Table 2.
HOMER-known motif analysis
| Sarcoma-specific binding sites | |||||||
|---|---|---|---|---|---|---|---|
| Rank | Name | P value | # Target sequences with motif | % of Targets sequences with motif | # Background sequences with motif | % of Background sequences with motif | Motif |
| 1 | Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer | 1e-1014 | 2618 | 34.76% | 2802.5 | 7.39% | Atf-related |
| 2 | Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer | 1e-918 | 2141 | 28.43% | 1983.2 | 5.23% | Atf-related |
| 3 | Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer | 1e-849 | 1776 | 23.58% | 1410.8 | 3.72% | Atf-related |
| 4 | c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-734 | 1580 | 20.98% | 1282.4 | 3.38% | Atf-related |
| 5 | CRE(bZIP)/Promoter/Homer | 1e-610 | 1238 | 16.44% | 912.8 | 2.41% | Atf-related |
| 6 | JunD(bZIP)/K562-JunD-ChIP-Seq/Homer | 1e-584 | 902 | 11.98% | 437.6 | 1.15% | Atf-related |
| 7 | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-414 | 1582 | 21.00% | 2270.4 | 5.99% | Atf-related |
| 8 | AP1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-411 | 1882 | 24.99% | 3136.4 | 8.27% | Atf-related |
| 9 | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-406 | 1730 | 22.97% | 2719.3 | 7.17% | Atf-related |
| 10 | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-403 | 1726 | 22.92% | 2720 | 7.17% | Atf-related |
| 11 | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-352 | 1143 | 15.18% | 1396 | 3.68% | Atf-related |
| 12 | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1.00E-287 | 881 | 11.70% | 1007.1 | 2.66% | Atf-related |
| 13 | EBF(EBF)/proBcell-EBF-ChIP-Seq(GSE21978)/Homer | 1.00E-126 | 412 | 5.47% | 489.1 | 1.29% | Sarcoma-specific |
| 14 | Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer | 1.00E-105 | 507 | 6.73% | 823.9 | 2.17% | |
| 15 | EBF1(EBF)/Near-E2A-ChIP-Seq(GSE21512)/Homer | 1.00E-100 | 1072 | 14.23% | 2697.6 | 7.11% | Sarcoma-specific |
| 16 | Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1.00E-95 | 466 | 6.19% | 762.9 | 2.01% | |
| 17 | Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer | 1.00E-90 | 527 | 7.00% | 970.4 | 2.56% | Atf-related |
| 18 | Nkx6.1(Homeobox)/Islet-Nkx6.1-ChIP-Seq(GSE40975)/Homer | 1.00E-69 | 2961 | 39.31% | 11288.6 | 29.77% | Sarcoma-specific |
| 19 | Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer | 1.00E-64 | 1362 | 18.08% | 4319.5 | 11.39% | Sarcoma-specific |
| 20 | Foxo1(Forkhead)/RAW-Foxo1-ChIP-Seq/Homer | 1.00E-62 | 1985 | 26.35% | 7022.5 | 18.52% | Sarcoma-specific |
