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Table 3 GPEA analysis of 1 Mb genomic regions gene sets for the Bead 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
chr8 q24.3 145000001 43 60 2.08131e-90 RECQL4
chr6 p22.2/p22.1 26000001 48 54 2.23839e-73  
chr6 p22.2 25500001 50 54 2.00277e-71  
chr1 q21.3 152500001 43 46 1.76715e-63  
chr17 q25.3 79500001 47 41 4.31970e-51 ASPSCR1
chr6 p22.1 27000001 32 34 7.06860e-51 HIST1H4I
chr8 q24.3 145500001 37 35 2.51328e-48 RECQL4
chr8 q24.3 144500001 39 30 1.02102e-37  
chr8 p11.23/p11.22 37500001 20 21 3.49503e-35 WHSC1L1
chr1 q23.3 161000001 36 27 2.04204e-34 FCGR2B, SDHC
chr11 q13.2 67000001 36 25 7.06860e-31  
chr17 q21.32 46000001 31 23 1.80642e-30  
chr17 q21.32/q21.33 46500001 31 23 1.80642e-30  
chr1 q21.3 153000001 43 27 3.29868e-30  
chr11 p15.5 1 50 29 1.06029e-29 HRAS
chr16 p13.3 1 52 29 1.02102e-28 AXIN1
chr19 q13.43 57500001 41 25 5.10510e-28  
chr1 q23.3 160500001 34 22 7.85400e-27 SDHC
chr1 p34.3/p34.2 40000001 23 18 2.74890e-26 MYCL1
chr6 p22.1 27500001 36 22 1.02102e-25  
chr1 p34.2 40500001 22 17 5.89050e-25  
chr1 q21.3 150500001 35 20 7.46130e-23 MLLT11, ARNT
chr1 q21.3/q22 154500001 42 22 9.42480e-23 MUC1
chr6 p21.32/p21.31 32500001 42 22 9.42480e-23 DAXX
chr9 q34.3 139500001 67 28 2.98452e-21  
chr19 q13.43 58000001 46 22 4.71240e-21  
chr1 q21.3 151000001 37 19 2.82744e-20 MLLT11
chr16 p13.3 500001 48 22 3.10233e-20  
chr3 p21.31 49500001 38 19 7.85400e-20  
chr1 q22 155000001 42 20 1.09956e-19 MUC1
chr11 q13.2 66500001 35 18 1.49226e-19  
chr5 q31.3 140000001 74 28 5.89050e-19  
chr22 q13.33 50000001 30 16 1.68861e-18  
chr4 q13.2/q13.3 69500001 9 9 2.67036e-17  
chr6 p21.1 42500001 33 16 3.69138e-17  
chr12 q15 69000001 15 11 3.76992e-17 MDM2
chr12 q13.3/q14.1 57500001 37 17 3.92700e-17 CDK4, DDIT3
chr17 q11.2 26500001 49 20 4.71240e-17  
chr19 p13.2 7500001 42 18 1.02102e-16  
chr9 q34.3 140000001 35 16 2.43474e-16  
chr20 q13.12 43500001 39 17 2.43474e-16 SDC4
chr22 q13.33 50500001 32 15 5.89050e-16  
chr5 q31.3 140500001 54 20 2.04204e-15  
chr1 q21.3 152000001 34 15 3.76992e-15  
chr7 p15.2/p15.1 27000001 22 12 3.76992e-15 JAZF1, HOXA11, HOXA13
chr16 q12.2/q13/q21 56500001 34 15 3.76992e-15 HERPUD1
chr2 q35 219500001 47 18 5.49780e-15 FEV
chr17 p13.1 7000001 68 23 5.89050e-15 TP53
chr11 q13.1 64500001 56 20 8.24670e-15 MEN1
chr8 p11.21 41500001 12 9 1.02102e-14 KAT6A
  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).