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 |
---|---|---|---|---|
50 | 416 | 0.65 (0.0E+00) |
2.88 (4.0E-03) |
Co-expression Survival |
Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
---|---|---|---|
1 | 2 | 101 | 4 |
Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
---|---|---|
Gravendeel, et al. 2009 | 0.61 (0.0E+00) | 2.25 (2.4E-02) |
Madhavan, et al. 2009 | 0.58 (0.0E+00) | 1.92 (5.5E-02) |
Murat, et al. 2008 | 0.56 (0.0E+00) | -1.13 (2.6E-01) |
Type | Name | Action | Prior Knowledge |
---|---|---|---|
TF | ELF1 | Activator | Yes |
Mutation | Regulator | Bicluster | ||
---|---|---|---|---|
NEUROTROPHIC_FACTOR_MEDIATED_TRK_RECEPTOR_SIGNALING | ELF1 | PITA_413 | ||
SIGNALING_EVENTS_MEDIATED_BY_THE_HEDGEHOG_FAMILY | ELF1 | PITA_413 |
GO Term | GO BP ID | Genes |
Cell activation | GO:0001775 | |
Cytokine production | GO:0001816 | CD4 PTAFR |
Regulation of cytokine production | GO:0001817 | |
Adaptive immune response | GO:0002250 | BTLA CD4 CD84 LILRA3 LILRB1 LILRB4 |
Immune effector process | GO:0002252 | |
Activation of immune response | GO:0002253 | |
Cell activation involved in immune response | GO:0002263 | |
Myeloid leukocyte activation | GO:0002274 | |
Myeloid cell activation involved in immune response | GO:0002275 | |
Leukocyte activation involved in immune response | GO:0002366 | |
Cytokine production involved in immune response | GO:0002367 | |
Cytokine secretion involved in immune response | GO:0002374 | |
Immune system process | GO:0002376 | |
Immunoglobulin production | GO:0002377 | |
Immune response-activating cell surface receptor signaling pathway | GO:0002429 | |
Production of molecular mediator of immune response | GO:0002440 | |
Leukocyte mediated immunity | GO:0002443 | |
Myeloid leukocyte mediated immunity | GO:0002444 | |
Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | GO:0002460 | |
Antigen processing and presentation of peptide or polysaccharide antigen via mhc class ii | GO:0002504 | |
Regulation of immune system process | GO:0002682 | |
Positive regulation of immune system process | GO:0002684 | |
Regulation of leukocyte activation | GO:0002694 | |
Positive regulation of leukocyte activation | GO:0002696 | |
Regulation of immune effector process | GO:0002697 | |
Positive regulation of immune effector process | GO:0002699 | |
Regulation of production of molecular mediator of immune response | GO:0002700 | |
Regulation of leukocyte mediated immunity | GO:0002703 | |
Regulation of cytokine production involved in immune response | GO:0002718 | |
Regulation of cytokine secretion involved in immune response | GO:0002739 | |
Negative regulation of cytokine secretion involved in immune response | GO:0002740 | IL10 LILRB1 |
Immune response-activating signal transduction | GO:0002757 | |
Immune response-regulating signaling pathway | GO:0002764 | |
Immune response-regulating cell surface receptor signaling pathway | GO:0002768 | BTLA FGR |
Regulation of adaptive immune response | GO:0002819 | |
Regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | GO:0002822 | |
Regulation of myeloid leukocyte mediated immunity | GO:0002886 | |
Response to stress | GO:0006950 | |
Defense response | GO:0006952 | CD84 CSF3R LILRA3 |
Inflammatory response | GO:0006954 | AOAH C3AR1 CCR5 IL10 NLRC4 PTAFR TLR5 TLR7 |
