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Table 3. DEGs inside the KEGG map “Pathways in cancer” identified in the most implicated signalings

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

Signaling Gene symbol Gene name Control mean counts MRS mean counts Fold change q- value
PI3K signaling BAD BCL2 associated agonist of cell death 826.17 116.74 − 2.82 5.74 e−05
  EGF Epidermal growth factor 62.50 700.46 3.49 2.01 e−04
  FGFR2 Fibroblast growth factor receptor 2 85.98 950.63 3.47 4.66 e−03
  FLT3LG fms related tyrosine kinase 3 ligand 92.37 0 − 4.90 4.48 e−02
  HRAS HRas proto− oncogene, GTPase 460.16 83.39 − 2.46 2.96 e−03
  IGF1R Insulin like growth factor 1 receptor 2771.65 11591.01 2.06 1.07 e−03
  PDGFA Platelet derived growth factor subunit A 29.57 150.10 2.37 1.98 e−02
  PDGFRB Platelet derived growth factor receptor beta 314.64 0 − 6.68 7.00 e−03
  PIK3R3 Phosphoinositide− 3− kinase regulatory subunit 3 152.15 0 − 5.62 2.17 e−02
  SOS1 SOS Ras/Rac guanine nucleotide exchange factor 1 1679.24 6804.51 2.02 1.61 e−10
  TGFA Transforming growth factor alpha 951.89 50.03 − 4.25 2.30 e−04
ERK signaling BRAF B− Raf proto− oncogene, serine/threonine kinase 1366.54 9206.10 2.75 1.26 e−17
  FGFR2 Fibroblast growth factor receptor 2 85.98 950.63 3.47 4.66 e−03
  FLT3LG fms related tyrosine kinase 3 ligand 92.37 0 − 4.90 4.48 e−02
  HRAS HRas proto− oncogene, GTPase 460.16 83.39 − 2.46 2.96 e−03
  IGF1R Insulin like growth factor 1 receptor 2771.65 11591.01 2.06 1.07 e−03
  MAPK3 Mitogen− activated protein kinase 3 5762.75 1334.22 − 2.11 1.12 e−04
  PDGFA Platelet derived growth factor subunit A 29.57 150.10 2.37 1.98 e−02
  PDGFB Platelet derived growth factor subunit B 171.69 0 − 5.81 1.63 e−02
  PDGFRB Platelet derived growth factor receptor beta 314.64 0 − 6.68 7.00 e−03
  SOS1 SOS Ras/Rac guanine nucleotide exchange factor 1 1679.24 6804.51 2.02 1.61 e−10
  TGFA Transforming growth factor alpha 951.89 50.03 − 4.25 2.30 e−04
JAK− STAT signaling EGF Epidermal growth factor 62.50 700.46 3.49 2.01 e−04
  FLT3LG fms related tyrosine kinase 3 ligand 92.37 0 − 4.90 4.48 e−02
  IFNAR2 Interferon alpha and beta receptor subunit 2 2464.19 83.39 − 4.89 6.69 e−11
  IL12RB1 Interleukin 12 receptor subunit beta 1 2509.33 617.08 − 2.02 1.76 e−05
  IL13RA1 Interleukin 13 receptor subunit alpha 1 5850.09 1184.12 − 2.30 2.81 e−05
  IL15 Interleukin 15 240.69 50.03 − 2.26 4.34 e−02
  IL2RB Interleukin 2 receptor subunit beta 8781.96 733.82 − 3.58 8.80 e−08
  IL2RG Interleukin 2 receptor subunit gamma 6894.04 33.36 − 7.69 1.12 e−11
  IL6R interleukin 6 receptor 19003.48 4036.01 − 2.24 3.77 e−07
Calcium signaling CAMK2D Calcium/calmodulin dependent protein kinase II delta 1091.52 5470.29 2.32 6.63 e−11
  EGF Epidermal growth factor 62.50 700.46 3.49 2.01 e−04
  PDGFA Platelet derived growth factor subunit A 29.57 150.10 2.37 1.98 e−02
  PDGFB Platelet derived growth factor subunit B 171.69 0 − 5.81 1.63 e−02
  PDGFRB Platelet derived growth factor receptor beta 314.64 0 − 6.68 7.00 e−03
  PRKCG Protein kinase C gamma 3.07 166.78 5.79 6.10 e−08
  TGFA Transforming growth factor alpha 951.89 50.03 − 4.25 2.30 e−04
Other RAS signaling EGF Epidermal growth factor 62.50 700.46 3.49 2.01 e−04
  HRAS HRas proto− oncogene, GTPase 460.16 83.39 − 2.46 2.96 e−03
  RALB RAS like proto− oncogene B 7354.73 1417.61 − 2.38 4.91 e−09
  RALGDS Ral guanine nucleotide dissociation stimulator 959.68 16.68 − 5.85 4.33 e−04
  RASSF1 Ras association domain family member 1 5456.91 717.14 − 2.93 1.40 e−13
  SOS1 SOS Ras/Rac guanine nucleotide exchange factor 1 1679.24 6804.51 2.02 1.61 e−10
WNT signaling APC APC regulator of WNT signaling pathway 1038.06 12174.73 3.55 1.22 e−15
  FZD1 Frizzled class receptor 1 271.89 50.03 − 2.44 2.45 e−02
  FZD6 Frizzled class receptor 6 64.00 517.01 3.01 1.78 e−05
  LRP6 LDL receptor related protein 6 55.66 1400.93 4.64 7.96 e−06
  WNT10B Wnt family member 10B 229.22 0 − 6.22 9.03 e−03
  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 signalings in KEGG map “Pathways in cancer”. All values are rounded to the second decimal digit
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Orphanet Journal of Rare Diseases

ISSN: 1750-1172