Annotation Extension Relation:has regulation target: Difference between revisions
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#REDIRECT [[Annotation]] | |||
'''USAGE OF THIS RELATION HAS BEEN DEPRECATED''' | |||
<pre style="color:#808080"> | |||
==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. | ||
==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> | |||
</pre> | |||
[[Category:Deprecated]] |
Latest revision as of 08:37, 27 September 2021
Redirect to:
USAGE OF THIS RELATION HAS BEEN DEPRECATED
==Definition== Identifies a gene or gene product affected by a regulation Biological Process or regulator Molecular Function. ==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 {| class="wikitable" border="1" |- ! Gene Name (col 2) ! GO ID (col 5) ! Reference (col 6) ! Evidence (col 7) ! Annotation Extension (col 16) |- | WBGene00000220 atf-2(tm467) |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> |} == 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 | | <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>