Immune response | GO:0006955 | CCR5 CD4 CMKLR1 HLA-DQA1 HLA-DQA2 HLA-DQB1 PTAFR |
Signal transduction | GO:0007165 | CD4 CSF3R LILRA3 LILRB1 LILRB4 |
Protein secretion | GO:0009306 | |
Response to external stimulus | GO:0009605 | |
Response to biotic stimulus | GO:0009607 | |
Response to wounding | GO:0009611 | |
Response to bacterium | GO:0009617 | |
Calcium-mediated signaling | GO:0019722 | CCR5 TREML1 |
Signaling | GO:0023052 | CCR5 |
Leukocyte chemotaxis | GO:0030595 | IL10 |
Negative regulation of b cell proliferation | GO:0030889 | BTLA IL10 MNDA |
Lymphocyte costimulation | GO:0031294 | |
T cell costimulation | GO:0031295 | BTLA CD4 HLA-DQA1 HLA-DQA2 HLA-DQB1 |
Regulation of defense response | GO:0031347 | |
Regulation of response to external stimulus | GO:0032101 | |
Interleukin-12 production | GO:0032615 | |
Negative regulation of interleukin-12 production | GO:0032695 | CMKLR1 IL10 |
Negative regulation of mononuclear cell proliferation | GO:0032945 | LILRB1 |
Response to interferon-gamma | GO:0034341 | CXCL16 |
Regulation of cytokine biosynthetic process | GO:0042035 | |
Cytokine biosynthetic process | GO:0042089 | |
Cytokine metabolic process | GO:0042107 | |
T cell activation | GO:0042110 | |
Negative regulation of tumor necrosis factor biosynthetic process | GO:0042536 | IL10 LILRB1 |
Leukocyte degranulation | GO:0043299 | |
Regulation of leukocyte degranulation | GO:0043300 | |
Symbiosis, encompassing mutualism through parasitism | GO:0044403 | |
Regulated secretory pathway | GO:0045055 | |
Innate immune response | GO:0045087 | CD4 CD84 FCER1G FGR NLRC4 TLR5 TLR7 TREML1 |
Leukocyte activation | GO:0045321 | |
Interferon-alpha biosynthetic process | GO:0045349 | |
Regulation of interferon-alpha biosynthetic process | GO:0045354 | |
Lymphocyte activation | GO:0046649 | |
Positive regulation of biological process | GO:0048518 | |
Regulation of response to stimulus | GO:0048583 | |
Positive regulation of response to stimulus | GO:0048584 | |
Cytokine secretion | GO:0050663 | |
Negative regulation of lymphocyte proliferation | GO:0050672 | |
Regulation of immune response | GO:0050776 | HCST LILRB1 TREML1 |
Positive regulation of immune response | GO:0050778 | |
Regulation of biological process | GO:0050789 | |
Regulation of calcium-mediated signaling | GO:0050848 | CMKLR1 |
Antigen receptor-mediated signaling pathway | GO:0050851 | |
T cell receptor signaling pathway | GO:0050852 | CD4 HLA-DQA1 HLA-DQA2 HLA-DQB1 |
Regulation of t cell activation | GO:0050863 | CD4 |
Regulation of cell activation | GO:0050865 | |
Positive regulation of cell activation | GO:0050867 | |
Positive regulation of t cell activation | GO:0050870 | |
Response to stimulus | GO:0050896 | |
Leukocyte migration | GO:0050900 | CD84 FCER1G |
Regulation of lymphocyte activation | GO:0051249 | |
Positive regulation of lymphocyte activation | GO:0051251 | |
Response to other organism | GO:0051707 | |
Cellular response to stimulus | GO:0051716 | |
Cell chemotaxis | GO:0060326 | |
Interferon-gamma-mediated signaling pathway | GO:0060333 | HLA-DQA1 HLA-DQA2 HLA-DQB1 PTAFR |
Biological regulation | GO:0065007 | |
Negative regulation of leukocyte proliferation | GO:0070664 | |
Leukocyte apoptosis | GO:0071887 | |
Regulation of response to stress | GO:0080134 | |
Regulation of leukocyte apoptosis | GO:2000106 |
|
Legend: Hanahan and Weinberg, Cell 2011 |