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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
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Orphanet Journal of Rare Diseases

ISSN: 1750-1172