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

Open Data