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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).