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Table 1 K90 GIL Collection Overview

From: Maximizing capture of gene co-expression relationships through pre-clustering of input expression samples: an Arabidopsis case study

GILA

Arrays

Datasets

Nodes

Edges

<k>

RMT

γ

ModulesB

GOc

Interpro

KEGGC

AraCycc

POC

GILA

Arrays

Datasets

Nodes

Edges

<k>

RMT

γ

ModulesB

GOc

Interpro

KEGGC

AraCycc

POC

1

48

7

2,563

7,051

5.50

0.929

1.99

616/294

153/225

192/112

192/112

19/18

21/13

46

116

28

n.a.

n.a.

n.a.

n.a.

n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

2

38

2

1,921

7,807

8.13

0.943

1.85

418/226

98/135

84/50

84/50

14/19

11/34

47

105

12

1,445

4,969

6.88

0.910

1.85

280/282

122/123

119/110

54/90

15/15

10/19

3

76

22

2,919

6,415

4.40

0.844

2.13

763/251

313/219

298/130

298/130

28/20

45/36

48

269

31

2,638

11,228

8.51

0.803

1.78

489/493

316/663

231/317

103/200

35/38

45/62

4

72

12

2,764

6,565

4.75

0.872

2.07

713/319

334/448

303/168

303/168

38/17

45/23

49

39

2

1,954

9,688

9.92

0.935

1.76

413/376

177/286

160/133

78/86

15/10

14/3

5

40

2

997

4,346

8.72

0.936

1.86

197/136

115/107

81/35

81/35

11/7

3/2

50

113

27

3,520

11,996

6.82

0.809

1.92

770/497

330/350

284/222

144/99

30/5

21/14

6

123

25

2,446

15,547

12.71

0.835

1.75

507/458

254/854

203/360

203/360

24/19

18/24

51

45

9

2,377

4,570

3.85

0.911

2.20

651/223

153/132

173/75

90/43

16/9

4/3

7

75

22

2,491

4,259

3.42

0.842

2.26

705/229

267/148

251/77

251/77

21/13

10/8

52

8

1

n.a.

n.a.

n.a.

n.a.

