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Table 4 GPEA analysis of 1 Mb genomic regions gene sets for the Oligo urothelial cancer 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
chr1 q23.3 161000001 36 27 4.82850e-30 FCGR2B, SDHC
chr17 q25.3 79500001 47 30 5.15040e-28 ASPSCR1
chr1 q21.3 150500001 35 25 1.80264e-27 MLLT11, ARNT
chr11 p15.5 1 50 25 8.36940e-20 HRAS
chr8 q24.3 145000001 43 22 8.04750e-19 RECQL4
chr1 p34.3/p34.2 40000001 23 15 6.11610e-18 MYCL1
chr1 q23.3 160500001 34 18 3.86280e-17 SDHC
chr19 q13.2/q13.31 43000001 20 13 4.18470e-16  
chr9 p21.1/p13.3 32500001 17 12 4.50660e-16  
chr16 p13.2 8000001 7 8 1.41636e-15  
chr6 p21.1 42500001 33 16 1.25541e-14  
chr1 q21.2/q21.3 150000001 27 14 3.54090e-14 ARNT
chr8 p11.21 42000001 17 11 4.18470e-14  
chr16 p13.2 8500001 9 8 2.06016e-13  
chr16 q21/q22.1 66500001 42 17 1.31979e-12 CBFB
chr17 q12/q21.1/q21.2 37500001 31 14 1.67388e-12 ERBB2, CDK12, RARA
chr4 q13.3 74500001 14 9 5.47230e-12  
chr6 p21.1 43000001 26 12 1.80264e-11  
chr1 q21.3/q22 154500001 42 16 2.44644e-11 MUC1
chr4 q13.3 74000001 16 9 7.40370e-11  
chr8 p11.23/p11.22 37500001 20 10 9.65700e-11 FGFR1, WHSC1L1
chr11 q13.2 67000001 36 14 1.03008e-10  
chr9 p21.3 20500001 24 11 1.06227e-10 MLLT3
chr1 p34.2 40500001 22 10 6.75990e-10  
chr11 p11.2 47000001 22 10 6.75990e-10 DDB2
chr13 q34 113500001 18 9 6.75990e-10  
chr2 p22.1 39000001 11 7 1.22322e-09  
chr13 q14.2 48500001 11 7 1.22322e-09 RB1
chr19 p13.12 15000001 27 11 1.41636e-09 BRD4
chr17 q25.3 80000001 23 10 1.67388e-09  
chr17 p13.3 500001 19 9 1.83483e-09 YWHAE
chr1 p34.3 37500001 20 9 4.82850e-09  
chr1 q22 155000001 42 14 6.75990e-09 MUC1
chr9 p21.3 21000001 25 10 9.01320e-09 CDKN2A
chr3 p25.3 9500001 34 12 1.06227e-08 VHL
chr16 q12.2/q13/q21 56500001 34 12 1.06227e-08 HERPUD1
chr19 q13.33/q13.41 51000001 49 15 3.21900e-08 KLK2
chr1 p34.3 38000001 18 8 3.86280e-08  
chr11 q13.1/q13.2 65000001 46 14 7.40370e-08  
chr11 q13.1/q13.2 65500001 46 14 7.40370e-08  
chr19 q13.31 44000001 37 12 7.72560e-08  
chr20 p13 3000001 28 10 8.69130e-08  
chr6 p21.32/p21.31 32500001 42 13 9.97890e-08 DAXX
chr12 q15 69000001 15 7 1.31979e-07 MDM2
chr20 q11.22/q11.23 33500001 24 9 1.35198e-07  
chr1 q21.3 153000001 43 13 1.80264e-07  
chr9 p21.1/p13.3 33000001 20 8 2.12454e-07  
chr22 q11.21 20500001 20 8 2.12454e-07  
chr8 q24.3 144500001 39 12 2.60739e-07  
chr11 q13.2 66500001 35 11 3.86280e-07  
  1. 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).