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 | 405 | 0.42 (0.0E+00) |
2.60 (9.4E-03) |
Co-expression Survival |
Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
---|---|---|---|
2 | 8 | 147 | 2 |
Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
---|---|---|
Gravendeel, et al. 2009 | 0.47 (0.0E+00) | 2.38 (1.8E-02) |
Madhavan, et al. 2009 | 0.50 (0.0E+00) | 2.00 (4.6E-02) |
Murat, et al. 2008 | 0.49 (0.0E+00) | -1.39 (1.7E-01) |
Mutation | Regulator | Bicluster | ||
---|---|---|---|---|
ATF_2_TRANSCRIPTION_FACTOR_NETWORK | IRF1 | PITA_150 | ||
DNAH5 | IKZF1 | PITA_150 | ||
EPHA2_FORWARD_SIGNALING | IRF1 | PITA_150 | ||
EPHRIN_B_REVERSE_SIGNALING | IRF1 | PITA_150 | ||
FGF_SIGNALING_PATHWAY | IRF1 | PITA_150 | ||
NEUROTROPHIC_FACTOR_MEDIATED_TRK_RECEPTOR_SIGNALING | IRF1 | PITA_150 | ||
SIGNALING_EVENTS_MEDIATED_BY_FOCAL_ADHESION_KINASE | IRF1 | PITA_150 | ||
SIGNALING_EVENTS_REGULATED_BY_RET_TYROSINE_KINASE | IRF1 | PITA_150 |
GO Term | GO BP ID | Genes |
Cell activation | GO:0001775 | |
Cytokine production | GO:0001816 | CD4 |
Regulation of cytokine production | GO:0001817 | |
Positive regulation of cytokine production | GO:0001819 | |
Activation of innate immune response | GO:0002218 | AIM2 |
Pattern recognition receptor signaling pathway | GO:0002221 | CLEC7A |
Response to molecule of bacterial origin | GO:0002237 | |
Response to molecule of fungal origin | GO:0002238 | TLR2 |
Adaptive immune response | GO:0002250 | CD4 LILRB2 SYK |
Immune effector process | GO:0002252 | |
Activation of immune response | GO:0002253 | |
Myeloid leukocyte activation | GO:0002274 | |
Immune system process | GO:0002376 | |
Immune response-activating cell surface receptor signaling pathway | GO:0002429 | |
Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | GO:0002460 | |
Monocyte chemotaxis | GO:0002548 | CCL13 CCL23 CCL7 FOLR2 |
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 | |
Positive regulation of immune effector process | GO:0002699 | |
Immune response-activating signal transduction | GO:0002757 | |
Innate immune response-activating signal transduction | GO:0002758 | |
Immune response-regulating signaling pathway | GO:0002764 | |
Immune response-regulating cell surface receptor signaling pathway | GO:0002768 | |
Leukotriene metabolic process | GO:0006691 | ALOX5AP |
Endocytosis | GO:0006897 | PSTPIP1 |
Phagocytosis | GO:0006909 | IRF8 |
Phagocytosis, recognition | GO:0006910 | CD36 CLEC7A |
Phagocytosis, engulfment | GO:0006911 | AIF1 FCER1G FCGR1A |
Response to stress | GO:0006950 | |
Defense response | GO:0006952 | HCP5 RNASE6 WAS |
Inflammatory response | GO:0006954 | AIF1 AIM2 CCL13 CCL23 CCL7 CLEC7A CXCL13 FOLR2 IL18 LY86 PSTPIP1 TLR2 TLR5 TLR7 |
Immune response | GO:0006955 | AIM2 CCL23 CD4 CXCL13 FCGR1A HLA-DRB5 IGKV1-5 IL18 IRF8 LILRB2 TLR2 WAS |
Response to external stimulus | GO:0009605 | |
Response to biotic stimulus | GO:0009607 | |
Response to wounding | GO:0009611 | CTSB |
Response to bacterium | GO:0009617 | |
Response to fungus | GO:0009620 | |
Membrane invagination | GO:0010324 | |
Cellular membrane organization | GO:0016044 | |
Vesicle-mediated transport | GO:0016192 | |
Leukotriene biosynthetic process | GO:0019370 | ALOX5AP SYK |
Antigen processing and presentation | GO:0019882 | |
Regulation of endocytosis | GO:0030100 | |
T cell differentiation | GO:0030217 | CD4 GIMAP1 |
Leukocyte chemotaxis | GO:0030595 | |
Regulation of defense response | GO:0031347 | |
Positive regulation of defense response | GO:0031349 | |
Regulation of response to external stimulus | GO:0032101 | |
Positive regulation of response to external stimulus | GO:0032103 | |
Response to bacterial lipoprotein | GO:0032493 | |
Response to lipopolysaccharide | GO:0032496 | CXCL13 |
Granulocyte macrophage colony-stimulating factor production | GO:0032604 | |
Interleukin-12 production | GO:0032615 | |
Interleukin-2 production | GO:0032623 | |
Interleukin-6 production | GO:0032635 | |
Interleukin-8 production | GO:0032637 | |
Tumor necrosis factor production | GO:0032640 | |
Regulation of granulocyte macrophage colony-stimulating factor production | GO:0032645 | |
Regulation of interleukin-12 production | GO:0032655 | |
Regulation of interleukin-6 production | GO:0032675 | |
Regulation of interleukin-8 production | GO:0032677 | |
Regulation of tumor necrosis factor production | GO:0032680 | |
Positive regulation of chemokine production | GO:0032722 | TLR2 TLR7 |
Positive regulation of interleukin-12 production | GO:0032735 | CD36 IRF8 TLR2 |
