ncbi.nlm.nih.gov/pubmed/19077548 Zhou Z, Lin IJ, Darst RP, Bungert J. Maneuver at the transcription start site: Mot1p and NC2 navigate TFIID/TBP to specific core promoter elements. Epigenetics. 2009 Jan;4(1):1-4. Epub 2009 Jan 27. PMID: 19077548]

= Reannotation suggestions =

==MF terms==
* 1 MERGE
*: <font color="red">Merge</font> '''RNA polymerase II transcription mediator activity''' (GO:0016455) into MF term '''RNA polymerase II transcription cofactor activity''' (GO:0001104)
*: Also consider annotating to the CC term '''mediator complex''' (GO:0016592)
* 6 OBSOLETIONS (as per modified proposal to obsolete instead of merge)
** For these three terms: <font color="red">done</font>
*** GO:0003704 '''specific RNA polymerase II transcription factor activity'''
*** GO:0016252 '''nonspecific RNA polymerase II transcription factor activity'''
*** GO:0016251 '''general RNA polymerase II transcription factor activity'''
**: <font color="red">Obsolete all 3 terms</font>
**: These three terms are all defined in terms of the process affected, but not in terms of how the function is carried out. Thus, although these terms have been present in the MF ontology, they actually represent BP information. Since the general/non-specific vs specific distinction is not valid with respect to process and these terms are all specific to RNAP II without conveying any additional detail, the BP term is the only term to which all annotations can be transferred without review.
*** consider the BP term '''transcription from RNA polymerase II promoter''' (GO:0006366) as the equivalent meaning
*** For reannotation in the MF tree, consider these terms and their children:
**** GO:0001076 - RNA polymerase II transcription factor binding transcription factor activity
**** GO:0000991 - core RNA polymerase II binding transcription factor activity
**** GO:0000981 - sequence-specific DNA binding RNA polymerase II transcription factor activity
** For these three terms:  <font color="red">done</font>
*** GO:0016566  '''specific transcriptional repressor activity'''
*** GO:0017163  '''basal transcription repressor activity'''
*** GO:0016565  '''general transcriptional repressor activity'''
**: <font color="red">Obsolete all 3 terms</font>
**: These three terms are all defined in terms of the process affected, but not in terms of how the function is carried out. Thus, although these terms have been present in the MF ontology, they actually represent BP information. Since the general/non-specific vs specific distinction is not valid with respect to process and these terms are all related to repression of transcription, the BP term is the only term to which all annotations can be transferred without review. Similarly to the merge of "transcription" and its regulation terms into "transcription, DNA-dependent" and its regulation terms, we are suggesting merging into the "DNA-dependent" form of the the term because we feel that the majority of the annotations are already intended to be for DNA-dependent transcription.
*** Consider BP term '''negative regulation of transcription, DNA-dependent''' (GO:0045892) as the equivalent meaning
*** For reannotation in the MF tree, consider these terms and their children <font color="red">or requesting similar terms under '''protein binding transcription factor activity''' (GO:0000988)</font>:
**** GO:0001141 - bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative 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

