TimeXNet: Identifying active gene sub-networks using time-course gene expression profiles

BMC Systems Biology

Table 1 TimeXNet evaluation for the mouse innate immune response.

Method	Experimentally confirmed regulators (3 datasets)			KEGG Pathways with predicted paths (maximum length^#)	Execution time (4 CPUs, 2.4Ghz, 12Gb RAM)	Prior knowledge required	Analysis of time-course data
TimexNet	49.6%¹	69.8%²	54.9%³	13 (7 edges)	3 min	None	Yes
ResponseNet ^ǂ	39.2%¹	53.5%²	39.2%³	0 (3 edges)	1 min	None	No
SDREM*	12.0%¹	32.6%²	11.8%³	2 (4 edges)	~10 days	Initial regulatory genes	Yes

ǂ Results of comparison with ResponseNet taken from Patil et al.[8].
*SDREM was run with 2 starting genes (MyD88 and TRIF) and 62 target genes identified by DREM using time-course gene expression profiles.
^# Length indicates the maximum number of consecutive directed edges identified in the pathway
¹ Regulatory genes from Amit et al., Science, 2009
² Regulatory genes from Chevrier et al., Cell, 2011
³ Target genes from Chevrier et al., Cell, 2011

ISSN: 1752-0509