Positive regulation of interleukin-6 production | GO:0032755 | CD36 FCER1G LILRB2 TLR2 TLR7 |
Positive regulation of interleukin-8 production | GO:0032757 | TLR2 TLR5 TLR7 |
Positive regulation of tumor necrosis factor production | GO:0032760 | CD36 FCER1G TLR2 |
Regulation of localization | GO:0032879 | |
Regulation of superoxide anion generation | GO:0032928 | SYK |
Regulation of mononuclear cell proliferation | GO:0032944 | |
Positive regulation of mononuclear cell proliferation | GO:0032946 | |
Response to cytokine stimulus | GO:0034097 | CXCL16 |
Regulation of toll-like receptor signaling pathway | GO:0034121 | |
Positive regulation of toll-like receptor signaling pathway | GO:0034123 | PIK3AP1 TLR2 TLR5 |
Response to interferon-gamma | GO:0034341 | CXCL16 |
Regulation of cytokine biosynthetic process | GO:0042035 | |
Cytokine biosynthetic process | GO:0042089 | |
Interleukin-2 biosynthetic process | GO:0042094 | IL18 |
T cell proliferation | GO:0042098 | |
Positive regulation of t cell proliferation | GO:0042102 | AIF1 CD4 LILRB2 |
Cytokine metabolic process | GO:0042107 | |
Positive regulation of cytokine biosynthetic process | GO:0042108 | |
T cell activation | GO:0042110 | CD80 CLEC7A WAS |
Macrophage activation | GO:0042116 | |
Regulation of t cell proliferation | GO:0042129 | |
Granulocyte macrophage colony-stimulating factor biosynthetic process | GO:0042253 | IL18 |
Defense response to bacterium | GO:0042742 | CXCL13 FCER1G GNLY IRF8 SYK TLR5 |
Cellular alkene metabolic process | GO:0043449 | |
Alkene biosynthetic process | GO:0043450 | |
Positive regulation of interleukin-2 biosynthetic process | GO:0045086 | CD4 CD80 |
Innate immune response | GO:0045087 | AIM2 CD36 CD4 CD80 CLEC7A CTSB FCER1G FCGR1A IGKV1-5 LY86 PSTPIP1 SYK TLR2 TLR5 TLR7 WAS |
Regulation of innate immune response | GO:0045088 | |
Positive regulation of innate immune response | GO:0045089 | |
Leukocyte activation | GO:0045321 | |
Regulation of granulocyte macrophage colony-stimulating factor biosynthetic process | GO:0045423 | |
Positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process | GO:0045425 | CD80 SYK |
Alpha-beta t cell proliferation | GO:0046633 | |
Regulation of alpha-beta t cell activation | GO:0046634 | |
Positive regulation of alpha-beta t cell activation | GO:0046635 | |
Regulation of alpha-beta t cell proliferation | GO:0046640 | |
Positive regulation of alpha-beta t cell proliferation | GO:0046641 | CD80 SYK |
Lymphocyte activation | GO:0046649 | |
Lymphocyte chemotaxis | GO:0048247 | CCL13 CCL23 CCL7 |
Positive regulation of biological process | GO:0048518 | |
Regulation of response to stimulus | GO:0048583 | |
Positive regulation of response to stimulus | GO:0048584 | |
Regulation of lymphocyte proliferation | GO:0050670 | |
Positive regulation of lymphocyte proliferation | GO:0050671 | |
Regulation of inflammatory response | GO:0050727 | PIK3AP1 |
Positive regulation of inflammatory response | GO:0050729 | CCL13 CCL23 CCL7 IL18 TLR2 TLR7 |
Regulation of phagocytosis | GO:0050764 | SYK |
Positive regulation of phagocytosis | GO:0050766 | FCER1G |
Regulation of immune response | GO:0050776 | FCGR1A IGKV1-5 LILRB2 |
Positive regulation of immune response | GO:0050778 | |
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 | |
Leukocyte migration | GO:0050900 | FCER1G |
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 | |
Cell chemotaxis | GO:0060326 | |
Membrane organization | GO:0061024 | |
Positive regulation of myeloid leukocyte cytokine production involved in immune response | GO:0061081 | |
Response to bacterial lipopeptide | GO:0070339 | |
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 bacterial lipoprotein | GO:0071220 | |
Cellular response to bacterial lipopeptide | GO:0071221 | TLR2 |
Cellular response to lipopolysaccharide | GO:0071222 | CD36 CD80 CXCL16 IRF8 LILRB2 NR1H3 TLR5 |
Cellular response to interferon-gamma | GO:0071346 | AIF1 CCL13 CCL23 CCL7 |
Tumor necrosis factor superfamily cytokine production | GO:0071706 | |
Lymphocyte migration | GO:0072676 | |
Regulation of response to stress | GO:0080134 | |
Regulation of superoxide metabolic process | GO:0090322 | |
Regulation of lymphocyte migration | GO:2000401 | |
Positive regulation of lymphocyte migration | GO:2000403 | |
Regulation of t cell migration | GO:2000404 | |
Positive regulation of t cell migration | GO:2000406 | AIF1 |
|
Legend: Hanahan and Weinberg, Cell 2011 |