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 | 400 | 0.59 (0.0E+00) |
2.36 (1.8E-02) |
Co-expression Survival |
Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
---|---|---|---|
4 | 1 | 14 | 2 |
Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
---|---|---|
Gravendeel, et al. 2009 | 0.53 (0.0E+00) | 2.05 (4.0E-02) |
Madhavan, et al. 2009 | 0.45 (1.2E-02) | 3.55 (3.9E-04) |
Murat, et al. 2008 | 0.44 (0.0E+00) | -1.09 (2.8E-01) |
Type | Name | Action | Prior Knowledge |
---|---|---|---|
miRNA | hsa-mir-181c | Repressor | Yes |
miRNA | hsa-mir-182 | Repressor | Yes |
miRNA | hsa-mir-128 | Repressor | Yes |
miRNA | hsa-mir-9 | Repressor | Yes |
Mutation | Regulator | Bicluster | ||
---|---|---|---|---|
TBC1D29 | hsa-mir-181c | PITA_314 |
GO Term | GO BP ID | Genes |
Immune system process | GO:0002376 | |
Response to stress | GO:0006950 | |
Defense response | GO:0006952 | |
Inflammatory response | GO:0006954 | C5AR1 CCL13 CCL23 CLEC7A IL10 IL2RA TLR8 |
Immune response | GO:0006955 | C5AR1 CCL23 IL2RA |
Response to external stimulus | GO:0009605 | |
Response to wounding | GO:0009611 | |
Leukocyte chemotaxis | GO:0030595 | IL10 |
Interferon-alpha biosynthetic process | GO:0045349 | |
Regulation of interferon-alpha biosynthetic process | GO:0045354 | |
Regulation of immune response | GO:0050776 | AMICA1 |
Negative regulation of immune response | GO:0050777 | IL2RA |
Leukocyte migration | GO:0050900 | AMICA1 |
Cell chemotaxis | GO:0060326 |
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Legend:![]() Hanahan and Weinberg, Cell 2011 |