Table 6

Functional TFBS constraints used in the promoter simulation

Name

Accession no.

Length (bp)

Strand

Location (min, max)

Copy no. (min, max)

Cutoff


YY1E2F

MA0095 (YY1)

MA0024 (E2F)

13

+

(20, 30)

(1, 1)

0.90

Pax6

MA0069

14

+

(50, 70)

(1, 1)

0.90

TP53

MA0106

20

+

(360, 400)

(1, 1)

0.90

IRF2

MA0051

18

+

(420, 480)

(1, 1)

0.90

PPARG

MA0066

20

+

(2000, 2080)

(1, 1)

0.90

ROAZ

MA0116

15

+

(2100, 2200)

(1, 1)

0.90


The accession numbers in the second column are from the JASPAR database [39]. 'Location' refers to the restriction on the upstream minimum and maximum distances to transcription start site. YY1E2F is a composite TFBS created by joining the YY1 and E2F sites.

Huang et al. Genome Biology 2007 8:R225   doi:10.1186/gb-2007-8-10-r225

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