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Table 3 Composite element in prostate specific promoters

From: MatrixCatch - a novel tool for the recognition of composite regulatory elements in promoters

Name1

Gene

Position2

Strand

S 1 3

S 2 3

CS

p-value

Sequence

Original composite element sequence

        ATGAGGCAAT           cggcact  GTTGCCACAT

uc002uum.1

MOB4

−346

+

0.972

0.976

0.012

3.801e-06

AGTTTGCGAAAAT              gctgtg     GTTTCTTAAGAGA

uc003jwu.1

OCLN

−213

+

0.973

0.949

0.202

9.234e-05

 AGATTCAGAAACA    gcgccaatg       TTTACACACGACT

uc003qcg.1

EPB41L2

−100

+

0.988

0.981

0.099

1.418e-06

 AGATTTTGAAATG          ctac          TTTTCACAAAATA

uc001iia.1

NET1

−369

+

0.991

0.765

0.207

1.091e-05

  ACCTTTGGTAATT      ggaaat          ATATCTCATATTG

uc002eby.1

ZNF843

−352

+

0.963

0.929

0.123

1.895e-04

   AGCCTAGGCAAAA        gagcacg     ATTCCGTCTCAAG

uc004dpe.1

SHROOM4

+3

+

0.961

0.915

0.140

3.402e-04

   TGCTATTGTAAAT         ggaactg   TTTTCTTTCTTTC

Sequence complementary to the original composite element sequence

           ATGTGGCAAC       agtgccg   ATTGCCTCAT

uc003edg.1

C3orf15

−317

-

0.946

0.959

0.110

1.347e-04

   TGGCTGAGAAAAT     caatgac      ATTGCTTATGAAA

uc003fsb.1

TP63

−345

-

0.924

0.972

0.228

2.397e-04

  ACAAAGAGTAAAA  agaaaag       TTTTCATAAAGGA

uc003gno.1

C1QTNF7

−27

-

0.947

0.997

0.234

4.040e-06

   AAACTGAGAAAGA     taa               CTTTCTGAAATGC

uc003xye.1

SULF1

−333

-

0.728

0.987

0.304

1.456e-04

   AAAGAAAGGTAGG      ca               GTTGCAAAACTTC

uc002tah.1

AFF3

−149

-

0.922

0.993

0.046

4.600e-06

   TCAGAAGGAAAAA      agtttag      ATTTCAAAATGTA

uc003sli.1

MAD1L1

+2

-

0.761

0.981

0.276

1.790e-04

    TGTCTAGGGGAGA   taaaat          CTTGCCTAAGCAA

uc003zwl.1

KIAA1539

−310

-

0.760

0.959

0.300

8.385e-04

     CTCCGTAGTCACC   agatttt          ATTTCACAAGGTG

uc001lwy.1

SLC22A18

−113

-

0.939

0.965

0.167

1.691e-04

    CGCTCCCGGAACT  tccat           TTTACATATGAGG

uc001wpn.1

SDR39U1

−12

-

0.767

0.993

0.313

3.045e-05

    TTAGTGAGACAAT      ggcg      ATTGCAAAGCGCG

uc004env.1

COL4A6

−44

-

0.752

0.981

0.285

2.156e-04

    TGAGATGGACATT        ttattttt      ATTGCCTAAACTG

  1. Composite regulatory element C/EBP / C/EBP recognized in promoters of genes active in prostate tissue. Nucleotides with significant conservation shown in bold (within binding motifs) and italics (intermediate sequence).
  2. 1 Names according to (Jacox et al., [12]).
  3. 2 Beginning of the element relative to TSS.
  4. 3S 1,2 - PWM scores for the first and second C/EBP motif, CS - composite score.
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BMC Bioinformatics

ISSN: 1471-2105

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