Difference between revisions of "Phenotype2GO Analysis"
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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 - what are the targets? || No || Possible downstream effect | | 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 - what are the targets? || No || Possible downstream effect | ||
|- | |- | ||
| − | | met-1 || locomotion (GO:0040011) || IMP || RNAi || 26635, Gottschalk, et al., 2005 || | + | | 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 || axon guidance, neuron migration || || sax-3 plays a role in neuron and muscle migration guidance || No || 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 | ||
Revision as of 18:23, 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 - what are the targets? | 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 | 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)