==BP terms==
* Two basic process terms trying to distinguish "gene-specific" vs "general" transcription
*: <font color="red">Merge</font> these two terms into '''transcription from RNA polymerase II promoter''' (GO:0006366)
**  '''gene-specific transcription from RNA polymerase II promoter''' (GO:0032569) <font color="red">done</font>
**  '''general transcription from RNA polymerase II promoter''' (GO:0032568) <font color="red">done</font>
*: These terms both relate to transcription from an RNAP II promoter. We are moving the annotations up to the parent term since "gene-specific transcription" and "general transription are not distinct processes. 
* Three regulation terms at the general level of "gene-specific transcription"
** <font color="red">Merge</font> '''regulation of gene-specific transcription''' (GO:0032583)  into '''regulation of transcription, DNA-dependent''' (GO:0006355) <font color="red">done</font>
** <font color="red">Merge</font> '''positive regulation of gene-specific transcription''' (GO:0043193) into '''positive regulation of transcription, DNA-dependent''' (GO:0045893) <font color="red">done</font>
** <font color="red">Merge</font> '''negative regulation of gene-specific transcription''' (GO:0032582) into '''negative regulation of transcription, DNA-dependent''' (GO:0045892) <font color="red">done</font>
*: These terms are all already defined in terms of DNA-dependent transcription, so if any annotations were made for "RNA-dependent transcription", they were made incorrectly. However, based on what we have seen, we feel that the vast majority of annotations will be for DNA-dependent transcription. Thus, we are moving the annotations up to the parent term since "gene-specific transcription" isn't a distinct process.
* Three regulation terms for "gene-specific transcription from RNA polymerase II promoter"
** <font color="red">Merge</font> '''regulation of gene-specific transcription from RNA polymerase II promoter''' (GO:0010551) into '''regulation of transcription from RNA polymerase II promoter''' (GO:0006357) <font color="red">done</font>
** <font color="red">Merge</font> '''positive regulation of gene-specific transcription from RNA polymerase II promoter''' (GO:0010552) into '''positive regulation of transcription from RNA polymerase II promoter''' (GO:0045944) [NOTE: fix def of 45994, use 'an' instead of 'the' to preface promoter.] <font color="red">done</font>
** <font color="red">Merge</font> '''negative regulation of gene-specific transcription from RNA polymerase II promoter''' (GO:0010553) into '''negative regulation of transcription from RNA polymerase II promoter''' (GO:0000122) <font color="red">done</font>
*: We are just moving all these annotations up to the corresponding parent terms since "gene-specific transcription" isn't a distinct process.
* Three regulation terms for "gene-specific transcription elongation from RNA polymerase II promoter"
** <font color="red">Merge</font> '''regulation of gene-specific transcription elongation from RNA polymerase II promoter''' (GO:0090039) into '''regulation of transcription elongation from RNA polymerase II promoter''' (GO:0034243) <font color="red">done</font>
** <font color="red">Merge</font> '''positive regulation of gene-specific transcription elongation from RNA polymerase II promoter''' (GO:0090040) into '''positive regulation of transcription elongation from RNA polymerase II promoter''' (GO:0032968) <font color="red">done</font>
** <font color="red">Merge</font> '''negative regulation of gene-specific transcription elongation from RNA polymerase II promoter''' (GO:0090041) into '''negative regulation of transcription elongation from RNA polymerase II promoter''' (GO:0034244) <font color="red">done</font>
* One term for a specific set of RNAP II genes
** '''positive regulation of gene-specific transcription involved in unfolded protein response''' (GO:0006990)
*: <font color="red">Rename</font> to '''positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response''' <font color="red">done; David please check cross-products</font>
*: This term is already defined in terms of RNAP II transcription and already has appropriate is_a parentage under a term that will not be affected by the transcription overhaul.

= Supporting information =
== Annotation counts ==

Annotation counts via GOOSE (Berkeley BOP) on 3/28/2011

=== grouped by term name and evidence code (non-IEA vs IEA)===
<pre>
Term name....................................................   aspect  non-IEA IEA     Grand Total

.......general RNA polymerase II transcription factor activity  MF      230     466     696
...nonspecific RNA polymerase II transcription factor activity  MF      1       -       1
......specific RNA polymerase II transcription factor activity  MF      596     72      668

.............RNA polymerase II transcription mediator activity  MF      166     1915    2081

........................basal transcription repressor activity  MF      33      16      49
....................general transcriptional repressor activity  MF      41      17      58
...................specific transcriptional repressor activity  MF      645     39431   40076

...gene-specific transcription from RNA polymerase II promoter  BP      142     16      158
.........general transcription from RNA polymerase II promoter  BP      59      60      119

.....................regulation of gene-specific transcription  BP      40      39      79
............positive regulation of gene-specific transcription  BP      400     253     653
............negative regulation of gene-specific transcription  BP      269     127     396

............regulation of gene-specific transcription from RNA  BP      118     45      163
        polymerase II promoter
...positive regulation of gene-specific transcription from RNA  BP      759     617     1376
        polymerase II promoter
...negative regulation of gene-specific transcription from RNA  BP      691     306     997
        polymerase II promoter

