Background
Methods
Data processing
Co-expression networks and modules
Hub genes and the functional annotations
Results
Pre-processing of the osteosarcoma datasets
Identification of gene co-expression networks and modules
Correlation between each modules
Functional enrichment and clustering analysis
Term | Gene counts | Percent | P value | Benjamini | |
---|---|---|---|---|---|
Module 1 | Cell cycle | 66 | 0.8 | 1.30E−10 | 3.10E−07 |
Negative regulation of cellular protein metabolic process | 28 | 0.4 | 2.80E−10 | 3.50E−07 | |
Negative regulation of protein metabolic process | 28 | 0.4 | 6.80E−10 | 5.60E−07 | |
Negative regulation of protein ubiquitination | 18 | 0.2 | 7.50E−10 | 4.70E−07 | |
Anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process | 16 | 0.2 | 7.10E−09 | 3.50E−06 | |
Module 2 | Translational elongation | 51 | 0.8 | 4.20E−53 | 8.70E−50 |
Translation | 61 | 0.9 | 2.60E−34 | 2.70E−31 | |
Generation of precursor metabolites and energy | 30 | 0.5 | 2.00E−09 | 1.40E−06 | |
Oxidative phosphorylation | 17 | 0.3 | 3.40E−09 | 1.70E−06 | |
Ribosomal large subunit biogenesis | 6 | 0.1 | 2.40E−06 | 1.00E−03 | |
Module 3 | ATP synthesis coupled proton transport | 6 | 0.3 | 9.40E−05 | 4.50E−02 |
Energy-coupled proton transport, down electrochemical gradient | 6 | 0.3 | 9.40E−05 | 4.50E−02 | |
Module 4 | Translational elongation | 14 | 0.7 | 1.40E−11 | 1.50E−08 |
Translation | 18 | 0.9 | 2.00E−08 | 1.10E−05 | |
Module 5 | Antigen processing and presentation | 12 | 1.7 | 1.30E−13 | 8.60E−11 |
Antigen processing and presentation of peptide or polysaccharide antigen via MHC class II | 8 | 1.1 | 1.50E−10 | 4.70E−08 | |
Immune response | 20 | 2.8 | 2.20E−10 | 4.70E−08 | |
Antigen processing and presentation of peptide antigen | 6 | 0.8 | 1.80E−07 | 2.90E−05 | |
Antigen processing and presentation of exogenous peptide antigen | 4 | 0.6 | 1.60E−05 | 2.10E−03 |
Term | Gene counts | Percent | P value | Benjamini | |
---|---|---|---|---|---|
Module 1 | Proteasome | 14 | 0.2 | 3.90E−07 | 6.10E−05 |
Module 2 | Ribosome | 46 | 0.7 | 1.80E−41 | 2.60E−39 |
Parkinson’s disease | 24 | 0.4 | 6.20E−10 | 4.50E−08 | |
Oxidative phosphorylation | 24 | 0.4 | 8.50E−10 | 4.10E-08 | |
Huntington’s disease | 26 | 0.4 | 2.70E−08 | 9.90E−07 | |
Alzheimer’s disease | 22 | 0.3 | 1.40E−06 | 4.00E−05 | |
Module 3 | Epithelial cell signaling in Helicobacter pylori infection | 9 | 0.4 | 1.80E−05 | 1.80E−03 |
Lysosome | 11 | 0.5 | 2.80E−05 | 1.30E−03 | |
Vibrio cholerae infection | 8 | 0.4 | 4.30E−05 | 1.30E−03 | |
Oxidative phosphorylation | 9 | 0.4 | 1.70E−03 | 4.00E−02 | |
Module 4 | Ribosome | 14 | 0.7 | 2.80E−11 | 1.90E−09 |
Module 5 | Type I diabetes mellitus | 10 | 1.4 | 3.30E−11 | 2.60E−09 |
Antigen processing and presentation | 12 | 1.7 | 4.20E−11 | 1.60E−09 | |
Viral myocarditis | 11 | 1.6 | 2.00E−10 | 5.10E−09 | |
Allograft rejection | 9 | 1.3 | 3.30E−10 | 6.50E−09 | |
Graft-versus-host disease | 9 | 1.3 | 6.70E−10 | 1.00E−08 |