PITA_150

Bicluster Network Summary

Legend:
= Somatically mutated gene/pathway
= TF; = miRNA; (Regulator edges: = Activation; T = Repression)
= Bicluster
= Hallmark of Cancer

Summary

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.
GenesPatient TumorsFPC Var. Exp.
(Perm. p-value)
Survival
(p-value)
Independent Replication
71405
0.42 (0.0E+00)
2.60 (9.4E-03)
Co-expression
Survival
RegulatorsCausal FlowsEnriched GO BPsEnriched
Hallmarks of Cancer
281472

Replication in independent datasets

StudyFPC 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)

Patients

  • TCGA.02.0001
  • TCGA.02.0003
  • TCGA.02.0004
  • TCGA.02.0006
  • TCGA.02.0007
  • TCGA.02.0009
  • TCGA.02.0010
  • TCGA.02.0011
  • TCGA.02.0014
  • TCGA.02.0015
  • TCGA.02.0016
  • TCGA.02.0021
  • TCGA.02.0023
  • TCGA.02.0024
  • TCGA.02.0025
  • TCGA.02.0026
  • TCGA.02.0027
  • TCGA.02.0028
  • TCGA.02.0033
  • TCGA.02.0034
  • TCGA.02.0037
  • TCGA.02.0038
  • TCGA.02.0039
  • TCGA.02.0043
  • TCGA.02.0046
  • TCGA.02.0047
  • TCGA.02.0048
  • TCGA.02.0052
  • TCGA.02.0054
  • TCGA.02.0055
  • TCGA.02.0057
  • TCGA.02.0058
  • TCGA.02.0059
  • TCGA.02.0060
  • TCGA.02.0068
  • TCGA.02.0069
  • TCGA.02.0070
  • TCGA.02.0071
  • TCGA.02.0074
  • TCGA.02.0075
  • TCGA.02.0079
  • TCGA.02.0080
  • TCGA.02.0083
  • TCGA.02.0085
  • TCGA.02.0086
  • TCGA.02.0089
  • TCGA.02.0099
  • TCGA.02.0102
  • TCGA.02.0104
  • TCGA.02.0107
  • TCGA.02.0113
  • TCGA.02.0114
  • TCGA.02.0115
  • TCGA.02.0116
  • TCGA.02.0289
  • TCGA.02.0321
  • TCGA.02.0330
  • TCGA.02.0332
  • TCGA.02.0337
  • TCGA.02.0422
  • TCGA.02.0430
  • TCGA.02.0432
  • TCGA.02.0440
  • TCGA.02.0446
  • TCGA.02.2466
  • TCGA.02.2470
  • TCGA.02.2483
  • TCGA.02.2485
  • TCGA.02.2486
  • TCGA.06.0122
  • TCGA.06.0124
  • TCGA.06.0125
  • TCGA.06.0126
  • TCGA.06.0128
  • TCGA.06.0129
  • TCGA.06.0132
  • TCGA.06.0133
  • TCGA.06.0137
  • TCGA.06.0138
  • TCGA.06.0139
  • TCGA.06.0140
  • TCGA.06.0141
  • TCGA.06.0142
  • TCGA.06.0143
  • TCGA.06.0145
  • TCGA.06.0146
  • TCGA.06.0148
  • TCGA.06.0150
  • TCGA.06.0151
  • TCGA.06.0152
  • TCGA.06.0154
  • TCGA.06.0155
  • TCGA.06.0156
  • TCGA.06.0157
  • TCGA.06.0158
  • TCGA.06.0159
  • TCGA.06.0160
  • TCGA.06.0165
  • TCGA.06.0166
  • TCGA.06.0167
  • TCGA.06.0168
  • TCGA.06.0171
  • TCGA.06.0173
  • TCGA.06.0174
  • TCGA.06.0176
  • TCGA.06.0178
  • TCGA.06.0184
  • TCGA.06.0185
  • TCGA.06.0187
  • TCGA.06.0188
  • TCGA.06.0189
  • TCGA.06.0190
