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 |
---|---|---|---|---|
64 | 410 | 0.55 (0.0E+00) |
1.55 (1.2E-01) | Co-expression |
Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
---|---|---|---|
2 | 2 | 16 | 2 |
Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
---|---|---|
Gravendeel, et al. 2009 | 0.57 (0.0E+00) | -0.11 (9.1E-01) |
Madhavan, et al. 2009 | 0.72 (0.0E+00) | -5.08 (3.7E-07) |
Murat, et al. 2008 | 0.50 (0.0E+00) | -0.88 (3.8E-01) |
Type | Name | Action | Prior Knowledge |
---|---|---|---|
miRNA | hsa-mir-27a | Repressor | Yes |
TF | EGR3 | Activator | Yes |
Mutation | Regulator | Bicluster | ||
---|---|---|---|---|
MUC16 | hsa-mir-27a | TFBS_DB_239 | ||
PKHD1 | EGR3 | TFBS_DB_239 |
GO Term | GO BP ID | Genes |
System process | GO:0003008 | |
Transport | GO:0006810 | ATP2B2 ATP2B3 GRIN2B |
Ion transport | GO:0006811 | SLC4A10 |
Cation transport | GO:0006812 | |
Cell communication | GO:0007154 | |
Cell-cell signaling | GO:0007267 | |
Synaptic transmission | GO:0007268 | CACNG3 GRIN2B HCN1 KCNA1 KCNS2 KCNV1 SYN2 SYT5 VAMP2 |
Transmission of nerve impulse | GO:0019226 | CACNG3 |
Signaling | GO:0023052 | |
Metal ion transport | GO:0030001 | |
Ion transmembrane transport | GO:0034220 | ATP2B2 ATP2B3 ATP6V0C ATP6V1B2 |
Multicellular organismal signaling | GO:0035637 | |
Regulation of synaptic plasticity | GO:0048167 | ATP2B2 YWHAG |
Neurological system process | GO:0050877 | |
Localization | GO:0051179 | |
Establishment of localization | GO:0051234 |
|
Legend: Hanahan and Weinberg, Cell 2011 |