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Table 4 EASE identifies the same themes in spite of the notable variability in gene lists resulting from different methods of data normalization and gene selection criteria

From: Identifying biological themes within lists of genes with EASE

Method A B C D E F G H   
Normalization MAS 4 MAS 4 dChip dChip Rank remap Rank remap NP NP   
Intensity calculation MAS 4 MAS 4 dChip dChip dChip dChip dChip dChip   
Gene selection t-test SAM t-test SAM t-test SAM t-test SAM System Category
  <0.0001 (1) 0.0002 (1) 0.0004 (1) <0.0001 (1) 0.0005 (2) <0.0001 (4) <0.0001 (1) <0.0001 (1) SWISS-PROT keyword Interferon induction
  0.0006 (2) 0.0027 (2) 0.0383 (4) < 0.0001 (2) <0.0001 (1) <0.0001 (1) <0.0001 (2) <0.0001 (3) Biological process Response to biotic stimulus
  0.0036 (5) 0.0061 (3) NS (5) < 0.0001 (4) 0.0005 (3) <0.0001 (2) <0.0001 (4) <0.0001 (4) Biological process Immune response
  0.0031 (4) 0.0081 (4) NS (7) < 0.0001 (5) 0.0006 (4) <0.0001 (3) <0.0001 (3) <0.0001 (2) Biological process Defense response
  0.0333 (6) NS (7) 0.0329 (3) < 0.0001 (3) 0.0128 (6) <0.0001 (5) 0.0003 (5) <0.0001 (5) Biological process Response to external stimulus
  0.0008 (3) 0.0101 (5) 0.0308 (2) < 0.0001 (6) 0.0078 (5) 0.0002 (6) 0.0558 (8) 0.0071 (8) Molecular function Antiviral response protein
  1. The six dominant categories over-represented in the genes upregulated in PBMCs of HIV patients one month after discontinuing therapy all implicate a vigorous immune response. EASE scores (corrected for multiplicity with the bootstrap function using 10,000 random trials) are shown along with the rank (in parentheses) of each category in each of the eight lists. The category outside of the top five for each list is indicated in italics. NS, p > 0.05.