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Table 1 Comparison of gene expression levels for pangenes located on the upper or lower halves of Chr 1

From: Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement

 

A. salmonicida

V. natriegens slow-growth

V. natriegens fast-growth

 

core

softcore

shell

cloud

core

softcore

shell

cloud

core

softcore

shell

cloud

Upper halfa

 Q1

152

118

42

42

188

126

21

5

249

170

36

37

 Q2

301

245

89

67

370

288

71

147

447

341

93

269

 Q3

853

633

197

197

1101

760

190

426

1059

719

241

581

 Max

34,254

34,254

6473

13,656

23,238

23,238

17,161

5533

35,274

35,274

28,737

4049

Lower halfa

 Q1

151

89

34

25

143

83

4

4

178

109

0

0

 Q2

309

207

65

47

360

192

28

18

328

232

26

17

 Q3

695

486

133

82

966

565

74

59

696

480

97

62

 Max

53,501

8098

19,837

23,646

14,116

14,116

15,800

463

16,521

17,549

17,550

535

P-value Q2 b

0.71

0.01

0.00

0.00

0.32

0.00

0.00

0.00

0.00

0.00

0.00

0.00

  1. a Q1 is the RPKM value at the first quartile. Q1 is defined as the middle number between the smallest number and the median (i.e., the second quartile Q2), if the data numbers (in this case RPKM values) are ordered from smallest to largest. The third quartile (Q3) is the middle value between the median (Q2) and the maximum (Max) value
  2. b Adjusted P-values from Wilcoxon signed-rank test, to test if Q2 values (median) of genes located on the upper half of Chr 1 are significantly different from Q2 values of genes located on the lower half. Values below 0.05 are considered significant