PITA_413

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
50416
0.65 (0.0E+00)
2.88 (4.0E-03)
Co-expression
Survival
RegulatorsCausal FlowsEnriched GO BPsEnriched
Hallmarks of Cancer
121014

Replication in independent datasets

StudyFPC 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)

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.02.0051
  • TCGA.02.0052
  • TCGA.02.0054
  • TCGA.02.0055
  • TCGA.02.0057
  • TCGA.02.0058
  • TCGA.02.0059
  • TCGA.02.0060
  • TCGA.02.0064
  • 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.06.0130
  • 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.06.0169
  • 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.06.0650
  • 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.06.1087
  • 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.06.2569
  • 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.12.1090
  • 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.14.0781
  • 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.14.0871
  • 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.14.1827
  • 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.19.1392
  • TCGA.19.1787
  • TCGA.19.1790
  • 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.26.1438
  • 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
TFELF1
Activator
Yes

Causal Flows

MutationRegulatorBicluster
NEUROTROPHIC_FACTOR_MEDIATED_TRK_RECEPTOR_SIGNALINGELF1PITA_413
SIGNALING_EVENTS_MEDIATED_BY_THE_HEDGEHOG_FAMILYELF1PITA_413

Enriched GO Biological Processes

GO TermGO BP IDGenes
Cell activationGO:0001775
Cytokine productionGO:0001816CD4 PTAFR
Regulation of cytokine productionGO:0001817
Adaptive immune responseGO:0002250BTLA CD4 CD84 LILRA3 LILRB1 LILRB4
Immune effector processGO:0002252
Activation of immune responseGO:0002253
Cell activation involved in immune responseGO:0002263
Myeloid leukocyte activationGO:0002274
Myeloid cell activation involved in immune responseGO:0002275
Leukocyte activation involved in immune responseGO:0002366
Cytokine production involved in immune responseGO:0002367
Cytokine secretion involved in immune responseGO:0002374
Immune system processGO:0002376
Immunoglobulin productionGO:0002377
Immune response-activating cell surface receptor signaling pathwayGO:0002429
Production of molecular mediator of immune responseGO:0002440
Leukocyte mediated immunityGO:0002443
Myeloid leukocyte mediated immunityGO:0002444
Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domainsGO:0002460
Antigen processing and presentation of peptide or polysaccharide antigen via mhc class iiGO:0002504
Regulation of immune system processGO:0002682
Positive regulation of immune system processGO:0002684
Regulation of leukocyte activationGO:0002694
Positive regulation of leukocyte activationGO:0002696
Regulation of immune effector processGO:0002697
Positive regulation of immune effector processGO:0002699
Regulation of production of molecular mediator of immune responseGO:0002700
Regulation of leukocyte mediated immunityGO:0002703
Regulation of cytokine production involved in immune responseGO:0002718
Regulation of cytokine secretion involved in immune responseGO:0002739
Negative regulation of cytokine secretion involved in immune responseGO:0002740IL10 LILRB1
Immune response-activating signal transductionGO:0002757
Immune response-regulating signaling pathwayGO:0002764
Immune response-regulating cell surface receptor signaling pathwayGO:0002768BTLA FGR
Regulation of adaptive immune responseGO:0002819
Regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domainsGO:0002822
Regulation of myeloid leukocyte mediated immunityGO:0002886
Response to stressGO:0006950
Defense responseGO:0006952CD84 CSF3R LILRA3
Inflammatory responseGO:0006954AOAH C3AR1 CCR5 IL10 NLRC4 PTAFR TLR5 TLR7
Immune responseGO:0006955CCR5 CD4 CMKLR1 HLA-DQA1 HLA-DQA2 HLA-DQB1 PTAFR
Signal transductionGO:0007165CD4 CSF3R LILRA3 LILRB1 LILRB4
Protein secretionGO:0009306
Response to external stimulusGO:0009605
Response to biotic stimulusGO:0009607
Response to woundingGO:0009611
Response to bacteriumGO:0009617
Calcium-mediated signalingGO:0019722CCR5 TREML1
SignalingGO:0023052CCR5
Leukocyte chemotaxisGO:0030595IL10
Negative regulation of b cell proliferationGO:0030889BTLA IL10 MNDA
Lymphocyte costimulationGO:0031294
T cell costimulationGO:0031295BTLA CD4 HLA-DQA1 HLA-DQA2 HLA-DQB1
Regulation of defense responseGO:0031347
Regulation of response to external stimulusGO:0032101
Interleukin-12 productionGO:0032615
Negative regulation of interleukin-12 productionGO:0032695CMKLR1 IL10
Negative regulation of mononuclear cell proliferationGO:0032945LILRB1
Response to interferon-gammaGO:0034341CXCL16
Regulation of cytokine biosynthetic processGO:0042035
Cytokine biosynthetic processGO:0042089
Cytokine metabolic processGO:0042107
T cell activationGO:0042110
Negative regulation of tumor necrosis factor biosynthetic processGO:0042536IL10 LILRB1
Leukocyte degranulationGO:0043299
Regulation of leukocyte degranulationGO:0043300
Symbiosis, encompassing mutualism through parasitismGO:0044403
Regulated secretory pathwayGO:0045055
Innate immune responseGO:0045087CD4 CD84 FCER1G FGR NLRC4 TLR5 TLR7 TREML1
Leukocyte activationGO:0045321
Interferon-alpha biosynthetic processGO:0045349
Regulation of interferon-alpha biosynthetic processGO:0045354
Lymphocyte activationGO:0046649
Positive regulation of biological processGO:0048518
Regulation of response to stimulusGO:0048583
Positive regulation of response to stimulusGO:0048584
Cytokine secretionGO:0050663
Negative regulation of lymphocyte proliferationGO:0050672
Regulation of immune responseGO:0050776HCST LILRB1 TREML1
Positive regulation of immune responseGO:0050778
Regulation of biological processGO:0050789
Regulation of calcium-mediated signalingGO:0050848CMKLR1
Antigen receptor-mediated signaling pathwayGO:0050851
T cell receptor signaling pathwayGO:0050852CD4 HLA-DQA1 HLA-DQA2 HLA-DQB1
Regulation of t cell activationGO:0050863CD4
Regulation of cell activationGO:0050865
Positive regulation of cell activationGO:0050867
Positive regulation of t cell activationGO:0050870
Response to stimulusGO:0050896
Leukocyte migrationGO:0050900CD84 FCER1G
Regulation of lymphocyte activationGO:0051249
Positive regulation of lymphocyte activationGO:0051251
Response to other organismGO:0051707
Cellular response to stimulusGO:0051716
Cell chemotaxisGO:0060326
Interferon-gamma-mediated signaling pathwayGO:0060333HLA-DQA1 HLA-DQA2 HLA-DQB1 PTAFR
Biological regulationGO:0065007
Negative regulation of leukocyte proliferationGO:0070664
Leukocyte apoptosisGO:0071887
Regulation of response to stressGO:0080134
Regulation of leukocyte apoptosisGO:2000106

Enriched Hallmarks of Cancer

Enriched Hallmarks
  • Tumor promoting inflammation Tumor promoting inflammation
  • Self sufficiency in growth signals Self sufficiency in growth signals
  • Evading immune detection Evading immune detection
  • Insensitivity to antigrowth signals Insensitivity to antigrowth signals
Legend:
 
Hallmarks of Cancer
Hanahan and Weinberg, Cell 2011