Carmen-Proteomics: Difference between revisions
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Preliminary results of GSEA runs by Amanda Larracuente (Qiu Lab) | Preliminary results of GSEA runs by Amanda Larracuente (Qiu Lab) | ||
* Methods | * Methods | ||
# Rank identified proteins by t-statistics, which is a measure of difference between WT and KO mice (3 individuals each). Most genes don't change, with t close to zero. t << 0 suggests down-regulation in KO mice relative to WT mice, and t >> 0 suggests up-regulation. (Need to | # Rank identified proteins by t-statistics, which is a measure of difference between WT and KO mice (3 individuals each). Most genes don't change, with t close to zero. t << 0 suggests down-regulation in KO mice relative to WT mice, and t >> 0 suggests up-regulation. (Could be the other way around. Need to confirm) | ||
# Download mice gene sets from a web resource | # Download mice gene sets from a web resource | ||
# Run GSEA by Broad Institute | # Run GSEA by Broad Institute | ||
* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490136739893 | * [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490136739893 Results using mice gene set with GO annotations] | ||
* [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490138021974 Results using mice gene set w/o GO annotations] | * [http://diverge.hunter.cuny.edu/~weigang/carmen-proteomics/mice.GseaPreranked.1490138021974 Results using mice gene set w/o GO annotations] | ||
Latest revision as of 14:06, 22 March 2017
Tuesday, March 21, 2017
Preliminary results of GSEA runs by Amanda Larracuente (Qiu Lab)
- Methods
- Rank identified proteins by t-statistics, which is a measure of difference between WT and KO mice (3 individuals each). Most genes don't change, with t close to zero. t << 0 suggests down-regulation in KO mice relative to WT mice, and t >> 0 suggests up-regulation. (Could be the other way around. Need to confirm)
- Download mice gene sets from a web resource
- Run GSEA by Broad Institute