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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
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