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Table 4 Chromosomal neighborhood-induced GPEA and GO analysis.

From: Functional and genetic analysis of the colon cancer network

chr

locus

start

Size

edges

pvalue

gcc

census

term

chr8

q24.3

145000001

35

52

3.6e-86

29

RECQL4

 

chr8

q24.3

145500001

31

37

3.3e-59

24

RECQL4

 

chr6

p22.2/p22.1

26000001

45

40

3.5e-52

23

 

nucleosome assembly (9)

chr6

p22.2

25500001

46

40

2.1e-51

24

 

nucleosome assembly (9)

chrX

q28

153000001

37

33

1.2e-45

18

  

chr19

q13.31

44000001

35

31

1.8e-43

15

 

regulation of transcription, DNA-

        

dependent (15)

chr7

p15.1/.2

27000001

17

21

4.4e-39

12

HOXA9, HOXA11, HOXA13, JAZF1

anterior/posterior pattern specification (9)

chr7

p15.2

26500001

18

21

6e-38

12

HOXA9, HOXA11, HOXA13

anterior/posterior pattern specification (9)

chr8

q24.3

144500001

30

26

1e-37

14

  

chr6

p21.1

42500001

32

26

3.3e-36

18

 

meiosis (3)

chr19

q13.31/q13.32

44500001

28

24

2.7e-35

12

BCL3, CBLC

regulation of transcription, DNA- dependent (12)

chr17

q12/q21.1/.2

37500001

26

22

8.4e-33

13

ERBB2,

 
       

RARA

 

chr17

p13.1

7000001

56

32

3.3e-32

22

TP53

 

chrX

q28

153500001

30

22

5.6e-30

14

MTCP1

 

chr1

q22

155000001

33

23

6.4e-30

20

MUC1

 

chr17

q11.2

26500001

34

23

2.6e-29

17

  

chr8

p11.21

42000001

16

16

3.3e-28

11

HOOK3

 

chr6

p21.31/.32

32500001

34

22

1.6e-27

7

DAXX

antigen processing and presentation of exogenous peptide antigen via MHC class II (6) proteasomal ubiquitin-dependent protein catabolic process (3)

chr9

q34.3

139500001

53

27

3.4e-26

15

  

chrX

p11.23

48500001

28

19

1.5e-25

14

WAS, GATA1, TFE3

 

chr17

q21.32

46000001

26

18

7.2e-25

7

 

embryonic skeletal system development (5)

chr16

p13.3

1500001

47

24

2.5e-24

15

TSC2

protein ubiquitination (4)

chr17

q21.32/.33

46500001

27

18

3e-24

7

 

embryonic skeletal system development (5)

chr17

p13.1

6500001

51

25

4e-24

20

  

chr8

q24.3

144000001

29

18

4e-23

7

 

heterocycle metabolic process (6)

chr6

p21.33

31000001

54

25

6.8e-23

13

  

chr6

p21.32/.33

31500001

54

25

6.8e-23

14

  

chr19

q13.43

58000001

40

21

9.2e-23

14

 

transcription, DNA-dependent (14) regulation of type I interferon- mediated signaling pathway (8) homophilic cell adhesion (8) cellular biosynthetic process (9)

chr9

p21.3

20500001

20

15

1e-22

8

MLLT3

 

chr5

q31.3

140000001

52

24

3e-22

8

  

chr17

q12

37000001

21

15

4.4e-22

13

LASP1, ERBB2

 

chr8

p11.22/.23

37500001

18

14

5.2e-22

8

WHSC1L1, FGFR1

 

chr19

q13.43

57500001

35

19

8.4e-22

10

 

regulation of transcription, DNA-dependent (10)

chr17

q25.3

79500001

46

22

1e-21

20

ASPSCR1

proteasomal ubiquitin-dependent protein catabolic process (3)

chrX

p11.23

48000001

28

16

5.6e-20

10

SSX1, WAS, GATA1, TFE3

 
  1. Each row corresponds to a window gene set. These windows are indexed by the chromosome, locus and base start. The number of genes in these windows and the edges between them are given in column four and five. Column six gives the p-value of the GPEA analysis (p-val) and column nine shows the most significant GO term for the genes in the GCC.