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 |
---|---|---|---|---|
35 | 416 | 0.61 (0.0E+00) |
3.21 (1.3E-03) |
Co-expression Survival |
Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
---|---|---|---|
1 | 11 | 179 | 3 |
Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
---|---|---|
Gravendeel, et al. 2009 | 0.63 (0.0E+00) | 3.19 (1.4E-03) |
Madhavan, et al. 2009 | 0.68 (0.0E+00) | 3.55 (3.8E-04) |
Murat, et al. 2008 | 0.61 (0.0E+00) | -0.92 (3.6E-01) |
Type | Name | Action | Prior Knowledge |
---|---|---|---|
TF | IRF1 | Activator | Yes |
Mutation | Regulator | Bicluster | ||
---|---|---|---|---|
CXCR3_MEDIATED_SIGNALING_EVENTS | IRF1 | TFBS_DB_589 | ||
EPHB_FORWARD_SIGNALING | IRF1 | TFBS_DB_589 | ||
ERBB2_ERBB3_SIGNALING_EVENTS | IRF1 | TFBS_DB_589 | ||
ERBB4_SIGNALING_EVENTS | IRF1 | TFBS_DB_589 | ||
GMCSF_MEDIATED_SIGNALING_EVENTS | IRF1 | TFBS_DB_589 | ||
IL23_MEDIATED_SIGNALING_EVENTS | IRF1 | TFBS_DB_589 | ||
IL2_MEDIATED_SIGNALING_EVENTS | IRF1 | TFBS_DB_589 | ||
IL2_SIGNALING_EVENTS_MEDIATED_BY_STAT5 | IRF1 | TFBS_DB_589 | ||
NEUROTROPHIC_FACTOR_MEDIATED_TRK_RECEPTOR_SIGNALING | IRF1 | TFBS_DB_589 | ||
SIGNALING_EVENTS_MEDIATED_BY_FOCAL_ADHESION_KINASE | IRF1 | TFBS_DB_589 | ||
SIGNALING_EVENTS_REGULATED_BY_RET_TYROSINE_KINASE | IRF1 | TFBS_DB_589 |
GO Term | GO BP ID | Genes |
Cell activation | GO:0001775 | |
B cell homeostasis | GO:0001782 | LYN |
Cytokine production | GO:0001816 | S100A8 |
Regulation of cytokine production | GO:0001817 | LYN |
Positive regulation of protein phosphorylation | GO:0001934 | AIF1 |
Response to molecule of bacterial origin | GO:0002237 | |
Adaptive immune response | GO:0002250 | CLEC4A LILRB2 LYN SYK |
Immune effector process | GO:0002252 | |
Activation of immune response | GO:0002253 | |
Myeloid leukocyte activation | GO:0002274 | |
Myeloid cell activation involved in immune response | GO:0002275 | |
Mast cell activation involved in immune response | GO:0002279 | |
Immune system process | GO:0002376 | |
Immune response-activating cell surface receptor signaling pathway | GO:0002429 | |
Fc receptor mediated stimulatory signaling pathway | GO:0002431 | FCER1G LYN |
Leukocyte mediated immunity | GO:0002443 | |
Myeloid leukocyte mediated immunity | GO:0002444 | |
Mast cell mediated immunity | GO:0002448 | |
Lymphocyte mediated immunity | GO:0002449 | |
Humoral immune response mediated by circulating immunoglobulin | GO:0002455 | |
Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | GO:0002460 | |
Antigen processing and presentation of peptide antigen via mhc class ii | GO:0002495 | |
Tolerance induction | GO:0002507 | |
Acute inflammatory response | GO:0002526 | ALOX5 S100A8 |
Production of molecular mediator involved in inflammatory response | GO:0002532 | |
Arachidonic acid metabolite production involved in inflammatory response | GO:0002538 | |
Leukotriene production involved in inflammatory response | GO:0002540 | ALOX5 |
Monocyte chemotaxis | GO:0002548 | CCL2 |
Platelet degranulation | GO:0002576 | LYN SERPING1 SRGN |
Regulation of antigen processing and presentation | GO:0002577 | |
Regulation of immune system process | GO:0002682 | |
Negative regulation of immune system process | GO:0002683 | |
Positive regulation of immune system process | GO:0002684 | |
Regulation of leukocyte migration | GO:0002685 | |
Positive regulation of leukocyte migration | GO:0002687 | TLR2 |
Regulation of leukocyte chemotaxis | GO:0002688 | |
Positive regulation of leukocyte chemotaxis | GO:0002690 | |
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 | |
Positive regulation of cytokine production involved in immune response | GO:0002720 | |
Immune response-activating signal transduction | GO:0002757 | |
Immune response-regulating signaling pathway | GO:0002764 | |
