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Table 4 Ranking of EPD human promoters containing predicted TFBSs by target functionality

From: Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions

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

  1. 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.
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BMC Bioinformatics

ISSN: 1471-2105

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