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 |
---|---|---|---|---|
37 | 387 | 0.39 (0.0E+00) |
-2.44 (1.5E-02) |
Co-expression Survival |
Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
---|---|---|---|
1 | 1 | 25 | 0 |
Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
---|---|---|
Gravendeel, et al. 2009 | 0.26 (0.0E+00) | -3.80 (1.5E-04) |
Madhavan, et al. 2009 | 0.25 (5.6E-01) | 0.45 (6.5E-01) |
Murat, et al. 2008 | 0.26 (0.0E+00) | 0.14 (8.9E-01) |
Type | Name | Action | Prior Knowledge |
---|---|---|---|
miRNA | hsa-mir-222 | Repressor | Yes |
Mutation | Regulator | Bicluster | ||
---|---|---|---|---|
E_CADHERIN_SIGNALING_IN_KERATINOCYTES | hsa-mir-222 | TFBS_DB_90 |
GO Term | GO BP ID | Genes |
Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | GO:0006139 | |
Transcription, dna-dependent | GO:0006351 | EPC1 EPC2 GATAD2B GPBP1 HMBOX1 JMJD1C KLF12 MED13L ZNF133 ZNF500 ZNF585A |
Regulation of transcription, dna-dependent | GO:0006355 | CREBBP GPBP1 JMJD1C ZNF133 ZNF500 ZNF585A |
Macromolecule biosynthetic process | GO:0009059 | |
Regulation of biosynthetic process | GO:0009889 | |
Gene expression | GO:0010467 | CASC3 CREBBP RBM5 TNRC6A |
Regulation of gene expression | GO:0010468 | |
Regulation of macromolecule biosynthetic process | GO:0010556 | |
Rna metabolic process | GO:0016070 | CASC3 |
Regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | GO:0019219 | |
Regulation of metabolic process | GO:0019222 | |
Regulation of cellular metabolic process | GO:0031323 | |
Regulation of cellular biosynthetic process | GO:0031326 | |
Rna biosynthetic process | GO:0032774 | |
Cellular nitrogen compound metabolic process | GO:0034641 | |
Cellular macromolecule biosynthetic process | GO:0034645 | |
Macromolecule metabolic process | GO:0043170 | |
Cellular macromolecule metabolic process | GO:0044260 | |
Regulation of nitrogen compound metabolic process | GO:0051171 | |
Regulation of rna metabolic process | GO:0051252 | |
Regulation of macromolecule metabolic process | GO:0060255 | |
Regulation of primary metabolic process | GO:0080090 | |
Nucleic acid metabolic process | GO:0090304 | |
Regulation of cellular macromolecule biosynthetic process | GO:2000112 | |
Regulation of rna biosynthetic process | GO:2001141 |
|
Legend: Hanahan and Weinberg, Cell 2011 |