Table 3

Percentage of genes whose transcription start site is within 5 kb of ChIP/chip peaks

Regulatory class

Factor antibody

% genes close to 1% FDR peaks

% genes close to 25% FDR peaks

A-P early

BCD 2

6.2

29.6

CAD 1

12.6

48.9

GT 2

7.7

27.2

HB 1

14.7

34.5

KNI 2

1.2

37.2

KR 2

27.0

65.3

HKB 1

9.0

41.3

TLL 1

2.8

20.8

D 1

52.6

84.1

A-P pair rule

FTZ 3

2.6

29.1

HRY 2

20.4

64.3

PRD 1

14.8

51.0

RUN 1

6.0

60.4

SLP1 1

11.4

52.4

D-V

DA 2

38.2

76.7

DL 3

66.5

87.0

MAD 2

1.6

73.5

MED 2

50.6

74.8

SHN 2

2.1

9.6

SNA 2

23.6

83.0

TWI 2

53.0

90.3

For those factors for which ChIP/chip data are available for more than one antibody, values shown are for the antibody that gave the most bound regions above the 1% FDR threshold using the symmetric null test.

MacArthur et al. Genome Biology 2009 10:R80   doi:10.1186/gb-2009-10-7-r80