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 |