Bicluster Expression of Patient Tumors
Expression of genes from patient tumors in bicluster on left side of red dashed line and out of bicluster on right of red dashed line. Each patient tumor is represented as a boxplot, ordered by their median expression for the bicluster genes (smallest to largest) and colored according to it's GBM subtype. |
Enrichment of Tumor Subtypes in Qunitiles
Patient tumors are sorted as on the left and broken into quintiles following the dashed grey lines. Then each quintile is tested for enrichment of each tumor subtype. The deviation from zero indicate -log10(enrichment p-value), and positive values indicate over-enrichment and negative values underenrichment. |
Genes | Patient Tumors | FPC Var. Exp. (Perm. p-value) | Survival (p-value) | Independent Replication |
---|---|---|---|---|
33 | 398 | 0.50 (0.0E+00) |
3.16 (1.6E-03) |
Co-expression Survival |
Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
---|---|---|---|
0 | 0 | 32 | 0 |
Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
---|---|---|
Gravendeel, et al. 2009 | 0.49 (0.0E+00) | 1.88 (5.9E-02) |
Madhavan, et al. 2009 | 0.49 (0.0E+00) | 2.77 (5.6E-03) |
Murat, et al. 2008 | 0.39 (0.0E+00) | -0.52 (6.0E-01) |
Type | Name | Action | Prior Knowledge |
---|---|---|---|
Mutation | Regulator | Bicluster |
---|
GO Term | GO BP ID | Genes |
Activation of immune response | GO:0002253 | |
Immune system process | GO:0002376 | |
Immune response-activating cell surface receptor signaling pathway | GO:0002429 | |
Antigen processing and presentation of peptide or polysaccharide antigen via mhc class ii | GO:0002504 | |
Immune response-activating signal transduction | GO:0002757 | |
Immune response-regulating signaling pathway | GO:0002764 | |
Immune response-regulating cell surface receptor signaling pathway | GO:0002768 | |
Response to stress | GO:0006950 | |
Defense response | GO:0006952 | |
Immune response | GO:0006955 | CXCL11 HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRB5 IFI44L IFI6 |
Cell surface receptor linked signaling pathway | GO:0007166 | IRF9 |
Response to virus | GO:0009615 | IFIT2 IFIT3 IFNGR1 OAS2 RSAD2 |
Response to organic substance | GO:0010033 | |
Cytokine-mediated signaling pathway | GO:0019221 | HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRB5 IFI6 IFIT2 IFIT3 IFNGR1 IRF9 OAS2 RSAD2 |
Lymphocyte costimulation | GO:0031294 | |
T cell costimulation | GO:0031295 | HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRB5 |
Response to cytokine stimulus | GO:0034097 | CXCL16 |
Response to type i interferon | GO:0034340 | |
Response to interferon-gamma | GO:0034341 | CXCL16 |
Response to interferon-alpha | GO:0035455 | |
Cellular response to interferon-alpha | GO:0035457 | IFIT2 IFIT3 |
Innate immune response | GO:0045087 | |
Antigen receptor-mediated signaling pathway | GO:0050851 | |
T cell receptor signaling pathway | GO:0050852 | HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRB5 |
Positive regulation of cell activation | GO:0050867 | |
Interferon-gamma-mediated signaling pathway | GO:0060333 | HLA-DQA1 HLA-DQA2 HLA-DQB1 HLA-DRB5 IFNGR1 IRF9 OAS2 |
Type i interferon-mediated signaling pathway | GO:0060337 | IFI6 IFIT2 IFIT3 IRF9 OAS2 RSAD2 |
Cellular response to chemical stimulus | GO:0070887 | |
Cellular response to organic substance | GO:0071310 | |
Cellular response to cytokine stimulus | GO:0071345 | |
Cellular response to interferon-gamma | GO:0071346 | |
Cellular response to type i interferon | GO:0071357 |
|
Legend: Hanahan and Weinberg, Cell 2011 |