...positive regulation of gene-specific transcription involved  BP      8       -       8
        in unfolded protein response

..........regulation of gene-specific transcription elongation  BP      7       5       12
        from RNA polymerase II promoter
.positive regulation of gene-specific transcription elongation  BP      14      6       20
        from RNA polymerase II promoter
.negative regulation of gene-specific transcription elongation  BP      15      10      25
        from RNA polymerase II promoter

Grand Total...................................................          4234    43401   47635
</pre>

=== grouped by source and evidence code (non-IEA vs IEA)===
<pre>
Source.............     non-IEA IEA     Grand Total
..............AspGD     20      119     139
................CGD     46      91      137
..........dictyBase     48      1       49
.............EcoCyc     158     2       160
..........EcoliWiki     126     1       127
............Ensembl     -       10      10
.................FB     318     9       327
.GeneDB_Pfalciparum     3       -       3
......GeneDB_Spombe     308     3       311
.....GeneDB_Tbrucei     1       -       1
...........JCVI_CMR     10      -       10
................MGI     760     16      776
................PDB     39      391     430
.............RefSeq     -       16      16
................RGD     506     176     682
................SGD     346     20      366
...............TAIR     30      19      49
...........TIGR_CMR     21      -       21
..........UniProtKB     1448    42485   43933
.................WB     40      17      57
...............ZFIN     6       25      31
Grand Total........     4234    43401   47635

</pre>

==Subsets==

'''Prokaryotic GO subset:'''
* GO:0016566    specific transcriptional repressor activity
* GO:0017163    basal transcription repressor activity
* GO:0043193    positive regulation of gene-specific transcription

'''Fission yeast GO slim:'''
* GO:0032569    gene-specific transcription from RNA polymerase II promoter

'''Not present in a subset:'''
* GO:0003704    specific RNA polymerase II transcription factor activity
* GO:0006990    positive regulation of gene-specific transcription involved in unfolded protein response
* GO:0010551    regulation of gene-specific transcription from RNA polymerase II promoter
* GO:0010552    positive regulation of gene-specific transcription from RNA polymerase II promoter
* GO:0010553    negative regulation of gene-specific transcription from RNA polymerase II promoter
* GO:0016251    general RNA polymerase II transcription factor activity
* GO:0016252    nonspecific RNA polymerase II transcription factor activity
* GO:0016455    RNA polymerase II transcription mediator activity
* GO:0016565    general transcriptional repressor activity
* GO:0032568    general transcription from RNA polymerase II promoter
* GO:0032582    negative regulation of gene-specific transcription
* GO:0032583    regulation of gene-specific transcription
* GO:0090039    regulation of gene-specific transcription elongation from RNA polymerase II promoter
* GO:0090040    positive regulation of gene-specific transcription elongation from RNA polymerase II promoter
* GO:0090041    negative regulation of gene-specific transcription elongation from RNA polymerase II promoter


==Non-definition dbxrefs==

'''GO:0016566 - specific transcriptional repressor activity (MF)'''
* InterPro:IPR003012
* InterPro:IPR004111
* InterPro:IPR005650
* InterPro:IPR012771
* InterPro:IPR015893
* JCVI_TIGRFAMS:TIGR00331
* JCVI_TIGRFAMS:TIGR02404
* JCVI_TIGRFAMS:TIGR03384
* Pfam:PF02909
* Pfam:PF03965
* PRINTS:PR00400

'''GO:0016251 - general RNA polymerase II transcription factor activity (MF)'''
* COG:K
* InterPro:IPR004600
* InterPro:IPR006751
* InterPro:IPR016640
* InterPro:IPR018381
* Pfam:PF03850
* Pfam:PF04658
* PIRSF:PIRSF015849

