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Table 3 Statistical significances for negative charge distribution skew on either side of the membrane in multi-pass TMHs

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

A)
Multi-pass Database-defined flanks Flanks after central alignment
Dataset IDs Helices Negative residues H statistic P value Negative residues H statistic P value
n μ σ Inside Outside Inside Outside
ExpAll 2205 15,563 7.07 3.95 9709 9598 0.04 8.43E-01 9648 9659 0.35 5.56E-01
UniHuman 1789 12,353 6.93 3.20 7196 9164 147.50 6.10E-34 6740 8968 179.77 5.43E-41
UniER 155 898 5.85 3.20 630 584 0.44 5.08E-01 578 576 0.03 8.58E-01
UniGolgi 61 383 6.28 2.97 274 261 0.02 8.75E-01 266 259 0.09 7.65E-01
UniPM 427 3079 7.22 3.30 1945 2499 47.98 4.30E-12 1791 2440 64.42 1.01E-15
UniCress 507 3823 7.55 3.32 2567 2426 0.73 3.93E-01 2398 2433 1.11 2.93E-01
UniFungi 1338 8685 6.50 3.75 5560 5266 5.83 1.57E-02 5140 5214 0.00 9.62E-01
UniBacilli 140 822 5.94 3.98 470 468 0.07 7.92E-01 450 471 0.92 3.38E-01
UniEcoli 529 3888 7.39 3.76 1990 1902 0.26 6.07E-01 1875 1887 0.18 6.71E-01
UniArch 59 327 5.97 2.73 245 175 7.98 4.72E-03 235 181 7.08 7.81E-03
B)
Multi-pass Overlapping flanks Database-defined viable* flanks
Dataset Negative residues H statistic P value N Negative residues H statistic P value
Inside Outside Inside Outside
ExpAll 11,969 12,615 22.54 2.05E-06 8808 6082 6916 59.93 9.81E-15
UniHuman 8645 11,181 254.30 3.00E-57 8183 5169 6915 179.71 5.60E-41
UniER 750 763 1.16 2.81E-01 516 398 441 3.16 7.55E-02
UniGolgi 333 369 7.12 7.64E-03 195 162 186 3.00 8.30E-02
UniPM 2319 3107 99.68 1.79E-23 1977 1343 1960 98.63 3.05E-23
UniCress 3142 3298 9.21 2.41E-03 2110 1626 1741 6.40 1.14E-02
UniFungi 6724 6814 0.46 4.96E-01 4581 3340 3411 0.41 5.22E-01
UniBacilli 585 636 2.65 1.04E-01 382 230 306 12.73 3.61E-04
UniEcoli 2574 2800 17.88 2.35E-05 1596 951 1114 16.57 4.69E-05
UniArch 342 248 14.67 1.28E-04 132 120 104 0.28 5.97E-01
  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 (A) the “Database-defined flanks” and in (B) the “Database-defined viable* flanks” and the “Overlapping flanks” columns, 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. (A) 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 with a maximum database defined flank length of 20 residues. The total number of proteins is given in the IDs column. The “Helices” column contains the total number of TMHs in the dataset (n), the average number of TMHs per protein in that population (μ) and the standard deviation of that average (σ). The Kruskal-Wallis scores were calculated for negative residues by comparing the number of negatively charged residues that were within 10 residues inside and 10 residues outside the helices
  2. *Here, viable indicates that in each TMH used for both flanks either side of the TMH has a flank length of at least half the maximum allowed flank length, in this case 10 (viable length = 5)
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