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 |
---|---|---|---|---|
71 | 413 | 0.55 (0.0E+00) |
3.28 (1.0E-03) |
Co-expression Survival |
Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
---|---|---|---|
2 | 12 | 102 | 2 |
Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
---|---|---|
Gravendeel, et al. 2009 | 0.51 (0.0E+00) | 2.63 (8.5E-03) |
Madhavan, et al. 2009 | 0.56 (0.0E+00) | 3.38 (7.3E-04) |
Murat, et al. 2008 | 0.44 (0.0E+00) | -1.38 (1.7E-01) |
Mutation | Regulator | Bicluster | ||
---|---|---|---|---|
DNAH5 | IKZF1 | TFBS_DB_326 | ||
EPHA2_FORWARD_SIGNALING | IRF1 | TFBS_DB_326 | ||
FGF_SIGNALING_PATHWAY | IRF1 | TFBS_DB_326 | ||
IL1_MEDIATED_SIGNALING_EVENTS | IRF1 | TFBS_DB_326 | ||
IL3_MEDIATED_SIGNALING_EVENTS | IRF1 | TFBS_DB_326 | ||
IL5_MEDIATED_SIGNALING_EVENTS | IRF1 | TFBS_DB_326 | ||
IL6_MEDIATED_SIGNALING_EVENTS | IRF1 | TFBS_DB_326 | ||
NONGENOTROPIC_ANDROGEN_SIGNALING | IRF1 | TFBS_DB_326 | ||
PLASMA_MEMBRANE_ESTROGEN_RECEPTOR_SIGNALING | IRF1 | TFBS_DB_326 | ||
REELIN_SIGNALING_PATHWAY | IRF1 | TFBS_DB_326 | ||
SIGNALING_EVENTS_REGULATED_BY_RET_TYROSINE_KINASE | IRF1 | TFBS_DB_326 | ||
VEGFR1_SPECIFIC_SIGNALS | IRF1 | TFBS_DB_326 |
GO Term | GO BP ID | Genes |
Cell activation | GO:0001775 | |
Cytokine production | GO:0001816 | |
Response to molecule of bacterial origin | GO:0002237 | |
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 | |
Immune system process | GO:0002376 | CD300LF |
Immune response-activating cell surface receptor signaling pathway | GO:0002429 | |
Leukocyte mediated immunity | GO:0002443 | |
Antigen processing and presentation of exogenous peptide antigen | GO:0002478 | |
Antigen processing and presentation of peptide antigen via mhc class ii | GO:0002495 | |
Antigen processing and presentation of peptide or polysaccharide antigen via mhc class ii | GO:0002504 | HLA-DRA |
Regulation of immune system process | GO:0002682 | |
Positive regulation of immune system process | GO:0002684 | |
Regulation of leukocyte activation | GO:0002694 | |
Immune response-activating signal transduction | GO:0002757 | |
Immune response-regulating signaling pathway | GO:0002764 | |
Immune response-regulating cell surface receptor signaling pathway | GO:0002768 | |
Response to stress | GO:0006950 | |
Defense response | GO:0006952 | CD74 CXCL9 |
Inflammatory response | GO:0006954 | CCR5 CXCL9 CYBB GBP5 HCK LGALS9 NCF1 NLRC4 SLC11A1 STAB1 TLR1 TLR2 TLR3 |
Immune response | GO:0006955 | ADAMDEC1 CCR5 CIITA CXCL9 HLA-DOA HLA-DPA1 HLA-DRA LCP2 TLR1 TLR2 TRIM22 |
Cellular defense response | GO:0006968 | CCR5 CXCL9 MNDA NCF1 NCF2 |
Detection of biotic stimulus | GO:0009595 | |
Response to biotic stimulus | GO:0009607 | |
Response to wounding | GO:0009611 | |
Response to bacterium | GO:0009617 | SLC11A1 |
Response to organic substance | GO:0010033 | |
Detection of bacterium | GO:0016045 | NLRC4 |
Cytokine-mediated signaling pathway | GO:0019221 | CIITA HCK HLA-DPA1 HLA-DRA TRIM22 UBE2L6 |
Antigen processing and presentation | GO:0019882 | |
Antigen processing and presentation of exogenous antigen | GO:0019884 | |
Antigen processing and presentation of exogenous peptide antigen via mhc class ii | GO:0019886 | CD74 FCER1G HLA-DMA HLA-DOA HLA-DPA1 HLA-DRA |
Lymphocyte costimulation | GO:0031294 | |
T cell costimulation | GO:0031295 | HLA-DPA1 HLA-DRA |
Positive regulation of defense response | GO:0031349 | |
Positive regulation of response to external stimulus | GO:0032103 | |
Response to lipopolysaccharide | GO:0032496 | CXCL9 EDNRA LGALS9 SLC11A1 |
Interleukin-6 production | GO:0032635 | |
Tumor necrosis factor production | GO:0032640 | |
Regulation of interleukin-6 production | GO:0032675 | |
Regulation of tumor necrosis factor production | GO:0032680 | |
Positive regulation of interleukin-6 production | GO:0032755 | FCER1G TLR2 TLR3 |
Response to cytokine stimulus | GO:0034097 | |
Response to interferon-gamma | GO:0034341 | CIITA SLC11A1 |
Modification of morphology or physiology of other organism | GO:0035821 | |
Macrophage activation | GO:0042116 | SLC11A1 TLR1 |
