Difference between revisions of "Phenotype2GO Analysis"

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| smg-8 || locomotion (GO:0040011) || IMP || RNAi || 37111, Izumi et al., 2010 || No manual annotation from 37111 ||  || smg-8 encodes a novel protein; only CC annotations exist || No || Downstream effect: phenotype used as output for more general cellular process: effect on locomotion apparently a result of unc-54 transcript stabilization; also incorrect evidence code
 
| smg-8 || locomotion (GO:0040011) || IMP || RNAi || 37111, Izumi et al., 2010 || No manual annotation from 37111 ||  || smg-8 encodes a novel protein; only CC annotations exist || No || Downstream effect: phenotype used as output for more general cellular process: effect on locomotion apparently a result of unc-54 transcript stabilization; also incorrect evidence code
 
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| mes-4 || determination of adult lifespan (GO:0008430) || IMP || RNAi || 33449, Curran et al., 2009 || No manual GO annotation for mes-4 from 33449 || || Affect on lifespan may be due to role in regulation of germline transcription || No || Downstream effect - regulating adult lifespan is not the main biological role of MES-4
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| mes-4 || determination of adult lifespan (GO:0008430) || IMP || RNAi || 33449, Curran et al., 2009 || No manual GO annotation for mes-4 from 33449 || || Affect on lifespan may be due to role in regulation of germline transcription, germ cell survival || No || Possible downstream effect - MES-4 is required for germ cell fate specification
 
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| gld-3 || apoptosis (obsolete) || IMP || RNAi || 38381 || maybe a germ cell development annotation? || IMP
 
| gld-3 || apoptosis (obsolete) || IMP || RNAi || 38381 || maybe a germ cell development annotation? || IMP

Revision as of 18:58, 3 June 2013

Named Genes with Phenotype2GO-Based Annotations

Gene Name Phenotype2GO Annotation Evidence Code Experiment Reference Manual GO Annotation Evidence Code Comment Recommend Keep Phenotype2GO Annotation? Class of P2GO
hsf-1 locomotion (GO:0040011) IMP RNAi in rrf-3 6395, Simmer et al., 2003, others No manual annotations from 6395 May reflect role in regulating transcription - what are the targets? No manual annotations to locomotion-related terms No Possible downstream effect
met-1 locomotion (GO:0040011) IMP RNAi 26635, Gottschalk, et al., 2005 No manual GO annotation from 26635 Role of met-1 not clear from this paper, but as a histone methyltransferase probably related to gene expression; manual annotations exist to cellular level processes and one vulval development annotation No Possible downstream effect
sax-3 locomotion (GO:0040011) IMP RNAi 5654, Kamath et al., 2003 No manual GO annotation from 5654 sax-3 plays a role in neuron and muscle migration guidance, manual annotations exist to axon guidance, neuron migration No Downstream effect
skn-1 embryonic development (GO:0009790) IMP RNAi 28492, Maduro et al., 2007 endodermal cell fate specification IMP P2GO annotation is correct, but less granular than manual annotation Not necessary - manual exists High-level term
smg-8 locomotion (GO:0040011) IMP RNAi 37111, Izumi et al., 2010 No manual annotation from 37111 smg-8 encodes a novel protein; only CC annotations exist No Downstream effect: phenotype used as output for more general cellular process: effect on locomotion apparently a result of unc-54 transcript stabilization; also incorrect evidence code
mes-4 determination of adult lifespan (GO:0008430) IMP RNAi 33449, Curran et al., 2009 No manual GO annotation for mes-4 from 33449 Affect on lifespan may be due to role in regulation of germline transcription, germ cell survival No Possible downstream effect - MES-4 is required for germ cell fate specification
gld-3 apoptosis (obsolete) IMP RNAi 38381 maybe a germ cell development annotation? IMP
fem-3 embryonic development ending in birth or egg hatching (GO:0009792) IMP RNAi 5599 large-scale screen small-scale experiment supports this but is not yet annotated (35459)

Strategy moving forward

From the Phenotype2GO (P2GO) annotation file we need the following information:

  • How many unique genes have P2GO annotations
  • How many of these genes have a manual or IEA (Process) annotation
  • How many genes have only P2GO annotations (will be obtained from the above)