'''GO:0016455 - RNA polymerase II transcription mediator activity (MF)'''
* InterPro:IPR007018
* InterPro:IPR008626
* InterPro:IPR008831
* InterPro:IPR009244
* InterPro:IPR009332
* InterPro:IPR009401
* InterPro:IPR011425
* InterPro:IPR013921
* InterPro:IPR013942
* InterPro:IPR013947
* InterPro:IPR014801
* InterPro:IPR016530
* InterPro:IPR016532
* InterPro:IPR016612
* InterPro:IPR016820
* InterPro:IPR018174
* InterPro:IPR019035
* InterPro:IPR019087
* InterPro:IPR019095
* InterPro:IPR019145
* InterPro:IPR019258
* InterPro:IPR019313
* InterPro:IPR019364
* InterPro:IPR019403
* InterPro:IPR019404
* InterPro:IPR019680
* InterPro:IPR020998
* Pfam:PF04934
* Pfam:PF05397
* Pfam:PF05669
* Pfam:PF05983
* Pfam:PF06333
* Pfam:PF07544
* Pfam:PF08612
* Pfam:PF08633
* Pfam:PF08638
* Pfam:PF08689
* Pfam:PF09497
* Pfam:PF09606
* Pfam:PF09637
* Pfam:PF09748
* Pfam:PF10018
* Pfam:PF10156
* Pfam:PF10232
* Pfam:PF10278
* Pfam:PF10280
* Pfam:PF10744
* Pfam:PF11593
* PIRSF:PIRSF007936
* PIRSF:PIRSF007945
* PIRSF:PIRSF013286
* PIRSF:PIRSF023869

'''GO:0032583 - regulation of gene-specific transcription (BP)'''
* InterPro:IPR016325
* PIRSF:PIRSF001863



== Term Stanzas ==

=== Molecular Function terms (7) ===
<pre>
id: GO:0016251
name: general RNA polymerase II transcription factor activity
namespace: molecular_function
alt_id: GO:0003703
def: "Any function that supports basal (unregulated) transcription of
  genes by core RNA polymerase II. Five general transcription factors
  are necessary and sufficient for such basal transcription in yeast:
  TFIIB, TFIID, TFIIE, TFIIF, TFIIH and TATA-binding protein (TBF)."
  [PMID:10384286, PMID:9774831]
is_a: GO:0003702 ! RNA polymerase II transcription factor activity

id: GO:0016252
name: nonspecific RNA polymerase II transcription factor activity
namespace: molecular_function
def: "Any function that supports transcription of genes by RNA
  polymerase II, and is not specific to a particular gene or gene set."
  [GOC:jl]
is_a: GO:0003702 ! RNA polymerase II transcription factor activity

id: GO:0003704
name: specific RNA polymerase II transcription factor activity
namespace: molecular_function
def: "Functions to enable the transcription of specific, or specific
  sets, of genes by RNA polymerase II." [GOC:ma]
is_a: GO:0003702 ! RNA polymerase II transcription factor activity

[Term]
id: GO:0016455
name: RNA polymerase II transcription mediator activity
namespace: molecular_function
def: "Functions to mediate the interaction of transcriptional
  activators with the RNA polymerase II-general RNA polymerase II
  transcription factor complex." [GOC:ma]
synonym: "thyroid receptor-associated protein" RELATED []
synonym: "TRAP protein" RELATED []
is_a: GO:0016251 ! general RNA polymerase II transcription factor activity

id: GO:0016566
name: specific transcriptional repressor activity
namespace: molecular_function
def: "Any activity that stops or downregulates transcription of
  specific genes or sets of genes." [GOC:mah]
subset: gosubset_prok
is_a: GO:0016564 ! transcription repressor activity

id: GO:0017163
name: basal transcription repressor activity
namespace: molecular_function
def: "Any transcription regulator activity that prevents or
  downregulates basal transcription. Basal transcription results from
  transcription that is controlled by the minimal complement of proteins
  necessary to reconstitute transcription from a minimal promoter."
  [GOC:dph, GOC:tb,
  http://tfib.med.harvard.edu/transcription/basaltx.html]
subset: gosubset_prok
is_a: GO:0016564 ! transcription repressor activity

id: GO:0016565
name: general transcriptional repressor activity
namespace: molecular_function
def: "Any activity that stops or downregulates transcription of genes
  globally, and is not specific to a particular gene or gene set."
  [GOC:mah]
is_a: GO:0016564 ! transcription repressor activity

