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 |
---|---|---|---|---|
23 | 379 | 0.49 (0.0E+00) |
2.87 (4.1E-03) |
Co-expression Survival |
Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
---|---|---|---|
1 | 12 | 21 | 0 |
Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
---|---|---|
Gravendeel, et al. 2009 | 0.46 (0.0E+00) | 2.36 (1.8E-02) |
Madhavan, et al. 2009 | 0.44 (3.0E-03) | 2.90 (3.8E-03) |
Murat, et al. 2008 | 0.47 (0.0E+00) | 0.73 (4.7E-01) |
Type | Name | Action | Prior Knowledge |
---|---|---|---|
TF | IRF1 | Activator | Yes |
Mutation | Regulator | Bicluster | ||
---|---|---|---|---|
EPHA2_FORWARD_SIGNALING | IRF1 | PITA_100 | ||
E_CADHERIN_SIGNALING_IN_THE_NASCENT_ADHERENS_JUNCTION | IRF1 | PITA_100 | ||
FAS_SIGNALING_PATHWAY | IRF1 | PITA_100 | ||
IGF1_PATHWAY | IRF1 | PITA_100 | ||
IL1_MEDIATED_SIGNALING_EVENTS | IRF1 | PITA_100 | ||
IL23_MEDIATED_SIGNALING_EVENTS | IRF1 | PITA_100 | ||
IL3_MEDIATED_SIGNALING_EVENTS | IRF1 | PITA_100 | ||
IL5_MEDIATED_SIGNALING_EVENTS | IRF1 | PITA_100 | ||
NECTIN_ADHESION_PATHWAY | IRF1 | PITA_100 | ||
NEUROTROPHIC_FACTOR_MEDIATED_TRK_RECEPTOR_SIGNALING | IRF1 | PITA_100 | ||
SIGNALING_EVENTS_REGULATED_BY_RET_TYROSINE_KINASE | IRF1 | PITA_100 | ||
VEGFR3_SIGNALING_IN_LYMPHATIC_ENDOTHELIUM | IRF1 | PITA_100 |
GO Term | GO BP ID | Genes |
Immune system process | GO:0002376 | |
Response to stress | GO:0006950 | |
Defense response | GO:0006952 | HCP5 MX1 |
Immune response | GO:0006955 | CXCL11 IFI44L IFI6 IFITM2 |
Response to biotic stimulus | GO:0009607 | |
Response to virus | GO:0009615 | CCL5 IFIT2 IFIT3 IFITM2 MX1 OAS2 RSAD2 |
Response to organic substance | GO:0010033 | |
Cytokine-mediated signaling pathway | GO:0019221 | IFI6 IFIT2 IFIT3 IFITM2 IRF9 MX1 OAS2 RSAD2 |
Response to cytokine stimulus | GO:0034097 | |
Response to type i interferon | GO:0034340 | MX1 |
Response to interferon-gamma | GO:0034341 | IFITM2 NUB1 |
Response to interferon-alpha | GO:0035455 | IFITM2 |
Cellular response to interferon-alpha | GO:0035457 | IFIT2 IFIT3 |
Innate immune response | GO:0045087 | MX1 PSMB10 |
Multi-organism process | GO:0051704 | |
Response to other organism | GO:0051707 | |
Type i interferon-mediated signaling pathway | GO:0060337 | IFI6 IFIT2 IFIT3 IFITM2 IRF9 MX1 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 type i interferon | GO:0071357 |
|
Legend: Hanahan and Weinberg, Cell 2011 |