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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  
  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).