</pre>

=== Biological Process terms (12) ===

<pre>
id: GO:0032569
name: gene-specific transcription from RNA polymerase II promoter
namespace: biological_process
def: "The specifically regulated synthesis of RNA from DNA encoding a
  specific gene or set of genes by RNA polymerase II (Pol II),
  originating at a Pol II-specific promoter. In addition to RNA
  polymerase II and the general transcription factors, specific
  transcription requires one or more specific factors that bind to
  specific DNA sequences or interact with the general transcription
  machinery." [GOC:mah]
subset: goslim_pombe
synonym: "specific transcription from RNA polymerase II promoter" EXACT [GOC:mah]
is_a: GO:0006366 ! transcription from RNA polymerase II promoter

id: GO:0032568
name: general transcription from RNA polymerase II promoter
namespace: biological_process
def: "The basal, non-specifically regulated synthesis of RNA from a
  DNA template by RNA polymerase II (Pol II), originating at a Pol
  II-specific promoter. Mediated by core RNA polymerase II and a set of
  general transcription factors; in Saccharomyces five transcription
  factors are necessary and sufficient for such basal transcription."
  [GOC:mah]
is_a: GO:0006366 ! transcription from RNA polymerase II promoter

id: GO:0032583
name: regulation of gene-specific transcription
namespace: biological_process
def: "Any process that modulates the DNA-dependent transcription of a
  specific gene or genes." [GOC:mah]
is_a: GO:0006355 ! regulation of transcription, DNA-dependent

id: GO:0043193
name: positive regulation of gene-specific transcription
namespace: biological_process
def: "Any process that activates or increases the frequency, rate or
  extent of the DNA-dependent transcription of a specific gene or
  genes." [GOC:jl]
subset: gosubset_prok
synonym: "activation of gene-specific transcription" NARROW []
synonym: "stimulation of gene-specific transcription" NARROW []
synonym: "up regulation of gene-specific transcription" EXACT []
synonym: "up-regulation of gene-specific transcription" EXACT []
synonym: "upregulation of gene-specific transcription" EXACT []
is_a: GO:0032583 ! regulation of gene-specific transcription
is_a: GO:0045893 ! positive regulation of transcription, DNA-dependent

id: GO:0032582
name: negative regulation of gene-specific transcription
namespace: biological_process
def: "Any process that stops, prevents or reduces the DNA-dependent
  transcription of a specific gene or genes." [GOC:mah]
synonym: "down regulation of gene-specific transcription" EXACT []
synonym: "down-regulation of gene-specific transcription" EXACT []
synonym: "downregulation of gene-specific transcription" EXACT []
synonym: "inhibition of gene-specific transcription" NARROW []
is_a: GO:0032583 ! regulation of gene-specific transcription
is_a: GO:0045892 ! negative regulation of transcription, DNA-dependent

id: GO:0010551
name: regulation of gene-specific transcription from RNA polymerase II promoter
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of the
  specifically regulated synthesis of RNA from DNA encoding a specific
  gene or set of genes by RNA polymerase II (Pol II), originating at a
  Pol II-specific promoter." [GOC:dph, GOC:tb]
is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter
is_a: GO:0032583 ! regulation of gene-specific transcription
intersection_of: GO:0065007 ! biological regulation
intersection_of: regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter
relationship: regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter

id: GO:0010552
name: positive regulation of gene-specific transcription from RNA polymerase II promoter
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of the
  specifically regulated synthesis of RNA from DNA encoding a specific
  gene or set of genes by RNA polymerase II (Pol II), originating at a
  Pol II-specific promoter." [GOC:dph, GOC:tb]
is_a: GO:0010551 ! regulation of gene-specific transcription from RNA polymerase II promoter
is_a: GO:0043193 ! positive regulation of gene-specific transcription
is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter
intersection_of: GO:0065007 ! biological regulation
intersection_of: positively_regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter
relationship: positively_regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter

