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Table 2 The numbers of genomic regions bound in blastoderm embryos

From: Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

   

Number of bound regions

Overlap between antibodies for the same factor

Regulatory class

Factor antibody

Amino acids recognized

1% FDR

25% FDR

% overlap

r

A-P early

BCD 1*

56-330

619

3,295

95

0.79

maternal

BCD 2*

330-489

702

3,404

93

0.81

 

CAD 1*

1-240

1,591

6,326

NA

NA

A-P early gap

GT 2*

182-353

1,070

3,968

NA

NA

 

HB 1*

1-305

1,832

4,707

86

0.64

 

HB 2*

306-758

1,718

6,675

92

0.80

 

KNI 1*

130-280

36

330

97

0.90

 

KNI 2*

281-425

197

5,167

83

0.86

 

KR 1*

1-230

3,593

11,323

96

0.91

 

KR 2*

350-502

4,084

12,255

93

0.93

A-P early terminal

HKB 1

1-100

1,012

5,339

99, 94

0.88, 0.64

 

HKB 2

101-200

614

4,241

99, 89

0.81, 0.34

 

HKB 3

201-297

638

3,766

99, 99

0.92, 0.99

 

TLL 1

110-259

429

2,650

NA

NA

A-P early gap-like

D 1

1-103

6,452

16,501

NA

NA

A-P pair rule

FTZ 3

All

403

3,721

NA

NA

 

HRY 1

123-221

1,704

6,053

97

0.80

 

HRY 2

254-337

2,729

10,979

80

0.73

 

PRD 1

355-450

2,061

7,145

96

0.93

 

PRD 2

450-613

1,273

5691

99

0.92

 

RUN 1

24-127, 240-318

921

8,809

77

0.79

 

RUN 2

319-510

172

2,903

99

0.75

 

SLP1 1

1-119

1,171

6,974

NA

NA

D-V maternal

DA 2

511-693

5,534

14,144

NA

NA

 

DL 3

All

9,358

18,113

NA

NA

D-V zygotic

MAD 2

144-254

204

10,969

NA

NA

 

MED 2

385-523, 630-713

5,458

9,273

NA

NA

 

SHN 2

1617-1750

341

1,400

47

0.70

 

SHN 3

2115-2279

121

363

87

0.38

 

SNA 1

75-166

596

4,868

100

0.87

 

SNA 2

167-258

2,800

15,811

61

0.82

 

TWI 1

1-178

6,686

17,486

99

0.98

 

TWI 2

259-363

7,416

19,605

98

0.98

General

Pol II H14*

CTD

3,108

7,991

NA

NA

 

TFIIB

All

1,943

6,002

NA

NA

  1. The number of bound regions at 1% and 25% false discovery rate (FDR) thresholds were determined by the symmetric null test [11]. The percentage overlap is defined as the percentage of 1% FDR 500-bp peak windows for one antibody that completely overlap a 25% FDR bound region for the other antibody/antibodies for the same factor. The Pearson correlation coefficient (r) is the correlation between the peak score from 1% FDR bound regions for one antibody and the corresponding 500 bp window score for the second antibody. Asterisks indicate previously published data [11]. NA, not applicable.