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

Baker, James Alexander; Wong, Wing-Cheong; Eisenhaber, Birgit; Warwicker, Jim; Eisenhaber, Frank

doi:10.1186/s12915-017-0404-4

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
Dataset	IDs	n	μ	σ	Inside	Outside	H statistic	P value	Inside	Outside	H statistic	P value
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
Dataset	Inside	Outside	H statistic	P value	N	Inside	Outside	H statistic	P value
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

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
*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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ISSN: 1741-7007

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