  • TCGA.06.0192
  • TCGA.06.0195
  • TCGA.06.0197
  • TCGA.06.0201
  • TCGA.06.0206
  • TCGA.06.0208
  • TCGA.06.0209
  • TCGA.06.0210
  • TCGA.06.0211
  • TCGA.06.0213
  • TCGA.06.0214
  • TCGA.06.0216
  • TCGA.06.0219
  • TCGA.06.0221
  • TCGA.06.0237
  • TCGA.06.0238
  • TCGA.06.0240
  • TCGA.06.0241
  • TCGA.06.0394
  • TCGA.06.0409
  • TCGA.06.0644
  • TCGA.06.0649
  • TCGA.06.0673
  • TCGA.06.0675
  • TCGA.06.0676
  • TCGA.06.0678
  • TCGA.06.0681
  • TCGA.06.0686
  • TCGA.06.0743
  • TCGA.06.0744
  • TCGA.06.0745
  • TCGA.06.0747
  • TCGA.06.0749
  • TCGA.06.0750
  • TCGA.06.0875
  • TCGA.06.0876
  • TCGA.06.0877
  • TCGA.06.0878
  • TCGA.06.0879
  • TCGA.06.0881
  • TCGA.06.0882
  • TCGA.06.1084
  • TCGA.06.1086
  • TCGA.06.1800
  • TCGA.06.1801
  • TCGA.06.1802
  • TCGA.06.1804
  • TCGA.06.1805
  • TCGA.06.2557
  • TCGA.06.2558
  • TCGA.06.2559
  • TCGA.06.2561
  • TCGA.06.2562
  • TCGA.06.2563
  • TCGA.06.2564
  • TCGA.06.2565
  • TCGA.06.2566
  • TCGA.06.2567
  • TCGA.06.2570
  • TCGA.06.5412
  • TCGA.06.5414
  • TCGA.06.5415
  • TCGA.06.5417
  • TCGA.06.5418
  • TCGA.06.5856
  • TCGA.06.5859
  • TCGA.06.6388
  • TCGA.06.6390
  • TCGA.06.6695
  • TCGA.06.6697
  • TCGA.06.6698
  • TCGA.06.6699
  • TCGA.06.6701
  • TCGA.08.0244
  • TCGA.08.0245
  • TCGA.08.0246
  • TCGA.08.0344
  • TCGA.08.0346
  • TCGA.08.0347
  • TCGA.08.0348
  • TCGA.08.0350
  • TCGA.08.0351
  • TCGA.08.0353
  • TCGA.08.0354
  • TCGA.08.0355
  • TCGA.08.0356
  • TCGA.08.0357
  • TCGA.08.0359
  • TCGA.08.0360
  • TCGA.08.0380
  • TCGA.08.0385
  • TCGA.08.0389
  • TCGA.08.0390
  • TCGA.08.0392
  • TCGA.08.0510
  • TCGA.08.0512
  • TCGA.08.0517
  • TCGA.08.0524
  • TCGA.08.0623
  • TCGA.08.0625
  • TCGA.08.0626
  • TCGA.08.0627
  • TCGA.12.0616
  • TCGA.12.0618
  • TCGA.12.0619
  • TCGA.12.0620
  • TCGA.12.0653
  • TCGA.12.0654
  • TCGA.12.0656
  • TCGA.12.0657
  • TCGA.12.0662
  • TCGA.12.0670
  • TCGA.12.0688
  • TCGA.12.0691
  • TCGA.12.0692
  • TCGA.12.0703
  • TCGA.12.0707
  • TCGA.12.0769
  • TCGA.12.0772
  • TCGA.12.0773
  • TCGA.12.0775
  • TCGA.12.0776
  • TCGA.12.0778
  • TCGA.12.0780
  • TCGA.12.0818
  • TCGA.12.0819
  • TCGA.12.0820
  • TCGA.12.0821
  • TCGA.12.0822
  • TCGA.12.0826
  • TCGA.12.0827
  • TCGA.12.0828
  • TCGA.12.0829
  • TCGA.12.1088
  • TCGA.12.1089
  • TCGA.12.1091
  • TCGA.12.1092
  • TCGA.12.1093
  • TCGA.12.1094
  • TCGA.12.1095
  • TCGA.12.1097
  • TCGA.12.1098
  • TCGA.12.1099
  • TCGA.12.1599
  • TCGA.12.1600
  • TCGA.12.1602
  • TCGA.12.3646
