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Table 3 Patterns for method 1, recognition of DNA regions induced by type I IFNs (IFNα, IFNβ)

From: Recognition of interferon-inducible sites, promoters, and enhancers

Site 1

Site 2

W = F1/F2 (weight for the pattern)

strongISGF3 (b)*

from -350 to +350**

-

3.25

ISGF3 (b)

from -200 to +50

-

3.89

ISGF3 (b)

from +130 to +350

-

1.83

STAT1 (+)

from -350 to +350

-

2.29

STAT1 (b)

from -300 to +1

-

1.68

STAT1 (-)

from +130 to +350

-

1.67

strong IRF1 (b)

from -350 to +350

-

2.76

strong IRF1 (+)

from -350 to +350

-

2.0

IRF1 (+)

from +130 to +350

-

2.16

strong NF-κB (-)

from -300 to +1

NF-κB (-)

from -300 to +1

1.8

IRF1 (b)

from -350 to +350

ISGF3 (b)

from -200 to +50

7.64

IRF1 (b)

from -500 to -300

ISGF3 (+)

from -200 to +50

4.25

IRF1 (b)

from -300 to +1

STAT1 (b)

from -350 to +350

9.4

ISGF3 (b)

from -200 to +50

AP1 (b)

from -500 to +1

3.74

IRF1 (b)

from -200 to +50

GATA1 (b)

from -600 to +1

3.45

IRF1 (+)

from -350 to +350

GATA1 (b)

from +45 to +350

2.1

ISGF3 (b)

from -200 to +50

OCT1 (b)

from -500 to +1

2.3

ISGF3 (b)

from -200 to +50

GATA1 (b)

from -600 to +1

2.35

ISGF3 (b)

from -200 to +50

AP1 (b)

from -500 to +1

5.31

ISGF3 (b)

from -200 to +50

OCT1 (b)

from -500 to +1

1.92

STAT1 (b)

from -350 to +350

ISGF3 (b)

from -200 to +50

4.53

STAT1 (b)

from -500 to +1

GATA1 (b)

from +45 to +350

1.92

STAT1 (+)

from -350 to +350

OCT1 (b)

from -500 to +1

2.66

  1. *b (both) - any direction of a site; + forward DNA strand; - reverse DNA strand;
  2. ** Location of a site with respect to the TSS
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BMC Bioinformatics

ISSN: 1471-2105

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