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Table 1 TimeXNet evaluation for the mouse innate immune response.

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

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
  1. ǂ Results of comparison with ResponseNet taken from Patil et al.[8].
  2. *SDREM was run with 2 starting genes (MyD88 and TRIF) and 62 target genes identified by DREM using time-course gene expression profiles.
  3. # Length indicates the maximum number of consecutive directed edges identified in the pathway
  4. 1 Regulatory genes from Amit et al., Science, 2009
  5. 2 Regulatory genes from Chevrier et al., Cell, 2011
  6. 3 Target genes from Chevrier et al., Cell, 2011