Annotation Extension Relation:has regulation target: Difference between revisions
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Back to [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation Annotation usage examples for each annotation extension relation] | |||
==Definition== | ==Definition== | ||
Identifies a gene or gene product affected by a regulation | Identifies a gene or gene product affected by a regulation Biological Process or regulator Molecular Function. | ||
==Comment== | |||
[http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_participant#Comment '''More details on the limited use of has_regulation_target with regulation of biological process annotations'''] | |||
==Child terms== | ==Child terms== | ||
* None | * None | ||
==Scope of use== | |||
===Domain=== | |||
GO:0065007 ! biological regulation | |||
===Range=== | |||
[[ENTITY_UNION:0000005]] ! chemical, gene product or complex | |||
==Annotation Extension Usage Examples== | ==Annotation Extension Usage Examples== | ||
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''Indeed, LGG-1 was massively upregulated in atf-2(tm467) mutant embryos, as compared with the wild type (Fig. 6A). We observed a similar extent of BEC-1 upregulation in the atf-2-deficient background (data not shown).'' | ''Indeed, LGG-1 was massively upregulated in atf-2(tm467) mutant embryos, as compared with the wild type (Fig. 6A). We observed a similar extent of BEC-1 upregulation in the atf-2-deficient background (data not shown).'' | ||
Expressed in LEGO: http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_6239-548253760000031 | |||
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! Annotation Extension (col 16) | ! Annotation Extension (col 16) | ||
|- | |- | ||
| WBGene00000220 | | WBGene00000220 atf-2(tm467) | ||
|GO:0000122 <span style="color:green">negative regulation of transcription from RNA polymerase II promoter</span> | |GO:0000122 <span style="color:green">negative regulation of transcription from RNA polymerase II promoter</span> | ||
| PMID:21502138 | | PMID:21502138 | ||
| IMP | |||
| has_regulation_target(WB:WBGene00000247 <span style="color:green">bec-1</span>) 'pipe' has_regulation_target(WB:WBGene00002980 <span style="color:green">lgg-1</span> | |||
|} | |||
== Using examples (from above) to demonstrate [[Folding_and_Unfolding]] using the relationship has_regulation_target == | |||
==== Specifying the gene which is a target of a transcription factor ==== | |||
'''gene transcription targets''' | |||
Statement example: | |||
''Indeed, LGG-1 was massively upregulated in atf-2(tm467) mutant embryos, as compared with the wild type (Fig. 6A). We observed a similar extent of BEC-1 upregulation in the atf-2-deficient background (data not shown).'' | |||
{| class="wikitable" border="1" | |||
|- | |||
! Folded/unfolded | |||
! Gene Name (col 2) | |||
! GO ID (col 5) | |||
! Reference (col 6) | |||
! Evidence (col 7) | |||
! Annotation Extension (col 16) | |||
! Parent terms of new folded GO term | |||
|- | |||
| Unfolded | |||
| WBGene00000220 <span style="color:green">atf-2(tm467)</span> | |||
| GO:0000122 <span style="color:green">negative regulation of transcription from RNA polymerase II promoter</span> | |||
| PMID:21502138 | |||
| IMP | |||
| has_regulation_target(WB:WBGene00000247 <span style="color:green">bec-1</span>)'pipe' has_regulation_target(WB:WBGene00002980 <span style="color:green">lgg-1</span> | |||
|- | |||
| Folded | |||
| WBGene00000220 <span style="color:green">atf-2(tm467)</span> | |||
| GO:0000122 <span style="color:green">negative regulation of transcription from RNA polymerase II promoter</span> | |||
| PMID:21502138 | |||
| IMP | | IMP | ||
| | | | ||
has_regulation_target | | <span style="color:red">No new GO term created</span> | ||
|- | |||
|} | |||
'''OWL class expression:''' GO:0000122 <span style="color:red">negative regulation of transcription from RNA polymerase II promoter</span> AND has_regulation_target SOME WB:WBGene00000247 <span style="color:red">bec-1</span> | |||
'''OWL class expression:''' GO:0000122 <span style="color:red">negative regulation of transcription from RNA polymerase II promoter</span> AND has_regulation_target SOME WB:WBGene00002980 <span style="color:red">lgg-1</span> | |||
Back to [http://wiki.geneontology.org/index.php/Annotation_Extension:_Capturing_participants Annotation Extension: Capturing participants] | Back to [http://wiki.geneontology.org/index.php/Annotation_Extension:_Capturing_participants Annotation Extension: Capturing participants] | ||
---- | |||
Back to [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extension_relation Annotation usage examples for each annotation extension relation] | |||
[[Category:relations]] | |||
[[Category:annotation extension]] |
Revision as of 08:44, 8 May 2015
Back to Annotation usage examples for each annotation extension relation
Definition
Identifies a gene or gene product affected by a regulation Biological Process or regulator Molecular Function.
Comment
Child terms
- None
Scope of use
Domain
GO:0065007 ! biological regulation
Range
ENTITY_UNION:0000005 ! chemical, gene product or complex
Annotation Extension Usage Examples
Loss of transcription factor activity affects gene expression:
Statements from paper:
Indeed, LGG-1 was massively upregulated in atf-2(tm467) mutant embryos, as compared with the wild type (Fig. 6A). We observed a similar extent of BEC-1 upregulation in the atf-2-deficient background (data not shown).
Expressed in LEGO: http://go-genkisugi.rhcloud.com/seed/model/gomodel:taxon_6239-548253760000031
Gene Name (col 2) | GO ID (col 5) | Reference (col 6) | Evidence (col 7) | Annotation Extension (col 16) |
---|---|---|---|---|
WBGene00000220 atf-2(tm467) | GO:0000122 negative regulation of transcription from RNA polymerase II promoter | PMID:21502138 | IMP | has_regulation_target(WB:WBGene00000247 bec-1) 'pipe' has_regulation_target(WB:WBGene00002980 lgg-1 |
Using examples (from above) to demonstrate Folding_and_Unfolding using the relationship has_regulation_target
Specifying the gene which is a target of a transcription factor
gene transcription targets
Statement example:
Indeed, LGG-1 was massively upregulated in atf-2(tm467) mutant embryos, as compared with the wild type (Fig. 6A). We observed a similar extent of BEC-1 upregulation in the atf-2-deficient background (data not shown).
Folded/unfolded | Gene Name (col 2) | GO ID (col 5) | Reference (col 6) | Evidence (col 7) | Annotation Extension (col 16) | Parent terms of new folded GO term |
---|---|---|---|---|---|---|
Unfolded | WBGene00000220 atf-2(tm467) | GO:0000122 negative regulation of transcription from RNA polymerase II promoter | PMID:21502138 | IMP | has_regulation_target(WB:WBGene00000247 bec-1)'pipe' has_regulation_target(WB:WBGene00002980 lgg-1 | |
Folded | WBGene00000220 atf-2(tm467) | GO:0000122 negative regulation of transcription from RNA polymerase II promoter | PMID:21502138 | IMP | No new GO term created |
OWL class expression: GO:0000122 negative regulation of transcription from RNA polymerase II promoter AND has_regulation_target SOME WB:WBGene00000247 bec-1 OWL class expression: GO:0000122 negative regulation of transcription from RNA polymerase II promoter AND has_regulation_target SOME WB:WBGene00002980 lgg-1
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