| 21 | CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer | 1.00E-60 | 928 | 12.32% | 2659 | 7.01% | Atf-related |
| 22 | FOXP1(Forkhead)/H9-FOXP1-ChIP-Seq(GSE31006)/Homer | 1.00E-52 | 612 | 8.13% | 1576.7 | 4.16% | Sarcoma-specific |
| 23 | NF1-halfsite(CTF)/LNCaP-NF1-ChIP-Seq(Unpublished)/Homer | 1.00E-48 | 1655 | 21.97% | 5889.6 | 15.53% | |
| 24 | MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer | 1.00E-40 | 1027 | 13.64% | 3381.4 | 8.92% | |
| 25 | FOXA1(Forkhead)/LNCAP-FOXA1-ChIP-Seq(GSE27824)/Homer | 1.00E-38 | 1384 | 18.37% | 4938.6 | 13.02% | Sarcoma-specific |
| 26 | Sox10(HMG)/SciaticNerve-Sox3-ChIP-Seq(GSE35132)/Homer | 1.00E-34 | 1664 | 22.09% | 6300.6 | 16.62% | Sarcoma-specific |
| 27 | Nur77(NR)/K562-NR4A1-ChIP-Seq(GSE31363)/Homer | 1.00E-33 | 276 | 3.66% | 607.9 | 1.60% | Sarcoma-specific |
| 28 | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1.00E-31 | 1187 | 15.76% | 4275 | 11.27% | |
| 29 | Lhx3(Homeobox)/Neuron-Lhx3-ChIP-Seq(GSE31456)/Homer | 1.00E-30 | 1778 | 23.61% | 6933.2 | 18.29% | Sarcoma-specific |
| 30 | FOXA1(Forkhead)/MCF7-FOXA1-ChIP-Seq(GSE26831)/Homer | 1.00E-30 | 1125 | 14.94% | 4027.9 | 10.62% | Sarcoma-specific |
| MEF-specific binding sites | |||||||
|---|---|---|---|---|---|---|---|
| Rank | Name | P value | # Target sequences with motif | % of Targets sequences with motif | # Background sequences with motif | % of Background sequences with motif | |
| 1 | Atf7(bZIP)/3T3L1-Atf7-ChIP-Seq(GSE56872)/Homer | 1e-2516 | 6796 | 26.36% | 1306.8 | 5.63% | Atf-related |
| 2 | Atf1(bZIP)/K562-ATF1-ChIP-Seq(GSE31477)/Homer | 1e-2430 | 7999 | 31.03% | 1895.2 | 8.16% | Atf-related |
| 3 | Atf2(bZIP)/3T3L1-Atf2-ChIP-Seq(GSE56872)/Homer | 1e-2415 | 5702 | 22.12% | 928.2 | 4.00% | Atf-related |
| 4 | c-Jun-CRE(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-2145 | 5184 | 20.11% | 858.6 | 3.70% | Atf-related |
| 5 | JunD(bZIP)/K562-JunD-ChIP-Seq/Homer | 1e-1716 | 2922 | 11.34% | 294.1 | 1.27% | Atf-related |
| 6 | Atf3(bZIP)/GBM-ATF3-ChIP-Seq(GSE33912)/Homer | 1e-1382 | 5991 | 23.24% | 1705.1 | 7.34% | Atf-related |
| 7 | BATF(bZIP)/Th17-BATF-ChIP-Seq(GSE39756)/Homer | 1e-1367 | 6005 | 23.30% | 1726.5 | 7.43% | Atf-related |
| 8 | Fra1(bZIP)/BT549-Fra1-ChIP-Seq(GSE46166)/Homer | 1e-1345 | 5400 | 20.95% | 1438 | 6.19% | Atf-related |
| 9 | AP1(bZIP)/ThioMac-PU.1-ChIP-Seq(GSE21512)/Homer | 1e-1309 | 6409 | 24.86% | 1996.5 | 8.60% | Atf-related |
| 10 | CRE(bZIP)/Promoter/Homer | 1e-1193 | 3207 | 12.44% | 575.2 | 2.48% | Atf-related |
