Investigator: Chad Johnson, Beachaump Lab

Description: 16 treatment pairs, pre- and 7 days post-treatment with Celebrex. Comparison of gene expression levels between these treatment pairs.

Tasks

Normalization (Zhouwen Liu).

Used RMA (in Biocondutor package) to normalize these data. Completed 9/20/05.

Permutation paired t-test (Zhouwen Liu).

Used AffyPaired software. Completed 9/21/05. There were 202 probes with differential experession p<0.01, and 15 probes with p<0.001. Decided to use 202 probe set for annotation and further examination of pathways.

Annotation (Aixiang Jiang).

Used Bioconductor GOTERMS package. Completed 11/17/05.

After meeting with Chad, it was decided that we would try to use KEGG terms instead. Tried the globaltest function - currently not functional for use with paired data (point to work on); no statistically significant pathways using this function. Most likely not powerful enough with small sample size (and we lose any power than might have been gained by using paired experimental design).

Report of 34 genes (those with unique LocusLink id's), with KEGG term description and direction of change was given to Chad Johnson on 1/18/06.