Skip to main content
. 2008 Mar 21;4(3):e1000021. doi: 10.1371/journal.pcbi.1000021

Table 1. Network of inferred transcription factor–cluster associations.

Clust TF TF Clust -log10 P scan Position-Weight Matrix Name FracBind Scan Hits -log10 P exp <θ> Mean Corr
1 Cebpg 22 5.74 V$CEBPGAMMA_Q6 0.41 40 0.03 13.5 −0.21
1 E2f1 2 2.84 V$E2F_02 0.44 43 0.82 75.4 0.72
1 E2f7 3 1.41 V$E2F1_Q4_01 0.41 40 4.42 73.4 0.86
1 Irf2 13 1.60 V$IRF_Q6_01 0.32 31 1.35 68.8 −0.74
1 Irf7 6 1.60 V$IRF_Q6_01 0.32 31 3.26 68.7 −0.83
1 Isgf3g 6 1.60 V$IRF_Q6_01 0.32 31 2.13 71.3 −0.80
1 Mef2a 2 2.73 V$MEF2_Q6_01 0.33 32 1.50 75.0 0.78
1 Mef2c 16 2.73 V$MEF2_Q6_01 0.33 32 2.23 67.4 0.81
1 Nfyc 4 6.08 V$NFY_Q6 0.48 47 0.17 78.1 0.59
2 E2f1 2 3.68 V$E2F_02 0.46 46 3.16 34.2 0.85
2 E2f6 10 2.97 V$E2F_03 0.47 47 2.72 65.9 0.82
2 E2f7 3 2.97 V$E2F_03 0.47 47 3.62 33.1 0.85
2 Myc 20 1.95 V$MYCMAX_01 0.34 34 1.36 18.4 0.74
2 Rxra 14 2.55 V$LXR_DR4_Q3 0.38 38 1.61 57.6 0.77
3 E2f1 2 3.86 V$E2F_Q6_01 0.53 54 2.39 47.2 0.83
3 E2f6 10 3.86 V$E2F_Q6_01 0.53 54 2.26 69.0 0.81
3 E2f7 3 3.86 V$E2F_Q6_01 0.53 54 8.00 33.5 0.93
3 Myc 20 1.32 V$MYCMAX_03 0.32 33 1.62 16.1 0.78
3 Nfic 19 3.98 V$NF1_Q6 0.46 47 0.26 77.6 0.63
3 Nfyc 4 7.73 V$NFY_Q6_01 0.54 55 0.28 58.3 0.65
3 Rxra 14 1.36 V$LXR_DR4_Q3 0.33 34 1.24 64.0 0.77
3 Stat1 6 2.12 V$STAT1_03 0.41 42 2.95 12.1 −0.86
4 Cebpa 19 2.05 V$CEBP_Q2 0.34 34 0.43 70.0 0.65
4 Foxm1 3 6.18 V$FOXM1_01 0.41 41 0.63 52.6 0.68
4 Mef2a 2 1.68 V$MEF2_04 0.30 30 1.56 40.2 0.79
4 Myc 20 1.99 V$MYCMAX_B 0.44 44 0.63 45.5 0.68
4 Nfyc 4 1.43 V$NFY_Q6_01 0.36 36 1.06 68.0 0.74
4 Tgif1 27 3.12 V$TGIF_01 0.32 32 0.16 42.5 0.10
5 E2f1 2 3.85 V$E2F1_Q6_01 0.52 45 2.31 50.3 0.81
5 E2f6 10 2.71 V$E2F_03 0.48 41 2.84 72.5 0.81
5 E2f7 3 2.71 V$E2F_03 0.48 41 1.27 47.3 0.76
5 Myc 20 2.54 V$MYCMAX_B 0.48 41 1.00 27.9 0.69
5 Rxra 14 1.87 V$PPARA_02 0.30 26 1.72 63.7 0.77
6 Irf1 25 3.65 V$IRF_Q6 0.40 35 0.09 79.1 0.56
6 Irf2 13 3.65 V$IRF_Q6 0.40 35 3.32 44.3 0.81
6 Irf3 12 3.65 V$IRF_Q6 0.40 35 0.05 35.4 −0.09
6 Irf5 6 3.65 V$IRF_Q6 0.40 35 1.21 68.4 0.75
6 Irf7 6 3.65 V$IRF_Q6 0.40 35 5.20 26.6 0.88
6 Isgf3g 6 1.84 V$IRF_Q6_01 0.33 29 3.24 25.0 0.84
7 Pou2f2 9 2.10 V$OCT_C 0.32 24 0.42 45.9 −0.64
9 Myc 20 1.54 V$MYC_Q2 0.36 26 1.26 29.3 −0.67
10 Atf1 14 1.73 V$CREB_Q3 0.34 25 0.86 38.1 0.73
10 Myc 20 2.18 V$MYCMAX_B 0.47 35 0.43 11.2 0.68
10 Nfyc 4 1.67 V$NFY_Q6_01 0.39 29 1.31 35.8 0.78
10 Nr3c1 6 2.79 V$GR_Q6_01 0.34 25 1.86 48.5 −0.79
11 Fos 27 3.23 V$AP1_Q2_01 0.45 29 0.11 47.0 −0.05
11 Jun 20 3.23 V$AP1_Q2_01 0.45 29 0.20 41.4 −0.37
11 Junb 28 3.23 V$AP1_Q2_01 0.45 29 0.05 70.3 0.24
13 Foxo3a 14 2.41 V$FOXO3_01 0.37 20 0.77 14.2 −0.75
13 Irf1 25 7.47 V$IRF_Q6_01 0.57 31 0.32 77.5 0.64
13 Irf3 12 7.47 V$IRF_Q6_01 0.57 31 0.07 42.8 0.07
13 Irf5 6 7.47 V$IRF_Q6_01 0.57 31 0.49 22.7 0.71
13 Nfkb1 15 2.32 V$NFKB_Q6_01 0.41 22 2.41 31.3 0.82
13 Rel 25 1.65 V$CREL_01 0.37 20 0.88 71.9 0.72