id: GO:0010553
name: negative regulation of gene-specific transcription from RNA polymerase II promoter
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of the
  specifically regulated synthesis of RNA from DNA encoding a specific
  gene or set of genes by RNA polymerase II (Pol II), originating at a
  Pol II-specific promoter." [GOC:dph, GOC:tb]
is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter
is_a: GO:0010551 ! regulation of gene-specific transcription from RNA polymerase II promoter
is_a: GO:0032582 ! negative regulation of gene-specific transcription
intersection_of: GO:0065007 ! biological regulation
intersection_of: negatively_regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter
relationship: negatively_regulates GO:0032569 ! gene-specific transcription from RNA polymerase II promoter

id: GO:0006990
name: positive regulation of gene-specific transcription involved in unfolded protein response
namespace: biological_process
def: "The activation of genes whose promoters contain a specific
  sequence elements such as the unfolded protein response element (UPRE;
  consensus CAGCGTG) or the ER stress-response element (ERSE;
  CCAAN(N)9CCACG), as a result of signaling via the unfolded protein
  response." [GOC:dph, GOC:mah, GOC:tb, PMID:12042763]
synonym: "positive regulation of transcription of target genes involved in unfolded protein response" EXACT [GOC:dph, GOC:tb]
synonym: "unfolded protein response, activation of target gene transcription" NARROW []
synonym: "unfolded protein response, positive regulation of target gene transcription" EXACT [GOC:tb]
synonym: "unfolded protein response, stimulation of target gene transcription" NARROW []
synonym: "unfolded protein response, target gene transcriptional activation" BROAD []
synonym: "unfolded protein response, up regulation of target gene transcription" EXACT []
synonym: "unfolded protein response, up-regulation of target gene transcription" EXACT []
synonym: "unfolded protein response, upregulation of target gene transcription" EXACT []
is_a: GO:0043193 ! positive regulation of gene-specific transcription
is_a: GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter
intersection_of: GO:0043193 ! positive regulation of gene-specific transcription
intersection_of: part_of GO:0030968 ! endoplasmic reticulum unfolded protein response
relationship: part_of GO:0030968 ! endoplasmic reticulum unfolded protein response

id: GO:0090039
name: regulation of gene-specific transcription elongation from RNA polymerase II promoter
namespace: biological_process
def: "Any process that modulates the frequency, rate or extent of
  gene-specific RNA elongation, the extension of an RNA molecule from a
  specific gene or genes after transcription initiation by the addition
  of ribonucleotides, catalyzed by RNA polymerase II." [GOC:dph, GOC:tb]
is_a: GO:0032583 ! regulation of gene-specific transcription
is_a: GO:0034243 ! regulation of transcription elongation from RNA polymerase II promoter
created_by: tanyaberardini
creation_date: 2009-08-03T11:39:30Z

id: GO:0090040
name: positive regulation of gene-specific transcription elongation from RNA polymerase II promoter
namespace: biological_process
def: "Any process that increases the frequency, rate or extent of
  gene-specific RNA elongation, the extension of an RNA molecule from a
  specific gene or genes after transcription initiation by the addition
  of ribonucleotides, catalyzed by RNA polymerase II." [GOC:dph, GOC:tb]
is_a: GO:0043193 ! positive regulation of gene-specific transcription
is_a: GO:0090039 ! regulation of gene-specific transcription elongation from RNA polymerase II promoter
created_by: tanyaberardini
creation_date: 2009-08-03T11:45:24Z

id: GO:0090041
name: negative regulation of gene-specific transcription elongation from RNA polymerase II promoter
namespace: biological_process
def: "Any process that decreases the frequency, rate or extent of
  gene-specific RNA elongation, the extension of an RNA molecule from a
  specific gene or genes after transcription initiation by the addition
  of ribonucleotides, catalyzed by RNA polymerase II." [GOC:dph, GOC:tb]
is_a: GO:0032582 ! negative regulation of gene-specific transcription
is_a: GO:0090039 ! regulation of gene-specific transcription elongation from RNA polymerase II promoter
created_by: tanyaberardini
creation_date: 2009-08-03T11:46:32Z
</pre>