Skip to main content

Advertisement

Table 3 Summary of pathway analyses

From: Gene expression analysis supports tumor threshold over 2.0 cm for T-category breast cancer

(Part A) Biological functions enriched in 5618 unique probes separating tumors below and above size 2.4 cm
 Associated network functions Score
  Cellular assembly and organization, cellular compromise, protein synthesis 26
  Cell signaling, nucleic acid metabolism, small molecule biochemistry 24
  Energy production, nucleic acid metabolism, small molecule biochemistry 24
  Hair and skin development and function, dermatological diseases and conditions, developmental disorder 22
  Post-translational modification, gene expression, infectious disease 22
 Top canonical pathways −log (FDR-corrected p value)
  Neuropathic pain signaling in dorsal horn neurons 1.13
  Role of NNFAT in cardiac hypertrophy 1.13
  Melatonin signaling 6.94 × 10−1
  Molecular mechanisms of cancer 6.94 × 10−1
  Calcium-induced T lymphocyte apoptosis 6.94 × 10−1
 Diseases and disorders FDR-corrected p value
  Cancer 3.95 × 10−1–5.44 × 10−1
  Hematological disease 3.95 × 10−1–5.44 × 10−1
  Immunological disease 5.13 × 10−1–5.44 × 10−1
  Hypersensitivity response 5.44 × 10−1–5.44 × 10−1
  Inflammatory response 5.44 × 10−1–5.44 × 10−1
 Molecular and cellular functions FDR-corrected p value
  Gene expression 2.03 × 10−1–5.44 × 10−1
  Cellular growth and proliferation 2.03 × 10−1–5.44 × 10−1
  Energy production 2.03 × 10−1–5.44 × 10−1
  Amino acid metabolism 2.03 × 10−1–5.44 × 10−1
  Small molecule biochemistry 2.03 × 10−1–5.44 × 10−1
(Part B) Biological functions enriched in 1914 unique probes separating tumors below and above size 2.0 cm
 Associated network functions Score
  Antigen presentation, cellular movement, hematological system development and function 29
  Cell assembly, and organization, cellular function and maintenance, protein synthesis 29
  Gene expression, infectious disease, small molecule biochemistry 29
  Cellular assembly and organization, cell signaling, gene expression 29
  Post-translational modification, protein folding, cell death 24
 Top canonical pathways −log (FDR-corrected p value)
  Tight junction signaling 9.13 × 10−1
  Germ cell-Sertoli cell junction signaling 8.69 × 10−1
  Cfc42 signaling 1.26 × 10−1
  Fatty acid biosynthesis 8.69 × 10−1
  Integrin signaling 8.69 × 10−1
 Diseases and disorders FDR-corrected p value
  Dermatological diseases and conditions 6.58 × 10−3–2.73 × 10−1
  Genetic disorder 6.58 × 10−3–2.73 × 10−1
  Infectious disease 1.14 × 10−2–2.73 × 10−1
  Inflammatory disease 3.38 × 10−2–2.73 × 10−1
  Inflammatory response 3.38 × 10−2–2.73 × 10−1
 Molecular and cellular functions FDR-corrected p value
  Antigen presentation 3.38 × 10−2–2.73 × 10−1
  Cell-to-cell signaling and interaction 3.38 × 10−2–2.73 × 10−1
  Cellular compromise 3.38 × 10−2–2.73 × 10−1
  Cellular function and maintenance 3.38 × 10−2–2.73 × 10−1
  Cellular movement 7.14 × 10−2–2.73 × 10−1
(Part C) Biological functions enriched in 6112 overlapping probes separating tumors below and above size 2.4 cm and 2.0 cm
 Associated network functions Score
  Protein synthesis, post-translational modification, cancer 26
  Cell signaling, nucleic acid metabolism, small molecule biochemistry 24
  Lipid metabolism, small molecule biochemistry, vitamin, and mineral metabolism 24
  Connective tissue development and function, embryonic development, skeletal and muscular system development and function 24
  Cancer, dematological diseases and conditions, tumor morphology 22
 Top canonical pathways −log (FDR-corrected p value)
  Cytotoxic T lymphocyte-mediated apoptosis of target cells 3.65
  Allograft rejection signaling 2.77
  Nur77 signaling in T lymphocytes 2.77
  Antigen presentation pathway 2.77
  T helper cell differentiation 1.75
 Diseases and disorders FDR-corrected p value
  Dermatological diseases and conditions 1.98 × 10−7–1.89 × 10−1
  Respiratory disease 7.98 × 10−5–1.89 × 10−1
  Cancer 4.49 × 10−4–1.89 × 10−1
  Genetic disorder 4.49 × 10−4–1.71 × 10−1
  Inflammatory response 4.49 × 10−4–1.89 × 10−1
 Molecular and cellular functions FDR-corrected p value
  Cell-to-cell signaling and interaction 2.68 × 10−4–1.89 × 10−1
  Cellular movement 8.02 × 10−4–1.89 × 10−1
  Cellular growth and proliferation 1.29 × 10−3–1.89 × 10−1
  Cellular development 2.99 × 10−3–1.89 × 10−1
  Cell death 4.1 × 10−3–1.89 × 10−1