14 Nfkb1 15 2.14 V$NFKB_C 0.34 19 3.37 51.3 −0.84
15 Rel 25 2.42 V$CREL_01 0.42 21 1.78 29.0 0.78
16 Cebpa 19 1.43 V$CEBP_C 0.32 16 1.05 73.4 0.74
16 E2f1 2 1.78 V$E2F_01 0.40 20 2.52 52.3 0.80
16 Jun 20 2.39 V$AP1_Q2_01 0.44 22 0.14 59.3 0.43
16 Myc 20 1.90 V$MYCMAX_02 0.40 20 0.83 20.5 0.63
16 Rxra 14 1.32 V$FXR_IR1_Q6 0.30 15 1.33 63.8 0.75
17 Nfatc1 14 1.71 V$NFAT_Q4_01 0.36 18 1.78 33.6 −0.79
17 Nfatc2 14 1.71 V$NFAT_Q4_01 0.36 18 1.60 12.2 −0.80
17 Nfkb1 15 2.02 V$NFKB_Q6 0.36 18 2.25 60.3 0.80
17 Sfpi1 17 1.35 V$ETS_Q6 0.42 21 1.34 14.8 0.78
18 Pou2f2 9 1.78 V$OCT_Q6 0.33 16 0.68 53.9 −0.67
19 Nr3c1 6 1.62 V$PR_Q2 0.33 16 1.24 37.2 −0.74
19 Rxra 14 1.61 V$T3R_Q6 0.37 18 1.65 14.6 0.79
19 Zfp161 19 2.98 V$ZF5_01 0.55 27 0.90 49.8 0.73
20 E2f7 3 2.11 V$E2F_03 0.50 24 0.64 66.5 0.66
20 Myc 20 2.36 V$MYCMAX_B 0.52 25 0.66 53.6 0.64
21 Nfkb1 15 2.13 V$NFKAPPAB_01 0.38 15 2.25 28.2 0.78
22 Stat1 6 3.22 V$STAT1_01 0.58 19 0.16 55.2 0.39
23 E2f1 2 3.24 V$E2F1_Q4_01 0.60 21 0.08 47.6 0.54
23 E2f6 10 3.24 V$E2F1_Q4_01 0.60 21 0.48 46.0 0.66
23 E2f7 3 3.24 V$E2F1_Q4_01 0.60 21 0.05 50.7 0.49
25 Irf1 25 1.41 V$IRF_Q6_01 0.40 10 1.42 15.1 0.79
26 Cebpa 19 2.50 V$CEBP_01 0.45 14 0.01 52.6 0.14
26 Tgif1 27 2.14 V$TGIF_01 0.39 12 0.28 49.4 0.36
27 Atf1 14 2.57 V$CREBATF_Q6 0.58 14 0.25 69.0 0.52
27 Cbfb 4 2.39 V$PEBP_Q6 0.50 12 0.45 65.3 0.52
27 E2f7 3 1.62 V$E2F_Q4_01 0.54 13 1.01 61.0 0.63
27 Egr1 27 2.62 V$KROX_Q6 0.58 14 1.37 16.0 0.75
27 Egr2 27 2.62 V$KROX_Q6 0.58 14 1.16 11.7 0.75
27 Jun 20 2.63 V$CREBP1CJUN_01 0.54 13 0.24 47.3 0.46
27 Rxra 14 2.46 V$PPARA_02 0.46 11 0.61 63.3 0.53
28 E2f1 2 2.75 V$E2F_01 0.54 14 0.05 37.9 −0.05
28 Nfkb1 15 4.48 V$NFKAPPAB_01 0.58 15 0.07 25.7 0.27
29 Cebpa 19 2.48 V$CEBP_01 0.48 12 0.04 65.9 −0.11
31 Mef2a 2 2.39 V$MEF2_03 0.58 7 0.16 35.9 −0.51

Column 1 indicates the target gene cluster. Column 2 indicates the transcription factor gene that is associated with the cluster, based on the two sources of evidence. Column 3 indicates the cluster of which the transcription factor gene is a member. Column 4 indicates the -log10 P value of the promoter scanning-based evidence. Column 5 indicates the name of the position-weight matrix that had the smallest scanning-based P value of association with the cluster, for the indicated transcription factor gene (the “V$” prefix is not shown). Column 6 indicates the fraction of scanned genes within the cluster that had at least one match for the indicated position-weight matrix. Column 7 contains the number of scanned genes within the cluster that had at least one match for the indicated position-weight matrix. Column 8 indicates the negative log10 P value of the time-lagged correlation evidence. Column 9 indicates the cluster-wide average time lag θ with respect to the indicated transcription factor gene. Column 10 contains the average optimal time-lagged correlation between the indicated transcription factor gene, and the genes within the cluster.