Changes between Version 3 and Version 4 of ListOfRelationsForGO


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Timestamp:
Apr 28, 2015, 12:00:15 PM (6 years ago)
Author:
mah79
Comment:

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  • ListOfRelationsForGO

    v3 v4  
    88||relation||brief explanation||example annotation||
    99||occurs_at||a sequence feature where a BP happens (note: used to be acts_at, then changed to occurs_at for BP and has_substrate for MF); NOTE: do not use occurs_at with CC annotations||hip3 GO:0030702 occurs_at(SO:0001799) = involved in 'chromatin silencing at centromere' at 'regional_centromere_outer_repeat_region'||
     10||(continued)||a sequence feature where DNA binding takes place||prz1 GO:0000978 occurs_at(SO:0001865) = has that crazy long-winded '... promoter proximal ... DNA binding' activity at 'CDRE_motif'||
    1011||exists_during||use for localization to CC at particular time (e.g. cell cycle phase or when another process is occurring)||cdr2 GO:0071341 exists_during(GO:0000085) = localizes to 'medial cortical node' during 'G2 phase of mitotic cell cycle'||
    1112||happens_during||use for function or process that takes place during a specific cell cycle phase or when another process is taking place||srw1 GO:0008054 happens_during(GO:0000080) = involved in 'cyclin catabolic process' during 'G1 phase of mitotic cell cycle'||
    12 ||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.)||none yet, but a few to change to this||
     13||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.||none yet, but a few to change to this||
    1314||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||
    1415||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