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Table 2. DEGs inside the KEGG map “Pathways in cancer” identified in the most implicated processes

From: Determining oncogenic patterns and cancer predisposition through the transcriptomic profile in Mitchell–Riley syndrome with heterotopic gastric mucosa and duodenal atresia: a case report

Biological implication

Gene symbol

Gene name

Control mean counts

MRS mean counts

Fold change

q-value

Evading apoptosis

BAD

BCL2 associated agonist of cell death

826.17

116.74

− 2.82

5.74e−05

 

BBC3

BCL2 binding component 3

1275.40

66.71

− 4.26

5.98e−06

 

EGF

Epidermal growth factor

62.50

700.46

3.49

2.01e−04

 

FGFR2

Fibroblast growth factor receptor 2

85.98

950.63

3.47

4.66e−03

 

FLT3LG

fms related tyrosine kinase 3 ligand

92.37

0

− 4.90

4.48e−02

 

HMOX1

heme oxygenase 1

3398.05

733.82

− 2.21

1.22e−03

 

HRAS

HRas proto− oncogene, GTPase

460.16

83.39

− 2.46

2.96e−03

 

IFNAR2

Interferon alpha and beta receptor subunit 2

2464.19

83.39

− 4.89

6.69e−11

 

IGF1R

Insulin like growth factor 1 receptor

2771.65

11591.01

2.06

1.07e−03

 

IL12RB1

Interleukin 12 receptor subunit beta 1

2509.33

617.08

− 2.02

1.76e−05

 

IL13RA1

Interleukin 13 receptor subunit alpha 1

5850.09

1184.12

− 2.30

2.81e−05

 

IL15

Interleukin 15

240.69

50.03

− 2.26

4.34e−02

 

IL2RB

Interleukin 2 receptor subunit beta

8781.96

733.82

− 3.58

8.80e−08

 

IL2RG

Interleukin 2 receptor subunit gamma

6894.04

33.36

− 7.69

1.12e−11

 

IL6R

Interleukin 6 receptor

19003.48

4036.01

− 2.24

3.77e−07

 

KEAP1

Kelch like ECH associated protein 1

1894.69

283.52

− 2.74

6.23e−07

 

MGST1

Microsomal glutathione S− transferase 1

385.27

16.68

− 4.52

8.22e−03

 

PDGFA

Platelet derived growth factor subunit A

29.57

150.10

2.37

1.98e−02

 

PDGFRB

Platelet derived growth factor receptor beta

314.64

0

− 6.68

7.00e−03

 

PIK3R3

Phosphoinositide− 3− kinase regulatory subunit 3

152.15

0

− 5.62

2.17e−02

 

RALB

RAS like proto− oncogene B

7354.73

1417.61

− 2.38

4.91e−09

 

RALGDS

Ral guanine nucleotide dissociation stimulator

959.68

16.68

− 5.85

4.33e−04

 

RASSF1

Ras association domain family member 1

5456.91

717.14

− 2.93

1.40e−13

 

SOS1

SOS Ras/Rac guanine nucleotide exchange factor 1

1679.24

6804.51

2.02

1.61e−10

 

TGFA

Transforming growth factor alpha

951.89

50.03

− 4.25

2.30e−04

 

TXNRD3

Thioredoxin reductase 3

18.50

133.42

2.78

1.63e−03

Proliferation

APC

APC regulator of WNT signaling pathway

1038.06

12174.73

3.55

1.22e−15

 

BRAF

B− Raf proto− oncogene, serine/threonine kinase

1366.54

9206.1

2.75

1.26e−17

 

CCND2

Cyclin D2

4458.14

66.71

− 6.06

2.79e−14

 

CCND3

Cyclin D3

16147.13

3485.64

− 2.21

1.37e−06

 

CCNE2

Cyclin E2

27.48

316.88

3.53

2.98e−03

 

FGFR2

Fibroblast growth factor receptor 2

85.98

950.63

3.47

4.66e−03

 

FLT3LG

fms related tyrosine kinase 3 ligand

92.37

0

− 4.90

4.48e−02

 

FZD1

Frizzled class receptor 1

271.89

50.03

− 2.44

2.45e−02

 