  • TCGA.12.3649
  • TCGA.12.5295
  • TCGA.14.0736
  • TCGA.14.0783
  • TCGA.14.0787
  • TCGA.14.0789
  • TCGA.14.0790
  • TCGA.14.0812
  • TCGA.14.0813
  • TCGA.14.0817
  • TCGA.14.0865
  • TCGA.14.0867
  • TCGA.14.1034
  • TCGA.14.1037
  • TCGA.14.1043
  • TCGA.14.1396
  • TCGA.14.1401
  • TCGA.14.1402
  • TCGA.14.1450
  • TCGA.14.1451
  • TCGA.14.1452
  • TCGA.14.1453
  • TCGA.14.1454
  • TCGA.14.1456
  • TCGA.14.1458
  • TCGA.14.1459
  • TCGA.14.1829
  • TCGA.14.2554
  • TCGA.14.3476
  • TCGA.14.4157
  • TCGA.15.0742
  • TCGA.15.1446
  • TCGA.15.1447
  • TCGA.15.1449
  • TCGA.16.0846
  • TCGA.16.0848
  • TCGA.16.0849
  • TCGA.16.0850
  • TCGA.16.0861
  • TCGA.16.1045
  • TCGA.16.1047
  • TCGA.16.1055
  • TCGA.16.1056
  • TCGA.16.1060
  • TCGA.16.1062
  • TCGA.16.1063
  • TCGA.19.0955
  • TCGA.19.0957
  • TCGA.19.0960
  • TCGA.19.0963
  • TCGA.19.0964
  • TCGA.19.1387
  • TCGA.19.1390
  • TCGA.19.1787
  • TCGA.19.1790
  • TCGA.19.1791
  • TCGA.19.2619
  • TCGA.19.2625
  • TCGA.19.2629
  • TCGA.19.2631
  • TCGA.19.5947
  • TCGA.19.5951
  • TCGA.19.5953
  • TCGA.19.5954
  • TCGA.19.5955
  • TCGA.19.5956
  • TCGA.19.5959
  • TCGA.26.1439
  • TCGA.26.1440
  • TCGA.26.1442
  • TCGA.26.1443
  • TCGA.26.5133
  • TCGA.26.5134
  • TCGA.26.5135
  • TCGA.26.5136
  • TCGA.26.5139
  • TCGA.26.6173
  • TCGA.27.1833
  • TCGA.27.1836
  • TCGA.27.1837
  • TCGA.27.1838
  • TCGA.27.2518
  • TCGA.27.2519
  • TCGA.27.2521
  • TCGA.27.2523
  • TCGA.27.2526
  • TCGA.27.2527
  • TCGA.27.2528
  • TCGA.28.1745
  • TCGA.28.1746
  • TCGA.28.1747
  • TCGA.28.1751
  • TCGA.28.1753
  • TCGA.28.1755
  • TCGA.28.1756
  • TCGA.28.2506
  • TCGA.28.2509
  • TCGA.28.2510
  • TCGA.28.2513
  • TCGA.28.2514
  • TCGA.28.5208
  • TCGA.28.5209
  • TCGA.28.5213
  • TCGA.28.5214
  • TCGA.28.5220
  • TCGA.28.6450
  • TCGA.32.1970
  • TCGA.32.1973
  • TCGA.32.1976
  • TCGA.32.1986
  • TCGA.32.1987
  • TCGA.32.1991
  • TCGA.32.2491
  • TCGA.32.2494
  • TCGA.32.2495
  • TCGA.32.2615
  • TCGA.32.4208
  • TCGA.32.4209
  • TCGA.32.4210
  • TCGA.32.4211
  • TCGA.32.4719
  • TCGA.41.2572
  • TCGA.41.2573
  • TCGA.41.2575
  • TCGA.41.3393
  • TCGA.41.3915
  • TCGA.41.4097
  • TCGA.41.5651
  • TCGA.74.6573
  • TCGA.74.6575
  • TCGA.74.6578
  • TCGA.76.4925
  • TCGA.76.4927
  • TCGA.76.4932
  • TCGA.76.4934
  • TCGA.76.4935
  • TCGA.76.6191
  • TCGA.76.6282
  • TCGA.76.6286
  • TCGA.76.6657
  • TCGA.76.6660
  • TCGA.76.6661
  • TCGA.76.6664
  • TCGA.81.5910
  • TCGA.81.5911
  • TCGA.87.5896

