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Table 2 CrmMiner's performance on the 154 heart-specific genes

From: Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs

n CNEs Controls PCRMs Controls(+) E-value h P-value
0 375 1875 41 30 6.8 1.4e−15
10 492 2460 46 55 4.2 4.3e−12
20 537 2685 19 8 11.2 7.3e−10
30 680 3400 50 47 5.3 1.3e−15
40 602 3010 41 45 4.6 1.3e−11
60 768 3840 40 58 3.5 8.4e−9
80 656 3280 38 43 4.5 1.4e−10
100 1107 5535 32 32 5.0 6.5e−10
All 892 4460 14 15 4.7 7.6e−5
  1. CrmMiner was evaluated on nine testing sets that were composed of CNEs found in 39 heart-specific gene loci. PCRMs stand for putative CRMs. Controls(+) stand for CRMs predicted among the control sequences. All mixed sets included CNEs in the region between -10 kbp and +10 kbp. Mixed sets were expanded as before. The number of CNEs in the mixed set did not always increase when the number of the closest CNEs, n, was increased because we randomly partitioned the loci into three sets every time n was increased. The Fisher's exact test was used to calculate the P-values.