FZD6

Frizzled class receptor 6

64.00

517.01

3.01

1.78e−05

 

HMOX1

Heme oxygenase 1

3398.05

733.82

− 2.21

1.22e−03

 

HRAS

HRas proto− oncogene, GTPase

460.16

83.39

− 2.46

2.96e−03

 

IGF1R

Insulin like growth factor 1 receptor

2771.65

11591.01

2.06

1.07e−03

 

KEAP1

Kelch like ECH associated protein 1

1894.69

283.52

− 2.74

6.23e−07

 

LRP6

LDL receptor related protein 6

55.66

1400.93

4.64

7.96e−06

 

MAPK3

Mitogen− activated protein kinase 3

5762.75

1334.22

− 2.11

1.12e−04

 

MGST1

Microsomal glutathione S− transferase 1

385.27

16.68

− 4.52

8.22e−03

 

PDGFA

Platelet derived growth factor subunit A

29.57

150.10

2.37

1.98e−02

 

PDGFB

Platelet derived growth factor subunit B

171.69

0

− 5.81

1.63e−02

 

PDGFRB

Platelet derived growth factor receptor beta

314.64

0

− 6.68

7.00e−03

 

RB1

RB transcriptional corepressor 1

1225.51

10390.22

3.08

8.52e−20

 

SOS1

SOS Ras/Rac guanine nucleotide exchange factor 1

1679.24

6804.51

2.02

1.61e−10

 

TGFA

Transforming growth factor alpha

951.89

50.03

− 4.25

2.30e−04

 

TXNRD3

Thioredoxin reductase 3

18.50

133.42

2.78

1.63e−03

 

WNT10B

Wnt family member 10B

229.22

0

− 6.22

9.03e−03

Sustained angiogenesis

BRAF

B− Raf proto− oncogene, serine/threonine kinase

1366.54

9206.10

2.75

1.26e−17

 

FGFR2

Fibroblast growth factor receptor 2

85.98

950.63

3.47

4.66e−03

 

FLT3LG

fms related tyrosine kinase 3 ligand

92.37

0

− 4.90

4.48e−02

 

HRAS

HRas proto− oncogene, GTPase

460.16

83.39

− 2.46

2.96e−03

 

IGF1R

Insulin like growth factor 1 receptor

2771.65

11591.01

2.06

1.07e−03

 

JAG1

Jagged canonical Notch ligand 1

99.62

517.01

2.37

2.68e−04

 

MAPK3

Mitogen− activated protein kinase 3

5762.75

1334.22

− 2.11

1.12e−04

 

NOTCH2

Notch receptor 2

8983.16

39609.57

2.14

6.81e−07

 

PDGFA

Platelet derived growth factor subunit A

29.57

150.10

2.37

1.98e−02

 

PDGFB

Platelet derived growth factor subunit B

171.69

0

− 5.81

1.63e−02

 

PDGFRB

Platelet derived growth factor receptor beta

314.64

0

− 6.68

7.00e−03

 

SOS1

SOS Ras/Rac guanine nucleotide exchange factor 1

1679.24

6804.51

2.02

1.61e−10

 

TGFA

Transforming growth factor alpha

951.89

50.03

− 4.25

2.30e−04

 

TGFB1

Transforming growth factor beta 1

28839.34

6287.5

− 2.20

1.64e−04

Genomic instability

BAD

BCL2 associated agonist of cell death

826.17

116.74

− 2.82

5.74e−05

 

BBC3

BCL2 binding component 3

1275.40

66.71

− 4.26

5.98e−06

Insensitivity to anti−growth signals

SMAD2

SMAD family member 2

2524.65

10957.26

2.12

3.49e−32

 

TGFB1

Transforming growth factor beta 1

28839.34

6287.5

− 2.20

1.64e−04

  1. We highlighted the transcripts mean counts obtained after DESeq2 normalization, the fold changes computed as log2 (MRS mean counts/Control mean counts) and the q-value for each of the DEGs in our analysis that take place in the most implicated process in KEGG map “Pathways in cancer”. All values are rounded to the second decimal digit