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
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BT_ATMminus vs. ATMplus Report
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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
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ATMminus vs. SCID Report
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SCID vs. ATMplus Report
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GSEA reports for "Log2_Ratio_of_Classes":


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