Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data

Matos Simoes, Ricardo de; Dalleau, Sabine; Williamson, Kate E; Emmert-Streib, Frank

doi:10.1186/s12918-015-0165-z

BMC Systems Biology

Table 2 GPEA analysis of 1 Mb genomic regions gene sets for the RNAseq UC GRN

From: Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data

chr	Locus	Start	Size	Edges	p-value	Census
chr5	q31.3	140000001	74	159	3.6673e-222
chr17	q21.2	39000001	61	136	7.6570e-204
chr17	q21.2	38500001	49	119	1.1284e-194	RARA, SMARCE1
chr6	p22.2	25500001	50	105	1.0881e-163
chr6	p22.2/p22.1	26000001	48	98	2.9016e-153
chr5	q31.3	140500001	54	103	1.6926e-152
chr19	q13.43	57500001	41	90	3.9091e-150
chr8	q24.3	145000001	43	81	1.5314e-127	RECQL4
chr19	q13.43	58000001	46	75	8.4630e-111
chr16	p11.2	30000001	54	80	4.0300e-109
chr21	q22.11	31500001	38	67	5.2390e-107
chr1	q21.3	152500001	43	69	2.0553e-103
chr9	q34.3	139500001	67	83	7.6570e-99
chr17	q25.3	79500001	47	67	3.9091e-94	ASPSCR1
chr19	q13.31	44000001	37	60	4.0300e-94
chr16	p11.2	30500001	49	68	1.7329e-93	FUS
chr8	q24.3	145500001	37	58	4.8360e-90	RECQL4
chr11	q13.1/q13.2	65000001	46	64	8.8660e-90
chr3	p25.3	9500001	34	55	3.1837e-88	FANCD2, VHL
chr5	q31.3	139500001	42	60	3.1434e-87
chr6	p22.1	27000001	32	51	8.8660e-83	HIST1H4I
chr1	q21.3	152000001	34	52	5.2390e-82
chr16	p11.2	29500001	45	59	1.1687e-81
chrX	p11.23	48500001	50	62	1.8941e-81	GATA1, TFE3, WAS
chr6	p21.33/p21.32	31500001	79	78	1.2896e-79
chr19	p13.3	500001	51	60	7.6570e-77	FSTL3, STK11
chr1	p36.33	1000001	48	58	1.7732e-76
chr19	p13.3	1000001	43	54	1.1687e-74	STK11, TCF3
chr1	q21.3	150500001	35	48	1.5314e-72	MLLT11, ARNT
chr1	q22	155000001	42	51	3.3852e-70	MUC1
chr8	q24.3	144500001	39	49	9.2690e-70
chr19	q13.41/q13.42	53000001	31	44	1.6926e-69
chr19	p13.11/p12	19000001	33	45	5.2390e-69
chr16	p13.3	1	52	56	5.6420e-69	AXIN1
chrX	p11.23/p11.22	49000001	44	51	4.4330e-68
chr11	q13.1/q13.2	65500001	46	52	7.6570e-68
chr6	p22.1	27500001	36	46	2.1359e-67
chr19	q13.33	49500001	70	64	2.9822e-66
chr1	q23.3	161000001	36	45	1.8941e-65	FCGR2B, SDHC
chr19	q13.31/q13.32	44500001	36	45	1.8941e-65	CBLC, BCL3
chr3	p21.31	48500001	42	48	1.1284e-64	NCKIPSD
chr19	q13.43	58500001	30	41	1.4911e-64
chr16	p13.3	1500001	59	57	2.1762e-64	TSC2, TRAF7
chr1	q21.3	151000001	37	45	2.4583e-64	MLLT11
chr11	p15.5	1	50	52	5.2390e-64	HRAS
chr1	q21.3/q22	154500001	42	47	7.6570e-63	MUC1
chr19	q13.12	36000001	48	50	1.9747e-62
chr11	q13.1	64500001	56	54	4.4330e-62	MEN1
chr19	p13.2	11500001	30	39	1.9747e-60
chr11	q13.2	67000001	36	42	1.1284e-59

For each significant genomic region the chromosome (chr), chromosome band (locus), nucleotide base start site of the genomic region (start), number of genes of the gene set (size), number of edges of the significant subnetwork (edges), Bonferroni adjusted p-value of the subnetwork (p-value) and a list of genes in the significant subnetwork that are present in the cancer census (census).

Back to article page

ISSN: 1752-0509

Contact us

General enquiries: ORSupport@springernature.com