Regulators

TypeNameActionPrior Knowledge
TFIRF1
Activator
Yes
TFIKZF1
Activator
Yes

Causal Flows

MutationRegulatorBicluster
ATF_2_TRANSCRIPTION_FACTOR_NETWORKIRF1PITA_150
DNAH5IKZF1PITA_150
EPHA2_FORWARD_SIGNALINGIRF1PITA_150
EPHRIN_B_REVERSE_SIGNALINGIRF1PITA_150
FGF_SIGNALING_PATHWAYIRF1PITA_150
NEUROTROPHIC_FACTOR_MEDIATED_TRK_RECEPTOR_SIGNALINGIRF1PITA_150
SIGNALING_EVENTS_MEDIATED_BY_FOCAL_ADHESION_KINASEIRF1PITA_150
SIGNALING_EVENTS_REGULATED_BY_RET_TYROSINE_KINASEIRF1PITA_150

Enriched GO Biological Processes

GO TermGO BP IDGenes
Cell activationGO:0001775
Cytokine productionGO:0001816CD4
Regulation of cytokine productionGO:0001817
Positive regulation of cytokine productionGO:0001819
Activation of innate immune responseGO:0002218AIM2
Pattern recognition receptor signaling pathwayGO:0002221CLEC7A
Response to molecule of bacterial originGO:0002237
Response to molecule of fungal originGO:0002238TLR2
Adaptive immune responseGO:0002250CD4 LILRB2 SYK
Immune effector processGO:0002252
Activation of immune responseGO:0002253
Myeloid leukocyte activationGO:0002274
Immune system processGO:0002376
Immune response-activating cell surface receptor signaling pathwayGO:0002429
Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domainsGO:0002460
Monocyte chemotaxisGO:0002548CCL13 CCL23 CCL7 FOLR2
Regulation of immune system processGO:0002682
Positive regulation of immune system processGO:0002684
Regulation of leukocyte activationGO:0002694
Positive regulation of leukocyte activationGO:0002696
Positive regulation of immune effector processGO:0002699
Immune response-activating signal transductionGO:0002757
Innate immune response-activating signal transductionGO:0002758
Immune response-regulating signaling pathwayGO:0002764
Immune response-regulating cell surface receptor signaling pathwayGO:0002768
Leukotriene metabolic processGO:0006691ALOX5AP
EndocytosisGO:0006897PSTPIP1
PhagocytosisGO:0006909IRF8
Phagocytosis, recognitionGO:0006910CD36 CLEC7A
Phagocytosis, engulfmentGO:0006911AIF1 FCER1G FCGR1A
Response to stressGO:0006950
Defense responseGO:0006952HCP5 RNASE6 WAS
Inflammatory responseGO:0006954AIF1 AIM2 CCL13 CCL23 CCL7 CLEC7A CXCL13 FOLR2 IL18 LY86 PSTPIP1 TLR2 TLR5 TLR7
Immune responseGO:0006955AIM2 CCL23 CD4 CXCL13 FCGR1A HLA-DRB5 IGKV1-5 IL18 IRF8 LILRB2 TLR2 WAS
Response to external stimulusGO:0009605
Response to biotic stimulusGO:0009607
Response to woundingGO:0009611CTSB
Response to bacteriumGO:0009617
Response to fungusGO:0009620
Membrane invaginationGO:0010324
Cellular membrane organizationGO:0016044
Vesicle-mediated transportGO:0016192
Leukotriene biosynthetic processGO:0019370ALOX5AP SYK
Antigen processing and presentationGO:0019882
Regulation of endocytosisGO:0030100
T cell differentiationGO:0030217CD4 GIMAP1
Leukocyte chemotaxisGO:0030595
Regulation of defense responseGO:0031347
Positive regulation of defense responseGO:0031349
Regulation of response to external stimulusGO:0032101
Positive regulation of response to external stimulusGO:0032103
Response to bacterial lipoproteinGO:0032493
Response to lipopolysaccharideGO:0032496CXCL13
Granulocyte macrophage colony-stimulating factor productionGO:0032604
Interleukin-12 productionGO:0032615
Interleukin-2 productionGO:0032623
Interleukin-6 productionGO:0032635
Interleukin-8 productionGO:0032637
Tumor necrosis factor productionGO:0032640
Regulation of granulocyte macrophage colony-stimulating factor productionGO:0032645
Regulation of interleukin-12 productionGO:0032655
Regulation of interleukin-6 productionGO:0032675
Regulation of interleukin-8 productionGO:0032677
Regulation of tumor necrosis factor productionGO:0032680
Positive regulation of chemokine productionGO:0032722TLR2 TLR7
Positive regulation of interleukin-12 productionGO:0032735CD36 IRF8 TLR2
Positive regulation of interleukin-6 productionGO:0032755CD36 FCER1G LILRB2 TLR2 TLR7
Positive regulation of interleukin-8 productionGO:0032757TLR2 TLR5 TLR7
Positive regulation of tumor necrosis factor productionGO:0032760CD36 FCER1G TLR2
Regulation of localizationGO:0032879
Regulation of superoxide anion generationGO:0032928SYK
Regulation of mononuclear cell proliferationGO:0032944
Positive regulation of mononuclear cell proliferationGO:0032946
