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 |
---|---|---|---|---|
34 | 406 | 0.49 (0.0E+00) |
-2.06 (3.9E-02) |
Co-expression Survival |
Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
---|---|---|---|
3 | 4 | 71 | 1 |
Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
---|---|---|
Gravendeel, et al. 2009 | 0.23 (1.0E-03) | -3.18 (1.5E-03) |
Madhavan, et al. 2009 | 0.25 (5.5E-01) | 1.54 (1.2E-01) |
Murat, et al. 2008 | 0.26 (0.0E+00) | 0.74 (4.6E-01) |
Type | Name | Action | Prior Knowledge |
---|---|---|---|
TF | PPARG | Repressor | Yes |
TF | ZNF148 | Activator | Yes |
TF | KLF12 | Activator | Yes |
Mutation | Regulator | Bicluster | ||
---|---|---|---|---|
RB1 | ZNF148 | TFBS_DB_281 | ||
SHP2_SIGNALING | PPARG | TFBS_DB_281 | ||
SIGNALING_EVENTS_MEDIATED_BY_TCPTP | KLF12 | TFBS_DB_281 | ||
SIGNALING_EVENTS_MEDIATED_BY_TCPTP | PPARG | TFBS_DB_281 |
GO Term | GO BP ID | Genes |
Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | GO:0006139 | |
Chromatin organization | GO:0006325 | CREBBP EP300 KIAA1267 MLL5 PHF21A SETD2 |
Transcription, dna-dependent | GO:0006351 | FOXN3 HIPK2 HMBOX1 MED13L MLL5 PHF21A ZNF275 ZNF398 ZNF500 |
Transcription initiation, dna-dependent | GO:0006352 | NCOA6 RSF1 TCF4 |
Regulation of transcription, dna-dependent | GO:0006355 | CREBBP EP300 INSR PHF21A SETD2 ZNF275 ZNF398 ZNF500 |
Regulation of transcription from rna polymerase ii promoter | GO:0006357 | FOXO3 MED13L |
Regulation of translation | GO:0006417 | CASC3 FOXO3 |
N-terminal protein amino acid acetylation | GO:0006474 | |
Nitrogen compound metabolic process | GO:0006807 | |
Response to dna damage stimulus | GO:0006974 | NCOA6 |
Organelle organization | GO:0006996 | |
Biosynthetic process | GO:0009058 | |
Macromolecule biosynthetic process | GO:0009059 | |
Embryo development | GO:0009790 | |
Regulation of biosynthetic process | GO:0009889 | |
Negative regulation of biosynthetic process | GO:0009890 | |
Positive regulation of biosynthetic process | GO:0009891 | |
Negative regulation of metabolic process | GO:0009892 | |
Positive regulation of metabolic process | GO:0009893 | |
Gene expression | GO:0010467 | CASC3 CREBBP EP300 TNRC6A |
Regulation of gene expression | GO:0010468 | |
Regulation of macromolecule biosynthetic process | GO:0010556 | |
Positive regulation of macromolecule biosynthetic process | GO:0010557 | |
Negative regulation of macromolecule biosynthetic process | GO:0010558 | |
Positive regulation of glycoprotein biosynthetic process | GO:0010560 | INSR |
Positive regulation of macromolecule metabolic process | GO:0010604 | |
Negative regulation of macromolecule metabolic process | GO:0010605 | |
Positive regulation of gene expression | GO:0010628 | |
Negative regulation of gene expression | GO:0010629 | INSR |
Viral reproduction | GO:0016032 | CREBBP EP300 |
Rna metabolic process | GO:0016070 | CASC3 |
Chromatin modification | GO:0016568 | CABIN1 PHF21A |
Covalent chromatin modification | GO:0016569 | |
Histone modification | GO:0016570 | |
N-terminal peptidyl-lysine acetylation | GO:0018076 | CREBBP EP300 |
Regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | GO:0019219 | |
Regulation of metabolic process | GO:0019222 | |
Erythrocyte differentiation | GO:0030218 | HIPK2 MLL5 |
Regulation of cellular metabolic process | GO:0031323 | |
Negative regulation of cellular metabolic process | GO:0031324 | |
Positive regulation of cellular metabolic process | GO:0031325 | |
Regulation of cellular biosynthetic process | GO:0031326 | |
Negative regulation of cellular biosynthetic process | GO:0031327 | |
Positive regulation of cellular biosynthetic process | GO:0031328 | |
N-terminal protein amino acid modification | GO:0031365 | |
Rna biosynthetic process | GO:0032774 | |
Erythrocyte homeostasis | GO:0034101 | |
Cellular nitrogen compound metabolic process | GO:0034641 | |
Cellular macromolecule biosynthetic process | GO:0034645 | |
Cellular biosynthetic process | GO:0044249 | |
Cellular macromolecule metabolic process | GO:0044260 | |
Negative regulation of transcription, dna-dependent | GO:0045892 | CBX1 FOXN3 HMBOX1 RSF1 |
Positive regulation of transcription, dna-dependent | GO:0045893 | CREBBP FOXO3 HIPK2 HMBOX1 INSR MLL5 NCOA6 RSF1 TCF4 ZNF398 |
Negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | GO:0045934 | |
Positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | GO:0045935 | |
Negative regulation of cellular process | GO:0048523 | |
Regulation of nitrogen compound metabolic process | GO:0051171 | |
Negative regulation of nitrogen compound metabolic process | GO:0051172 | |
Positive regulation of nitrogen compound metabolic process | GO:0051173 | |
Regulation of rna metabolic process | GO:0051252 | |
Negative regulation of rna metabolic process | GO:0051253 | |
Positive regulation of rna metabolic process | GO:0051254 | |
Chromosome organization | GO:0051276 | |
Regulation of macromolecule metabolic process | GO:0060255 | |
Protein-dna complex assembly | GO:0065004 | TCF4 |
Protein-dna complex subunit organization | GO:0071824 | |
Regulation of primary metabolic process | GO:0080090 | |
Nucleic acid metabolic process | GO:0090304 | |
Regulation of cellular macromolecule biosynthetic process | GO:2000112 | |
Negative regulation of cellular macromolecule biosynthetic process | GO:2000113 | |
Regulation of rna biosynthetic process | GO:2001141 |
|
Legend: Hanahan and Weinberg, Cell 2011 |