Table 4.
Ranking of EPD human promoters containing predicted TFBSs by target functionality
| TF type, Stringency | Known targets | Very possible targets | Possible targets | BSs of homologous TFs | Possibly unrelated | Unknown |
| E2F, 60% | MCM7, MCM5, MCM2, Cyclin D1, RAD51, TYMS2 | MCM3 | SLC1A5, ALDOA E3P2, GORASP2, BTG1, RAE1, ZNF9, CDC37 | MYL6, COX7B, COX8, YME1L1, MFGE8, TPMT | CBARA1, AUP1, SFRS10, PGD, TARS, PRPS1, RNASE4, PAPOLA2, MRPS7 | |
| HNF4, 50% | hepatic lipase | apolipop. B, apolipop. A1, glucagon, HPD, GLUL | HGD, HBXIP, CSTB, Cyclin D1, CCNB1, CCNB2, UBL5, TAPBP, IFI27, NDUFA6 | histone H4-A1, PRM2, STIP1, RPS8, CASQ2, TOMM22, AUP1, SNX6, TRAP1, RPL23 | CEA, FLJ13154, FLJ10276, LOC57862, COPS4, BLCAP, SLC22A8 | |
| IRF1, 80% | complement f. B, b'-interferon, HLA C, HLA B, IFI27, SP100, IFIT1, IFI 54K, IFI 6–162, ISG 15K | BST2, B2M | Haptoglob Hp1F, haptoglob HpR, IL-4 (BSF-1), TAPBP, NDUFC2, PHGDH, GLRX2, | † CSF-1, PCNA | APOL3, SRP54, GTF2H4, DNASE2, NDUFB4 | |
| ISGF3, 70% | IFI272, IFI 54K, IFI 6–162, ISG 15K | Complement f. B, IFIT1 | SSBP1, ATP5J, SCARB2, ESRRBL1, CTNNBL1, STX10, PMAIP1 | TNP1, B4GALT4, KNS2, PPP1CA, | MGC2714 | |
| PPAR, 70% | ATIII | apolipop. CIII, PCK2 | SDHD, CIR, LOC51064 | histone H2B, BAP29, CHEK1, HNMT, HLA DPB1, MT-IB, MRPL11, SERPINA3, SGT, TNP1, TAPBP, TCL1A, UBL5, VPS29, ARAF1 | CDW52, CSNK1A1, KIAA0971, PCBP2, STIP1, TAF9, TM4SF2, TMP21 | |
| SF-1, 60% | CG/LH/FSH/TSH-a, CYP11A, HSD3B2 | ACPP, PSMD8 | gastrin, FXYD3, CKMT2, MYL2, TGFB1, FXR1, VAPA, TPI1, CDC42EP2, MRPL11, MRPS21, S100A2 | # CTRB1, PPGB, ATF4 | SAT, CNTF, PPA12, RPLP1, FARSL, SERPIND1, CASQ2, TXN, CCT7, SNRP70 | ATP6V0D1, IGF II E3P3, ERH, OS, HU, JM5 |
| STAT1, 60% | complement f. B, AGT3, CD14, FLJ20244, CDKN1A | TNF-b', C4BP b', ARHGDIB, CTNNA1, C1S, SERPINB6 | MCP, BLCAP, DEK, DUT | ‡ DDH hepatic, PGK1, PTTG1 | SAP18, PRSS1, | CG/LH/FSH/TSH a', ALDH1A1, LOC51231, PWP1, EIF3S6, TARS, DC6, GGPS1 |
Prediction for potential targets of E2F, IRF1, ISGF3, HNF4, PPAR, SF-1 and STAT1 were done by combined PWM & SiteGA approach. For each TFs stringencies for SiteGA and PWM are in terms of the same fixed TP rate (50–80%). Known targets – experimentally confirmed targets; very possible or possible targets – a lot of or some indirect evidence on the target functionality; BSs of homologous TFs – potential targets of homologous TFs approved or may be supposed; possibly unrelated – presumably false positives, unknown – no information on the target functionality. 2 – gene have two predicted sites; 3 – gene have three predicted sites; † – potential targets of members of IRF family; # – potential targets of LRH-1, that is homolog of SF-1; ‡ – potential targets of members of STAT family.