Phenotype2GO Analysis
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Revision as of 18:50, 3 June 2013 by Vanaukenk (talk | contribs) (→Named Genes with Phenotype2GO-Based Annotations)
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 | No | Downstream effect - regulating adult lifespan is not the main biological role of MES-4 | |
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)