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
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

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.

Hosack et al. Genome Biology 2003 4:R70   doi:10.1186/gb-2003-4-10-r70

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