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 |
---|---|---|---|---|
30 | 399 | 0.49 (0.0E+00) |
-2.03 (4.3E-02) |
Co-expression Survival |
Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
---|---|---|---|
4 | 4 | 18 | 1 |
Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
---|---|---|
Gravendeel, et al. 2009 | 0.23 (2.0E-03) | -3.23 (1.2E-03) |
Madhavan, et al. 2009 | 0.25 (5.1E-01) | -2.46 (1.4E-02) |
Murat, et al. 2008 | 0.33 (0.0E+00) | 0.29 (7.7E-01) |
Type | Name | Action | Prior Knowledge |
---|---|---|---|
TF | E2F3 | Activator | Yes |
TF | SMAD9 | Activator | Yes |
TF | KLF1 | Repressor | Yes |
TF | KLF17 | Repressor | Yes |
Mutation | Regulator | Bicluster | ||
---|---|---|---|---|
HMCN1 | KLF1 | TFBS_DB_203 | ||
HMCN1 | KLF17 | TFBS_DB_203 | ||
MUC17 | SMAD9 | TFBS_DB_203 | ||
OBSCN | E2F3 | TFBS_DB_203 |
GO Term | GO BP ID | Genes |
Chromatin organization | GO:0006325 | MLL MLL5 MYST4 SETD2 |
Protein methylation | GO:0006479 | |
One-carbon metabolic process | GO:0006730 | |
Organelle organization | GO:0006996 | |
Protein alkylation | GO:0008213 | |
Chromatin modification | GO:0016568 | JMJD1C |
Covalent chromatin modification | GO:0016569 | |
Histone modification | GO:0016570 | |
Histone methylation | GO:0016571 | |
Peptidyl-lysine methylation | GO:0018022 | |
Peptidyl-lysine trimethylation | GO:0018023 | |
Regulation of cellular metabolic process | GO:0031323 | |
Methylation | GO:0032259 | |
Histone lysine methylation | GO:0034968 | |
Macromolecule methylation | GO:0043414 | |
Chromosome organization | GO:0051276 | |
Histone h3-k4 methylation | GO:0051568 | MLL MLL5 WDR82 |
Regulation of primary metabolic process | GO:0080090 |
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Legend: Hanahan and Weinberg, Cell 2011 |