Phenotype2GO Analysis

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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
ham-1 locomotion (GO:0040011) IMP RNAi in rrf-3 6395, Simmer et al., 2003 transcription, but nothing about locomotion ISS Member of SWI/SNF complex regulating transcription No Possible downstream effect
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
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 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)