Set 02: ATM / BT_ATM

Phenotypes:

ATM_minus: ATM^-/- Tumor - 4 Samples (actually from Set 01)
BT_ATM_minus: ATM^-/- cell before Tumor - 5 Samples
ATM_plus: ATM^+/+ normal thymocytes - 3 Samples from Set_01 (littermates) and 4 new Samples (age-matched)

Platform: Affymetrix MOE430 v2

GSEA-preRanked reports for "moderated t-Test":

	MSigDB.c2	MSigDB.c3.tft	MSigDB.c5	Pathways
ATMminus vs. BT_ATMminus	Report	Report	Report	Report
BT_ATMminus vs. ATMplus	Report	Report	Report	Report

Note: In this GSEA-preRanked analysis we have used only those four ATMplus (wt) samples from the second Experiment (age matched mice) and not those also included in the Set_01 (littermate ATMplus).

Note 2:
The ranked gene lists were extracted from a files named "pvals.txt" with the R-Code posted on:
http://baderlab.org/CancerStemCellProject/CodeRepository#extract_moderated_tStatisctic_to_RNK_Set02_ATM_BTATM.R
The R-Code to calculate the moderated t-Test is archived on:
http://baderlab.org/CancerStemCellProject/CodeRepository#moderated_t_Statistic_for_Set_02

GSEA reports for "GSEA t-Test":

	MSigDB.c2	MSigDB.c3.tft	MSigDB.c5	Pathways
ATMminus vs. ATMplus	Report	Report	Report	Report
ATMminus vs. SCID	Report	Report	Report	Report
SCID vs. ATMplus	Report	Report	Report	Report

GSEA reports for "Log2_Ratio_of_Classes":

	MSigDB.c2	MSigDB.c3.tft	MSigDB.c5	Pathways
ATMminus vs. ATMplus	Report	Report	Report	Report
ATMminus vs. SCID	Report	Report	Report	Report
SCID vs. ATMplus	Report	Report	Report	Report