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 | ||
|- | |- | ||
− | | ham-1 || NOTE: this annotation is no longer on the | + | | ham-1 || NOTE: this annotation is no longer on the ham-1 gene page as of 2013-06-03 locomotion (GO:0040011) || IMP || RNAi in rrf-3 || 6395, Simmer et al., 2003 || no manual annotations from this large-scale paper || || Member of SWI/SNF complex regulating transcription || No || Possible downstream effect, if ever existed |
|- | |- | ||
| 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 | | 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 |
Revision as of 18:06, 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 |
---|---|---|---|---|---|---|---|---|---|
ham-1 | NOTE: this annotation is no longer on the ham-1 gene page as of 2013-06-03 locomotion (GO:0040011) | IMP | RNAi in rrf-3 | 6395, Simmer et al., 2003 | no manual annotations from this large-scale paper | Member of SWI/SNF complex regulating transcription | No | Possible downstream effect, if ever existed | |
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 | 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)