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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).
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BMC Systems Biology

ISSN: 1752-0509

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