Difference between revisions of "Phenotype2GO Analysis"

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! Gene Name !! Phenotype2GO Annotation !! Evidence Code !! Experiment !! Reference !! Manual GO Annotation !! Evidence Code !! Comment !! Recommend Keep Phenotype2GO Annotation? || Class of P2GO
 
! Gene Name !! Phenotype2GO Annotation !! Evidence Code !! Experiment !! Reference !! Manual GO Annotation !! Evidence Code !! Comment !! Recommend Keep Phenotype2GO Annotation? || Class of P2GO
 
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| hsf-1 || locomotion (GO:0040011) || IMP || RNAi in rrf-3 || 6395, Simmer et al., 2003, others || Nothing related to locomotion || || Reflects role in regulating protein homeostasis? || No || Possible downstream effect
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| hsf-1 || locomotion (GO:0040011) || IMP || RNAi in rrf-3 || 6395, Simmer et al., 2003, others || Nothing related to locomotion || || May reflect role in regulating transcription || No || Possible downstream effect
 
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| met-1 || locomotion (GO:0040011) || IMP || RNAi || 26635, Gottschalk, et al., 2005 ||  no manual GO annotation || || role of met-1 not clear from this paper, but as a histone methyltransferase probably related to gene expression; contrast physiological process vs developmental process || No || Possible downstream effect
 
| met-1 || locomotion (GO:0040011) || IMP || RNAi || 26635, Gottschalk, et al., 2005 ||  no manual GO annotation || || role of met-1 not clear from this paper, but as a histone methyltransferase probably related to gene expression; contrast physiological process vs developmental process || No || Possible downstream effect

Revision as of 18:16, 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 Nothing related to locomotion May reflect role in regulating transcription No Possible downstream effect
met-1 locomotion (GO:0040011) IMP RNAi 26635, Gottschalk, et al., 2005 no manual GO annotation role of met-1 not clear from this paper, but as a histone methyltransferase probably related to gene expression; contrast physiological process vs developmental process No Possible downstream effect
sax-3 locomotion (GO:0040011) IMP RNAi 5654, Kamath et al., 2003 axon guidance, neuron migration sax-3 plays a role in neuron and muscle migration guidance No Downstream effect
skn-1 embryonic development (GO:0009790) IMP RNAi 28492, Maduaro 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 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184) IGI smg-8 encodes a novel protein; manual annotation still needs to be added; affect on locomotion apparently a result of unc-54 transcript stabilization No Phenotype used as output for more general cellular process; incorrect evidence code
mes-4 determination of adult lifespan (GO:0008430) IMP RNAi 33449 no GO annotation here? expt about germline fates
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)