| 11 | Fosl2(bZIP)/3T3L1-Fosl2-ChIP-Seq(GSE56872)/Homer | 1e-1052 | 3678 | 14.27% | 853 | 3.67% | Atf-related |
| 12 | Jun-AP1(bZIP)/K562-cJun-ChIP-Seq(GSE31477)/Homer | 1e-922 | 2881 | 11.18% | 596.2 | 2.57% | Atf-related |
| 13 | Bach2(bZIP)/OCILy7-Bach2-ChIP-Seq(GSE44420)/Homer | 1e-387 | 1701 | 6.60% | 459.1 | 1.98% | |
| 14 | Chop(bZIP)/MEF-Chop-ChIP-Seq(GSE35681)/Homer | 1.00E-297 | 1603 | 6.22% | 497.1 | 2.14% | |
| 15 | Atf4(bZIP)/MEF-Atf4-ChIP-Seq(GSE35681)/Homer | 1.00E-271 | 1769 | 6.86% | 615.5 | 2.65% | Atf-related |
| 16 | CEBP:AP1(bZIP)/ThioMac-CEBPb-ChIP-Seq(GSE21512)/Homer | 1.00E-189 | 3147 | 12.21% | 1642.2 | 7.07% | Atf-related |
| 17 | RUNX-AML(Runt)/CD4 + -PolII-ChIP-Seq/Homer | 1.00E-182 | 3251 | 12.61% | 1732.1 | 7.46% | MEF-specific |
| 18 | RUNX(Runt)/HPC7-Runx1-ChIP-Seq(GSE22178)/Homer | 1.00E-126 | 3229 | 12.53% | 1891.4 | 8.14% | MEF-specific |
| 19 | NF-E2(bZIP)/K562-NF-E2-ChIP-Seq(GSE31477)/Homer | 1.00E-111 | 507 | 1.97% | 139.8 | 0.60% | MEF-specific |
| 20 | RUNX1(Runt)/Jurkat-RUNX1-ChIP-Seq(GSE29180)/Homer | 1.00E-109 | 4110 | 15.94% | 2629 | 11.32% | MEF-specific |
| 21 | TEAD(TEA)/Fibroblast-PU.1-ChIP-Seq(Unpublished)/Homer | 1.00E-108 | 2673 | 10.37% | 1546.3 | 6.66% | MEF-specific |
| 22 | RUNX2(Runt)/PCa-RUNX2-ChIP-Seq(GSE33889)/Homer | 1.00E-106 | 3823 | 14.83% | 2419.9 | 10.42% | MEF-specific |
| 23 | Bach1(bZIP)/K562-Bach1-ChIP-Seq(GSE31477)/Homer | 1.00E-103 | 477 | 1.85% | 132.4 | 0.57% | MEF-specific |
| 24 | Nrf2(bZIP)/Lymphoblast-Nrf2-ChIP-Seq(GSE37589)/Homer | 1.00E-97 | 452 | 1.75% | 126.4 | 0.54% | MEF-specific |
| 25 | MafA(bZIP)/Islet-MafA-ChIP-Seq(GSE30298)/Homer | 1.00E-93 | 3410 | 13.23% | 2158.3 | 9.29% | |
| 26 | TEAD4(TEA)/Tropoblast-Tead4-ChIP-Seq(GSE37350)/Homer | 1.00E-88 | 3115 | 12.08% | 1954.8 | 8.42% | MEF-specific |
| 27 | Meis1(Homeobox)/MastCells-Meis1-ChIP-Seq(GSE48085)/Homer | 1.00E-84 | 6677 | 25.90% | 4835.6 | 20.82% | MEF-specific |
| 28 | MITF(bHLH)/MastCells-MITF-ChIP-Seq(GSE48085)/Homer | 1.00E-75 | 3891 | 15.09% | 2623.1 | 11.30% | |
| 29 | NF1(CTF)/LNCAP-NF1-ChIP-Seq(Unpublished)/Homer | 1.00E-65 | 1052 | 4.08% | 536.5 | 2.31% | |
| 30 | Tbx20(T-box)/Heart-Tbx20-ChIP-Seq(GSE29636)/Homer | 1.00E-64 | 1069 | 4.15% | 549.7 | 2.37% | MEF-specific |
Motifs appearing in sarcoma-specific and MEF-specific EWS/ATF1 binding sites are shown
MEF mouse embryonic fibroblasts, ChIP-seq chromatin immunoprecipitation-sequencing, CRE cyclic AMP response element, HOMER (Hypergeometric Optimization of Motif EnRichment)