Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples

Gorlov, Ivan P.; Pikielny, Claudio W.; Frost, Hildreth R.; Her, Stephanie C.; Cole, Michael D.; Strohbehn, Samuel D.; Wallace-Bradley, David; Kimmel, Marek; Gorlova, Olga Y.; Amos, Christopher I.

doi:10.1186/s12859-018-2455-0

BMC Bioinformatics

Table 1 Pair-wise correlations between gene characteristics

From: Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples

	% “A”	% “G”	% “C”	% “T”	ND	% “CpG”	CDS	SNPD	EC	NPS	NPM	AGE	LAGE	RRT	HA	NSM
% “A”	1.00	− 0.71	− 0.88	0.47	0.35	− 0.72	0.11	− 0.22	0.09	0.27	0.12	0.19	0.18	−0.26	− 0.04	− 0.01
% “G”	−0.71	1.00	0.60	−0.78	−0.46	0.76	−0.11	0.20	−0.06	− 0.22	− 0.12	− 0.06	− 0.04	0.27	0.06	−0.03
% “C”	− 0.88	0.60	1.00	−0.69	− 0.44	0.74	− 0.06	0.22	− 0.13	− 0.22	−0.07	− 0.24	−0.23	0.25	0.04	0.06
% “T”	0.47	−0.78	−0.69	1.00	0.54	−0.71	0.04	−0.18	0.10	0.13	0.04	0.11	0.10	−0.24	−0.06	− 0.04
ND	0.35	−0.46	−0.44	0.54	1.00	−0.60	0.08	−0.09	0.16	0.12	0.09	0.10	0.09	−0.09	−0.02	0.09
% “CpG”	−0.72	0.76	0.74	−0.71	−0.60	1.00	−0.13	0.15	−0.04	− 0.24	−0.14	− 0.09	−0.08	0.19	0.04	−0.03
CDS	0.11	−0.11	−0.06	0.04	0.08	−0.13	1.00	−0.10	0.08	0.97	1.00	−0.09	−0.07	− 0.05	−0.01	0.81
SNPD	−0.22	0.20	0.22	−0.18	−0.09	0.15	−0.10	1.00	−0.17	− 0.13	−0.10	− 0.13	−0.13	0.09	0.02	0.02
EC	0.09	−0.06	−0.13	0.10	0.16	−0.04	0.08	−0.17	1.00	0.08	0.09	0.27	0.27	0.08	−0.01	0.01
NPS	0.27	−0.22	−0.22	0.13	0.12	−0.24	0.97	−0.13	0.08	1.00	0.97	−0.06	−0.04	− 0.09	− 0.02	0.74
NPM	0.12	−0.12	−0.07	0.04	0.09	−0.14	1.00	−0.10	0.09	0.97	1.00	−0.09	−0.07	− 0.05	− 0.01	0.81
AGE	0.19	−0.06	−0.24	0.11	0.10	−0.09	−0.09	− 0.13	0.27	− 0.06	−0.09	1.00	0.98	0.19	0.07	−0.26
LAGE	0.18	−0.04	−0.23	0.10	0.09	−0.08	−0.07	− 0.13	0.27	− 0.04	−0.07	0.98	1.00	0.20	0.08	−0.26
RRT	−0.26	0.27	0.25	−0.24	−0.09	0.19	−0.05	0.09	0.08	−0.09	− 0.05	0.19	0.20	1.00	0.18	−0.17
HA	−0.04	0.06	0.04	−0.06	−0.02	0.04	−0.01	0.02	−0.01	− 0.02	− 0.01	0.07	0.08	0.18	1.00	−0.05
NSM	−0.01	−0.03	0.06	−0.04	0.09	−0.03	0.81	0.02	0.01	0.74	0.81	−0.26	−0.26	− 0.17	−0.05	1.00

ND- Nucleotide diversity, CDS CDS size, SNPD - SNP density, EC - Evolutionary conservation, NPS - N potential stops, NPM - N potential missense, AGE - Average gene expression, LAGE - LOG of average gene expression, RRT - Relative replication time, HA - Chromatin accessibility, NSM - N of silent mutations

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