Response to chemical stimulus | GO:0042221 | |
Detection of bacterial lipoprotein | GO:0042494 | |
Detection of triacyl bacterial lipopeptide | GO:0042495 | TLR1 TLR2 |
Superoxide anion generation | GO:0042554 | CYBB NCF1 NCF2 |
Defense response to bacterium | GO:0042742 | FCER1G NLRC4 SLAMF8 SLC11A1 STAB1 TLR3 |
Leukocyte degranulation | GO:0043299 | HCK |
Modification by symbiont of host morphology or physiology | GO:0044003 | |
Symbiosis, encompassing mutualism through parasitism | GO:0044403 | |
Interspecies interaction between organisms | GO:0044419 | |
Positive thymic t cell selection | GO:0045059 | CD74 HLA-DMA |
Innate immune response | GO:0045087 | CYBB CYFIP1 FCER1G HCK LCP2 NCF1 NCF2 NLRC4 TLR1 TLR2 TLR3 TNFAIP8L2 TREM2 UBE2L6 |
Leukocyte activation | GO:0045321 | |
Respiratory burst | GO:0045730 | CYBB NCF1 NCF2 SLC11A1 |
Antigen processing and presentation of peptide antigen | GO:0048002 | SLC11A1 |
Positive regulation of response to stimulus | GO:0048584 | |
Positive regulation of inflammatory response | GO:0050729 | EDNRA TLR2 TLR3 |
Regulation of phagocytosis | GO:0050764 | HCK ITGAV |
Positive regulation of phagocytosis | GO:0050766 | FCER1G SLC11A1 |
Regulation of immune response | GO:0050776 | CD300LF TREM2 |
Positive regulation of immune response | GO:0050778 | HLA-DMA |
Antigen receptor-mediated signaling pathway | GO:0050851 | |
T cell receptor signaling pathway | GO:0050852 | HLA-DPA1 HLA-DRA LCP2 |
Chaperone mediated protein folding requiring cofactor | GO:0051085 | CD74 HLA-DMA |
Interaction with host | GO:0051701 | |
Multi-organism process | GO:0051704 | |
Response to other organism | GO:0051707 | |
Modification of morphology or physiology of other organism involved in symbiotic interaction | GO:0051817 | |
Modulation by symbiont of host defense response | GO:0052031 | |
Pathogen-associated molecular pattern dependent induction by symbiont of host innate immunity | GO:0052033 | |
Positive regulation by symbiont of host innate immunity | GO:0052166 | |
Modulation by symbiont of host innate immunity | GO:0052167 | |
Pathogen-associated molecular pattern dependent modulation by symbiont of host innate immunity | GO:0052169 | |
Modulation by organism of defense response of other organism involved in symbiotic interaction | GO:0052255 | |
Pathogen-associated molecular pattern dependent induction by organism of innate immunity of other organism involved in symbiotic interaction | GO:0052257 | |
Positive regulation by organism of innate immunity in other organism involved in symbiotic interaction | GO:0052305 | |
Modulation by organism of innate immunity in other organism involved in symbiotic interaction | GO:0052306 | |
Pathogen-associated molecular pattern dependent modulation by organism of innate immunity in other organism involved in symbiotic interaction | GO:0052308 | |
Positive regulation by symbiont of host defense response | GO:0052509 | |
Positive regulation by organism of defense response of other organism involved in symbiotic interaction | GO:0052510 | |
Modulation by organism of immune response of other organism involved in symbiotic interaction | GO:0052552 | |
Modulation by symbiont of host immune response | GO:0052553 | |
Positive regulation by organism of immune response of other organism involved in symbiotic interaction | GO:0052555 | |
Positive regulation by symbiont of host immune response | GO:0052556 | |
Interferon-gamma-mediated signaling pathway | GO:0060333 | CIITA HCK HLA-DPA1 HLA-DRA TRIM22 |
Detection of bacterial lipopeptide | GO:0070340 | |
Cellular response to chemical stimulus | GO:0070887 | |
Cellular response to molecule of bacterial origin | GO:0071219 | |
Cellular response to cytokine stimulus | GO:0071345 | |
Cellular response to interferon-gamma | GO:0071346 | GBP5 HLA-DPA1 LGALS9 TLR3 |
Tumor necrosis factor superfamily cytokine production | GO:0071706 | |
Response to triacyl bacterial lipopeptide | GO:0071725 | |
Cellular response to triacyl bacterial lipopeptide | GO:0071727 | TLR1 TLR2 |
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Legend:![]() Hanahan and Weinberg, Cell 2011 |