Identifying biological themes within lists of genes with EASE

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.

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