RNA ENRICH RESULTS

LRPath Adjusted for Average Gene Count

• Results

NEW! Gene by Gene Ontology Tables

• Download Here
• Note: zip file contains an RData object
• GO Terms have been filtered so that only terms that are significant in at least 1 trait are present

NEW!: Some results regarding statins

• LRPath Results
WRONG WRONG WRONG
• DE Results

Differential Expression Results

• Results (FDR < 0.05)
• NEW! Same as above but with no PEER factors

LRpath Stuff

All Traits

Note: these are incorrect, as these analyses are not adjusted for average gene count (see RNA enrich results)

• LRpath Results!
• LRpath Results -- K=0!
• LRpath Results -- no IEA (k==0)
• Revigo trimmed lists
• LRpath Results -- only experimental evidence codes (k==0)

GOSEQ RELATED DOCUMENTS

All Traits

First Analysis - FDR 0.1 as cutoff; Wallenius approximation

• http://csg.sph.umich.edu/beckandy/report.html

report_n[y].html - For all traits, top y genes marked as differentially expressed; Wallenius approximation

• http://csg.sph.umich.edu/beckandy/report_n300.html
• http://csg.sph.umich.edu/beckandy/report_n500.html
• http://csg.sph.umich.edu/beckandy/report_n1000.html
• http://csg.sph.umich.edu/beckandy/report_n2000.html

Number DE by Q Value Cutoff

• http://csg.sph.umich.edu/beckandy/numDE.html

Decile Table - For each trait, how many genes are DE in each decile? 

• http://csg.sph.umich.edu/beckandy/decTab1.html

Direction Table - For each trait, what proportion of DE genes have (positive/negative) effect? + % of genes DE

• http://csg.sph.umich.edu/beckandy/direction.html

Wallenius Summary - Number of over/under enriched goterms based on various cutoffs (top 300/500/1000 or FDR < 0.1)

• http://csg.sph.umich.edu/beckandy/wallTable.html
  • Also w/ exclusion of categories with > 1000 genes

Single Traits

http://csg.sph.umich.edu/beckandy/reports/

• Reports with a trait name have goseq results when

1. Top 1000 genes marked DE
2. Genes in top 1000 with positive effect marked DE
3. Genes in top 1000 with negative effect marked DE 

http://csg.sph.umich.edu/beckandy/t2d_ngt.html

• Older report for NGT_v_T2D
• Uses various cutoffs for DE and also looked at using median count for bias correction
• Only shows overenriched categories

Other Documents

• http://csg.sph.umich.edu/beckandy/deciles.html
  • 10 analyses; For analysis i, mark the genes in decile i as differentially expressed and run goseq
  • http://csg.sph.umich.edu/beckandy/decileTable.html
    • Count of over/under enriched categories (and when excluding cats with > 1000 genes)
• http://csg.sph.umich.edu/beckandy/InsuDirByDecile.html
  • For the differentially expressed genes for insulin, how many are in each decile?
• http://csg.sph.umich.edu/beckandy/Insu30DirByDecile.html
  • For the differentially expressed genes for 30 minute insulin, how many are in each decile?
• http://csg.sph.umich.edu/beckandy/reports/etc_genes_exploration.html
  • Analysis of Respiratory ETC category results from NGT_V_T2D and Insulin
  • CSV FILE
• http://csg.sph.umich.edu/beckandy/oxreduc.html
  • Analysis of Oxidation-Reduction category results from NGT_V_T2D and Insulin
  • CSV FILE