Immune response-inhibiting signal transduction | GO:0002765 | |
Immune response-inhibiting cell surface receptor signaling pathway | GO:0002767 | LILRB2 |
Immune response-regulating cell surface receptor signaling pathway | GO:0002768 | LYN |
Fc receptor mediated inhibitory signaling pathway | GO:0002774 | LILRB2 LYN |
Regulation of myeloid leukocyte mediated immunity | GO:0002886 | |
Fatty acid biosynthetic process | GO:0006633 | |
Unsaturated fatty acid biosynthetic process | GO:0006636 | |
Icosanoid metabolic process | GO:0006690 | |
Leukotriene metabolic process | GO:0006691 | ALOX5 ALOX5AP |
Exocytosis | GO:0006887 | |
Phagocytosis | GO:0006909 | |
Phagocytosis, engulfment | GO:0006911 | AIF1 FCER1G |
Chemotaxis | GO:0006935 | CCL2 |
Response to stress | GO:0006950 | |
Defense response | GO:0006952 | CD74 |
Inflammatory response | GO:0006954 | AIF1 CCL2 CHI3L1 CYBB LY96 PSTPIP1 S100A8 TLR2 |
Immune response | GO:0006955 | FCGR2B LCP2 LILRB2 TLR2 |
Complement activation | GO:0006956 | C1QB C1S |
Complement activation, classical pathway | GO:0006958 | C1QB C1S SERPING1 |
Humoral immune response | GO:0006959 | CCL2 |
Blood coagulation | GO:0007596 | AMICA1 CD74 FCER1G LCP2 LYN SERPING1 SRGN SYK |
Hemostasis | GO:0007599 | |
Protein secretion | GO:0009306 | |
Response to external stimulus | GO:0009605 | |
Response to biotic stimulus | GO:0009607 | |
Response to wounding | GO:0009611 | CCL2 CTSB |
Response to bacterium | GO:0009617 | CCL2 |
Response to organic substance | GO:0010033 | |
Positive regulation of phosphorus metabolic process | GO:0010562 | |
Immunoglobulin mediated immune response | GO:0016064 | CD74 FCER1G |
Leukotriene biosynthetic process | GO:0019370 | ALOX5 ALOX5AP SYK |
B cell mediated immunity | GO:0019724 | |
Antigen processing and presentation | GO:0019882 | |
Antigen processing and presentation of exogenous peptide antigen via mhc class ii | GO:0019886 | CD74 FCER1G |
Platelet activation | GO:0030168 | FCER1G LCP2 LYN SERPING1 SRGN SYK |
Neutrophil chemotaxis | GO:0030593 | AMICA1 CCL2 FCER1G S100A8 SYK |
Leukocyte chemotaxis | GO:0030595 | |
Regulation of defense response | GO:0031347 | |
Lipopolysaccharide-mediated signaling pathway | GO:0031663 | CCL2 LY96 LYN TLR2 |
Regulation of response to external stimulus | GO:0032101 | |
Positive regulation of response to external stimulus | GO:0032103 | |
Detection of molecule of bacterial origin | GO:0032490 | |
Response to lipopolysaccharide | GO:0032496 | IL10RA LY96 S100A8 |
Interleukin-6 production | GO:0032635 | |
Regulation of interleukin-6 production | GO:0032675 | |
Positive regulation of interleukin-6 production | GO:0032755 | FCER1G LILRB2 TLR2 |
Regulation of homeostatic process | GO:0032844 | |
Mononuclear cell proliferation | GO:0032943 | |
Regulation of mononuclear cell proliferation | GO:0032944 | |
Positive regulation of mononuclear cell proliferation | GO:0032946 | |
Regulation of mast cell activation | GO:0033003 | LYN |
Positive regulation of mast cell activation | GO:0033005 | |
Regulation of mast cell activation involved in immune response | GO:0033006 | |
Positive regulation of mast cell activation involved in immune response | GO:0033008 | |
Unsaturated fatty acid metabolic process | GO:0033559 | |
Response to cytokine stimulus | GO:0034097 | |
Regulation of homotypic cell-cell adhesion | GO:0034110 | |
Toll-like receptor 2 signaling pathway | GO:0034134 | LY96 TLR2 |
Toll-like receptor 4 signaling pathway | GO:0034142 | LY96 TLR2 |
Wound healing | GO:0042060 | S100A8 |
Positive regulation of t cell proliferation | GO:0042102 | AIF1 LILRB2 |
T cell activation | GO:0042110 | |
Macrophage activation | GO:0042116 | |
Response to chemical stimulus | GO:0042221 | |
Positive regulation of phosphorylation | GO:0042327 | |
Taxis | GO:0042330 | |
