Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells

BMC Bioinformatics

Table 1 Comparison of the selected gene lists obtained with different methods of selection.

	Sliding window 20¹	Sliding window 30¹	EDGE 0.01²	EDGE 0.001²	BATS #1³	BATS #2⁴	timecourse 1000⁵	timecourse 1500⁵
Sliding window 20¹	1563	997	1126	667	903	1069	140	209
Sliding window 30¹		997	825	540	690	797	85	128
EDGE 0.01²			2595	1145	936	1086	232	343
EDGE 0.001²				1145	590	659	104	154
BATS #1³					1478	1397	157	157
BATS #2⁴						1660	232	243
timecourse 1000⁵							1000	1000
timecourse 1500⁵								1500

¹DiffScore threshold. ²q-value threshold. ³Error model = normal, λ=12. ⁴Error model = double-exponential, λ=9. ⁵Number of ranked genes selected.

Numbers indicate the genes obtained by pairwise intersection of different methods of selection. In bold are the selected gene lists for each method.

ISSN: 1471-2105