n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

8

42

4

1,596

5,282

6.62

0.964

1.92

315/217

90/72

88/65

88/65

13/13

19/15

53

143

32

1,898

5,518

5.81

0.826

1.96

438/232

231/186

192/94

86/64

17/15

19/12

9

84

2

1,859

16,072

17.29

0.876

1.64

327/374

121/927

90/165

90/165

22/92

24/39

54

85

13

1,983

3,849

3.88

0.859

2.23

522/206

166/80

191/52

70/36

22/14

18/9

10

147

16

1,804

9,878

10.95

0.898

1.70

317/329

168/543

111/98

111/98

16/44

46/93

55

87

29

3,811

16,013

8.40

0.802

1.83

815/668

373/580

311/261

137/170

38/27

28/14

11

63

1

1,971

16,547

16.79

0.889

1.62

351/484

175/1070

148/402

148/402

19/39

15/46

56

40

4

1,414

13,540

19.15

0.965

1.54

206/448

87/540

63/87

23/103

8/3

46/265

12

124

14

1,257

5,985

9.52

0.875

1.75

212/294

63/93

47/43

47/43

5/16

12/8

57

27

3

1,944

7,628

7.85

0.916

1.91

506/229

106/319

125/65

52/81

13/17

32/36

13

49

5

1,293

3,808

5.89

0.952

1.96

295/158

59/84

79/39

79/39

7/16

1/2

58

131

17

1,861

8,262

8.88

0.865

1.81

367/360

283/694

183/200

79/186

38/84

33/73

14

87

10

3,286

37,336

22.72

0.867

1.58

583/779

218/1186

190/328

190/328

24/44

69/117

59

50

13

926

2,415

5.22

0.927

2.05

229/102

41/27

63/20

20/6

7/0

6/5

15

46

10

1,925

10,961

11.39

0.941

1.75

382/350

86/71

123/48

123/48

8/6

21/51

60

44

13

1,703

6,996

8.22

0.916

1.83

381/267

199/404

165/85

75/118

17/10

34/64

16

64

9

1,552

5,071

6.53

0.926

1.94

359/220

98/60

114/35

114/35

3/8

6/3

61

59

4

2,006

10,532

10.50

0.891

1.69

327/391

175/582

102/192

44/137

13/54

30/38

17

37

7

1,895

12,248

12.93

0.945

1.66

347/472

109/465

72/129

72/129

14/49

19/29

62

73

16

1,185

4,543

7.67

0.886

1.91

278/213

139/177

143/79

74/70

13/6

6/2

18

43

6

1,783

6,340

7.11

0.943

1.90

416/322

78/86

120/69

120/69

15/14

12/14

63

131

23

2,448

6,632

5.42

0.850

1.98

538/303

234/279

193/143

98/93

18/32

31/45

19

166

33

2,866

9,723

6.79

0.795

1.89

628/393

323/278

293/116

293/116

36/33

40/44

64

197

30

3,122

11,982

7.68

0.781

1.81

589/435

361/484

257/234

114/147

33/35

48/66

20

142

34

3,440

12,799

7.44

0.783

1.88

752/432

336/385

294/196

132/149

34/35

36/52

65

30

3

332

1,685

10.15

0.988

1.69

60/85

64/263

23/54

11/61

5/27

1/4

21

71

9

1,525

12,678

16.63

0.922

1.62

263/332

121/354

84/98

30/75

16/53

29/68

66

23

4

2,523

20,630

16.35

0.954

1.86

626/325

132/64

158/34

72/27

16/5

26/34

22

70

9

2,465

6,898

5.60

0.903

2.03

633/288

191/200

231/109

99/67

19/18

15/37

67

215

41

3,254

16,033

9.85

0.762

1.78

617/461

377/533

285/298

128/172

48/68

63/66

23

24

1

402

3,010

14.98

0.983

1.60

66/97

3/15

8/10

7/8

0/0

0/5

68

86

18

1,283

7,209

11.24

0.893

1.69

223/268

171/767

99/230

47/172

19/43

24/22

24

87

6

2,347

5,280

4.50

0.905

2.09

599/298

169/184

172/133

86/78

12/5

14/15

69

192

19

3,597

40,668

22.61

0.823

1.59

585/597

301/504

269/264

103/77

26/58

78/946

25

72

14

3,512

10,063

5.73

0.856

2.06

895/319

338/203

295/93

146/59

37/25

43/54

70

37

8

n.a.

n.a.

n.a.

n.a.