Leukocyte degranulation | GO:0043299 | |
Regulation of leukocyte degranulation | GO:0043300 | |
Positive regulation of leukocyte degranulation | GO:0043302 | |
Mast cell degranulation | GO:0043303 | |
Regulation of mast cell degranulation | GO:0043304 | LYN |
Positive regulation of mast cell degranulation | GO:0043306 | FCER1G SYK |
Cellular alkene metabolic process | GO:0043449 | |
Alkene biosynthetic process | GO:0043450 | |
Regulated secretory pathway | GO:0045055 | |
T cell selection | GO:0045058 | CD74 |
Innate immune response | GO:0045087 | C1QB C1S CLEC4A CTSB CYBB FCER1G LCP2 LY96 LYN PSTPIP1 S100A8 SERPING1 SYK TLR2 |
Regulation of innate immune response | GO:0045088 | |
Leukocyte activation | GO:0045321 | |
Mast cell activation | GO:0045576 | FCER1G LCP2 |
Regulation of t cell differentiation | GO:0045580 | |
Positive regulation of t cell differentiation | GO:0045582 | CD74 |
Positive regulation of lymphocyte differentiation | GO:0045621 | |
Positive regulation of phosphate metabolic process | GO:0045937 | |
Icosanoid biosynthetic process | GO:0046456 | |
Lymphocyte activation | GO:0046649 | |
Lymphocyte proliferation | GO:0046651 | |
Secretion | GO:0046903 | |
Positive regulation of biological process | GO:0048518 | |
Regulation of response to stimulus | GO:0048583 | |
Positive regulation of response to stimulus | GO:0048584 | |
Homeostasis of number of cells | GO:0048872 | |
Cytokine secretion | GO:0050663 | LCP2 LYN |
Regulation of lymphocyte proliferation | GO:0050670 | |
Positive regulation of lymphocyte proliferation | GO:0050671 | |
Regulation of immune response | GO:0050776 | AMICA1 FCGR2B LILRB2 |
Positive regulation of immune response | GO:0050778 | |
Regulation of behavior | GO:0050795 | |
Coagulation | GO:0050817 | |
Regulation of t cell activation | GO:0050863 | |
Regulation of cell activation | GO:0050865 | |
Positive regulation of cell activation | GO:0050867 | |
Positive regulation of t cell activation | GO:0050870 | CCL2 |
Regulation of body fluid levels | GO:0050878 | |
Response to stimulus | GO:0050896 | |
Leukocyte migration | GO:0050900 | AMICA1 CD74 FCER1G LYN |
Regulation of chemotaxis | GO:0050920 | |
Positive regulation of chemotaxis | GO:0050921 | |
Regulation of multicellular organismal process | GO:0051239 | |
Positive regulation of multicellular organismal process | GO:0051240 | |
Regulation of lymphocyte activation | GO:0051249 | |
Positive regulation of lymphocyte activation | GO:0051251 | |
Multi-organism process | GO:0051704 | |
Response to other organism | GO:0051707 | |
Nitric-oxide synthase biosynthetic process | GO:0051767 | |
Regulation of nitric-oxide synthase biosynthetic process | GO:0051769 | |
Positive regulation of nitric-oxide synthase biosynthetic process | GO:0051770 | CCL2 TLR2 |
Cell chemotaxis | GO:0060326 | |
Positive regulation of myeloid leukocyte cytokine production involved in immune response | GO:0061081 | |
Erk1 and erk2 cascade | GO:0070371 | |
Regulation of erk1 and erk2 cascade | GO:0070372 | LYN SYK |
Platelet aggregation | GO:0070527 | |
Leukocyte proliferation | GO:0070661 | |
Regulation of leukocyte proliferation | GO:0070663 | |
Positive regulation of leukocyte proliferation | GO:0070665 | |
Cellular response to chemical stimulus | GO:0070887 | |
Cellular response to biotic stimulus | GO:0071216 | |
Cellular response to molecule of bacterial origin | GO:0071219 | |
Cellular response to lipopolysaccharide | GO:0071222 | CCL2 LILRB2 |
Protein activation cascade | GO:0072376 | |
T cell migration | GO:0072678 | |
Regulation of response to stress | GO:0080134 | |
Regulation of monocyte chemotaxis | GO:0090025 | LYN |
Regulation of platelet aggregation | GO:0090330 | LYN SYK |
Dendritic cell differentiation | GO:0097028 | LYN |
|
Legend: Hanahan and Weinberg, Cell 2011 |