Response to cytokine stimulusGO:0034097CXCL16
Regulation of toll-like receptor signaling pathwayGO:0034121
Positive regulation of toll-like receptor signaling pathwayGO:0034123PIK3AP1 TLR2 TLR5
Response to interferon-gammaGO:0034341CXCL16
Regulation of cytokine biosynthetic processGO:0042035
Cytokine biosynthetic processGO:0042089
Interleukin-2 biosynthetic processGO:0042094IL18
T cell proliferationGO:0042098
Positive regulation of t cell proliferationGO:0042102AIF1 CD4 LILRB2
Cytokine metabolic processGO:0042107
Positive regulation of cytokine biosynthetic processGO:0042108
T cell activationGO:0042110CD80 CLEC7A WAS
Macrophage activationGO:0042116
Regulation of t cell proliferationGO:0042129
Granulocyte macrophage colony-stimulating factor biosynthetic processGO:0042253IL18
Defense response to bacteriumGO:0042742CXCL13 FCER1G GNLY IRF8 SYK TLR5
Cellular alkene metabolic processGO:0043449
Alkene biosynthetic processGO:0043450
Positive regulation of interleukin-2 biosynthetic processGO:0045086CD4 CD80
Innate immune responseGO:0045087AIM2 CD36 CD4 CD80 CLEC7A CTSB FCER1G FCGR1A IGKV1-5 LY86 PSTPIP1 SYK TLR2 TLR5 TLR7 WAS
Regulation of innate immune responseGO:0045088
Positive regulation of innate immune responseGO:0045089
Leukocyte activationGO:0045321
Regulation of granulocyte macrophage colony-stimulating factor biosynthetic processGO:0045423
Positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic processGO:0045425CD80 SYK
Alpha-beta t cell proliferationGO:0046633
Regulation of alpha-beta t cell activationGO:0046634
Positive regulation of alpha-beta t cell activationGO:0046635
Regulation of alpha-beta t cell proliferationGO:0046640
Positive regulation of alpha-beta t cell proliferationGO:0046641CD80 SYK
Lymphocyte activationGO:0046649
Lymphocyte chemotaxisGO:0048247CCL13 CCL23 CCL7
Positive regulation of biological processGO:0048518
Regulation of response to stimulusGO:0048583
Positive regulation of response to stimulusGO:0048584
Regulation of lymphocyte proliferationGO:0050670
Positive regulation of lymphocyte proliferationGO:0050671
Regulation of inflammatory responseGO:0050727PIK3AP1
Positive regulation of inflammatory responseGO:0050729CCL13 CCL23 CCL7 IL18 TLR2 TLR7
Regulation of phagocytosisGO:0050764SYK
Positive regulation of phagocytosisGO:0050766FCER1G
Regulation of immune responseGO:0050776FCGR1A IGKV1-5 LILRB2
Positive regulation of immune responseGO:0050778
Regulation of t cell activationGO:0050863CD4
Regulation of cell activationGO:0050865
Positive regulation of cell activationGO:0050867
Positive regulation of t cell activationGO:0050870
Leukocyte migrationGO:0050900FCER1G
Positive regulation of multicellular organismal processGO:0051240
Regulation of lymphocyte activationGO:0051249
Positive regulation of lymphocyte activationGO:0051251
Multi-organism processGO:0051704
Response to other organismGO:0051707
Cell chemotaxisGO:0060326
Membrane organizationGO:0061024
Positive regulation of myeloid leukocyte cytokine production involved in immune responseGO:0061081
Response to bacterial lipopeptideGO:0070339
Regulation of leukocyte proliferationGO:0070663
Positive regulation of leukocyte proliferationGO:0070665
Cellular response to chemical stimulusGO:0070887
Cellular response to biotic stimulusGO:0071216
Cellular response to molecule of bacterial originGO:0071219
Cellular response to bacterial lipoproteinGO:0071220
Cellular response to bacterial lipopeptideGO:0071221TLR2
Cellular response to lipopolysaccharideGO:0071222CD36 CD80 CXCL16 IRF8 LILRB2 NR1H3 TLR5
Cellular response to interferon-gammaGO:0071346AIF1 CCL13 CCL23 CCL7
Tumor necrosis factor superfamily cytokine productionGO:0071706
Lymphocyte migrationGO:0072676
Regulation of response to stressGO:0080134
Regulation of superoxide metabolic processGO:0090322
Regulation of lymphocyte migrationGO:2000401
Positive regulation of lymphocyte migrationGO:2000403
Regulation of t cell migrationGO:2000404
Positive regulation of t cell migrationGO:2000406AIF1

Enriched Hallmarks of Cancer

Enriched Hallmarks
  • Tumor promoting inflammation Tumor promoting inflammation
  • Evading immune detection Evading immune detection
Legend:
 
Hallmarks of Cancer
Hanahan and Weinberg, Cell 2011