n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

26

32

5

1,792

26,789

29.90

0.920

1.62

413/280

41/23

72/32

33/9

11/11

28/244

71

235

24

2,034

7,791

7.66

0.859

1.85

410/282

231/250

202/141

78/70

16/33

39/137

27

72

1

634

2,043

6.44

0.966

1.91

128/103

52/52

57/46

24/24

4/3

6/3

72

24

2

1,314

4,931

7.51

0.948

1.88

279/262

47/39

68/28

22/25

7/18

13/6

28

75

9

593

5,428

18.31

0.961

1.57

96/128

21/21

28/20

12/24

5/16

1/3

73

114

16

2,145

13,061

12.18

0.836

1.76

454/403

131/126

176/131

70/66

18/43

21/41

29

129

22

2,798

9,343

6.68

0.814

1.91

595/366

299/282

254/153

118/107

37/26

23/12

74

42

7

1,244

3,508

5.64

0.956

2.00

284/183

55/26

92/16

46/34

8/13

4/0

30

104

9

2,107

21,381

20.30

0.870

1.60

363/495

128/314

115/168

66/88

18/73

19/28

75

161

44

2,689

13,042

9.70

0.791

1.84

554/342

247/579

262/247

112/158

34/15

12/12

31

40

10

2,715

7,370

5.43

0.895

2.06

725/293

147/156

217/144

100/103

32/27

23/54

76

34

4

1,198

8,819

14.72

0.930

1.66

215/313

46/104

65/190

22/14

9/24

7/32

32

104

9

1,918

6,878

7.17

0.910

1.86

420/387

247/488

154/106

82/137

16/39

13/13

77

70

9

2,340

5,730

4.90

0.893

2.07

591/291

239/315

194/103

110/77

20/19

10/5

33

61

4

1,409

5,306

7.53

0.923

1.94

349/200

81/35

111/36

44/13

12/5

7/4

78

172

31

3,513

15,437

8.79

0.777

1.76

665/570

451/880

361/392

150/287

53/45

40/107

34

34

4

2,213

7,181

6.49

0.932

1.92

524/238

111/109

153/74

56/29

16/13

52/56

79

26

6

2,599

5,542

4.26

0.927

2.22

741/225

124/67

186/44

85/25

12/5

14/13

35

49

9

2,004

6,306

6.29

0.935

1.93

458/297

217/394

155/125

88/107

19/41

9/16

80

112

30

3,288

23,432

14.25

0.821

1.75

628/621

294/324

246/134

124/75

31/29

23/19

36

18

1

1,365

7,141

10.46

0.952

1.79

2889/198

79/98

68/60

30/38

13/10

15/18

81

18

1

678

2,830

8.35

0.959

1.83

146/132

11/2

34/17

6/8

1/6

0/3

37

55

6

2,450

7,970

6.51

0.941

1.94

556/318

138/269

166/84

75/72

21/38

9/4

82

125

22

1,979

9,804

9.91

0.841

1.80

416/306

189/314

152/116

60/90

19/21

14/10

38

18

2

1,904

4,469

4.69

0.955

2.13

575/229

39/26

145/24

49/10

17/9

5/11

83

54

2

915

4,027

8.80

0.948

1.79

164/115

106/291

67/36

25/51

11/28

8/12

39

54

7

1,780

5,460

6.13

0.871

1.97

443/236

144/129

159/126

68/74

7/5

28/19

84

116

12

2,531

9,667

7.64

0.866

1.86

554/413

204/232

189/174

89/85

22/17

29/24

40

60

7

1,867

5,686

6.09

0.903

1.94

415/212

241/227

174/78

96/89

32/24

13/7

85

34

5

1,749

6,155

7.04

0.939

1.92

424/237

137/138

129/54

64/65

19/21

12/15

41

73

13

2,045

4,463

4.36

0.897

2.14

558/217

166/162

179/47

86/57

21/26

5/11

86

99

20

2,979

10,234

6.87

0.812

1.91

671/439

282/432

253/149

106/129

37/58

35/23

42

74

3

1,757

8,417

9.58

0.902

1.78

346/322

150/449

134/257

59/162

16/49

26/12

87

18

5

1,871

2,559

2.74

0.968

2.60

619/147

58/35

117/29

62/13

10/3

12/6

43

127

1

n.a.

n.a.

n.a.

n.a.

n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

n.a./n.a.

88

77

16

2,926

10,935

7.47

0.860

1.89

650/326

304/413

224/153

108/109

20/17

39/53

44

24

1

428

6,269

29.29

0.978

1.43

60/128

16/44

20/18

10/17

4/1

0/1

89

20

2

1,359

6,848

10.08

0.957

1.73

270/265

71/24

72/63

38/25

7/18

17/39

45

177

40

2,436

9,984

8.20

0.808

1.81

478/392

248/590

211/198

92/183

28/29

24/15

90

54

7

612

1,398

4.57

0.957

2.07

139/87

49/42

51/32

25/9

7/4

2/0

  1. AGene Interaction Layers 43,46,52,72 failed to construct; BModules counts are listed as MCL/LCM; CNumber of enriched terms in MCL/LCM modules.