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Table 2 Statistical significances for negative charge distribution skew on either side of the membrane in single-pass TMHs

From: Charged residues next to transmembrane regions revisited: “Positive-inside rule” is complemented by the “negative inside depletion/outside enrichment rule”

Single-pass

Database-defined flanks

Flanks after central alignment

Dataset

Helices

Negative residues

H statistic

P value

Negative residues

H statistic

P value

  

Inside

Outside

  

Inside

Outside

  

ExpAll

1544

848

1648

258.59

3.47E-58

735

1541

262.29

5.44E-59

UniHuman

1705

780

1922

421.53

1.13E-93

652

1865

501.86

3.74E-111

UniER

132

78

156

23.76

1.09E-06

76

150

21.62

3.33E-06

UniGolgi

206

60

240

104.45

1.61E-24

54

239

107.18

4.06E-25

UniPM

493

197

578

177.68

1.56E-40

161

569

215.18

1.02E-48

UniCress

632

314

450

18.23

1.96E-05

231

444

55.80

8.01E-14

UniFungi

729

449

631

28.15

1.12E-07

413

627

38.08

6.79E-10

UniBacilli

124

90

113

3.73

5.35E-02

86

106

2.53

1.12E-01

UniEcoli

54

32

77

17.24

3.30E-05

30

74

14.74

1.24E-04

UniArch

48

113

8

49.66

1.83E-12

96

7

45.62

1.43E-11

  1. The “Helices” column refers to the total TMHs contained in each dataset (ExpALL, TMHs from TOPDB [50]; UniHuman, human representative proteome; UniER, human endoplasmic reticulum representative proteome; UniGolgi, human Golgi representative proteome; UniPM, human plasma membrane representative proteome; UniCress, Arabidopsis thaliana (mouse-ear cress) representative proteome; UniFungi, fungal representative proteome; UniBacilli, Bacilli class representative proteome; UniEcoli, Escherichia coli representative proteome; UniArch, Archaea representative proteome; see Methods for details). In the “Database-defined flanks” column, the “Negative residues” column refers to the total number of negative residues found in the ±10 flanking residues on either side of the TMH and does not include residues found in the helix itself. In the “Flanks after central alignment” column, the “Negative residues” column refers to the total number of negative residues found in the –20 to –10 residues and the +10 to +20 residues from the centrally aligned residues of the TMH. Unlike the other tables, the global averages are derived from the ±20 datasets. The Kruskal-Wallis scores were calculated for negative residues by comparing the number of negatively charged residues that were within the 10 inside residues and the 10 outside residues in either case