Investigator: Chad Johnson, Beachaump Lab

Description: Comparison between stage 1/2 tumors with stage 4 tumors, all GI (includes rectal ca).

Tasks

Normalization (Zhouwen).

Used RMA (in Biocondutor package) to normalize these data. Completed 12/1/05.

KEGG annotation and significance testing.

Tried to use GOcluster, package bombed. Apparently the package is not being updated (search done by Bonnie on 12/15/05). Used SAFE analysis instead (completed by Aixiang on 12/21/05).

Completed

• Report with SAFE analysis, directional information and genes in the significant pathways given to Chad on 1/18/06.

Additional requests

(email from 1/27/06)

Finally, you sent me the KEGG pathway list for the Stage I/II vs. IV project last time. (Again, thank you for that.) Could you please send me the list of Affy probes (genes) with their p-values from your global comparison of the groups? I'm talking about just the significantly different genes in the two groups with their p-values much like the first one you sent me from the celecoxib study (1350 genes with a p-value <0.05), without function or pathway information.

Aixiang finished this, and added in the direction of the change on 2/2/06; email was sent to Chad on the same day.