Changes between Version 5 and Version 6 of ListOfRelationsForGO


Ignore:
Timestamp:
Apr 28, 2015, 12:06:19 PM (6 years ago)
Author:
mah79
Comment:

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  • ListOfRelationsForGO

    v5 v6  
    1313||has_regulation_target||a gene product whose activity (MF) is regulated by a 'regulator' MF; a gene product whose participation in a process is regulated by a 'regulation of' BP; or a gene whose expression is regulated by a 'regulation of gene expression' BP (regulation of transcription, regulation of translation, etc.) NOTE: GO has more specific "chained" relations under discussion, which are intended to distinguish among these and other cases.||ubc4 GO:0042787 has_regulation_target(PomBase:SPAC1783.07c) = involved in 'protein ubiquitination involved in ubiquitin-dependent protein catabolic process' and acts on Pap1 [[BR]] ace2 GO:0001077 has_regulation_target(PomBase:SPAC6F12.12) = has that crazily-named "RNA pol II transcription factor yada yada" activity, and regulates transcription of par2 [[BR]] could probably add more ... ||
    1414||has_direct_input||formerly has_substrate; a gene product or other molecule that a function or process acts on||set11 GO:0016279 has_substrate(PomBase:SPCC31H12.04c| PomBase:SPCC16C4.13c) = 'protein-lysine N-methyltransferase activity' with substrates Rpl1201 & Rpl1202||
    15 ||independent_of||only used for localization to date, where it can mean localization to a CC happens whether a particular BP occurs or not, OR  localization to a CC happens whether another gene product is present or not||pxl1 GO:0005826 independent_of(GO:0031028) = located at 'actomyosin contractile ring' whether 'septation initiation signaling cascade' happens or not
     15||coincident_with||use for localization to chromatin at a specific sequence or type of sequence region (SO ID); particularly useful for annotating ChIP results||orc1 GO:0000790 coincident_with (SO:0000296) = localizes to 'nuclear chromatin' at 'origin_of_replication'||
     16||independent_of||only used for localization to date, where it can mean localization to a CC happens whether a particular BP occurs or not, OR  localization to a CC happens whether another gene product is present or not||pxl1 GO:0005826 independent_of(GO:0031028) = located at 'actomyosin contractile ring' whether 'septation initiation signaling cascade' happens or not||
    1617||has_indirect_input||was indirectly_localizes (now a narrow synonym); describes the downstream substrate of a localization process; NOTE this is not for use with transporters which use has_substrate it is possible these terms will merge into their parents; NOTE: GO may obsolete this relation and use has_input||gene A methylates gene B and the methylation of geneB is responsible for its subsequent localization of Gene B (i.e. an output of the gene is doing the localizing, not the gene product itself), or if there are numerous steps between a modification and the localization event||
    1718||localization_dependent_on||various sorts of requirement for localization; deprecated (as of early 2014) except where the information can't be captured by a phenotype annotation||examples on next few lines||