TARGETSCAN_12
Bicluster Network Summary
Legend:
= Somatically mutated gene/pathway = TF; = miRNA; (Regulator edges: = Activation; T = Repression)
= Bicluster
= Hallmark of Cancer
= 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. |
| Genes | Patient Tumors | FPC Var. Exp. (Perm. p-value) | Survival (p-value) | Independent Replication |
|---|---|---|---|---|
| 32 | 406 | 0.60 (0.0E+00) |
3.61 (3.1E-04) |
Co-expression Survival |
| Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
|---|---|---|---|
| 2 | 3 | 50 | 2 |
Replication in independent datasets
| Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
|---|---|---|
| Gravendeel, et al. 2009 | 0.61 (0.0E+00) | 2.97 (3.0E-03) |
| Madhavan, et al. 2009 | 0.69 (0.0E+00) | 5.10 (3.5E-07) |
| Murat, et al. 2008 | 0.60 (0.0E+00) | 0.75 (4.5E-01) |
Genes
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.02.0051
- 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.06.0211
- 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.06.1805
- 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.08.0512
- 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.12.0828
- 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.14.1034
- 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.14.4157
- 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.19.5959
- 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.32.1986
- 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
| Type | Name | Action | Prior Knowledge |
|---|---|---|---|
| miRNA | hsa-mir-495 | Repressor | Yes |
| TF | IRF1 | Activator | Yes |
Causal Flows
| Mutation | Regulator | Bicluster | ||
|---|---|---|---|---|
| ATF_2_TRANSCRIPTION_FACTOR_NETWORK | IRF1 | TARGETSCAN_12 | ||
| NF1 | IRF1 | TARGETSCAN_12 | ||
| PIK3CA | IRF1 | TARGETSCAN_12 |
Enriched GO Biological Processes
| GO Term | GO BP ID | Genes |
| Immune effector process | GO:0002252 | |
| Immune system process | GO:0002376 | |
| Antigen processing and presentation of peptide antigen via mhc class i | GO:0002474 | B2M HLA-A HLA-B HLA-E HLA-F HLA-G TAP1 |
| Antigen processing and presentation of exogenous peptide antigen | GO:0002478 | |
| Antigen processing and presentation of exogenous peptide antigen via mhc class i, tap-dependent | GO:0002479 | B2M HLA-A HLA-B HLA-E HLA-F HLA-G TAP1 |
| Antigen processing and presentation of exogenous peptide antigen via mhc class i, tap-independent | GO:0002480 | B2M HLA-A HLA-B HLA-E HLA-F HLA-G |
| T cell tolerance induction | GO:0002517 | |
| Regulation of tolerance induction | GO:0002643 | |
| Regulation of t cell tolerance induction | GO:0002664 | |
| Regulation of immune system process | GO:0002682 | |
| Regulation of immune effector process | GO:0002697 | |
| Regulation of response to biotic stimulus | GO:0002831 | |
| Response to stress | GO:0006950 | |
| Defense response | GO:0006952 | HLA-B TAP1 |
| Immune response | GO:0006955 | HLA-A HLA-B |
| Cell surface receptor linked signaling pathway | GO:0007166 | |
| Response to biotic stimulus | GO:0009607 | |
| Response to virus | GO:0009615 | IFI44 IRF7 OAS3 |
| Response to organic substance | GO:0010033 | |
| Viral reproduction | GO:0016032 | B2M HLA-A HLA-B SP100 SP110 |
| Cytokine-mediated signaling pathway | GO:0019221 | B2M GBP1 HERC5 HLA-A HLA-B HLA-E HLA-F HLA-G IRF7 OAS3 SP100 TRIM21 |
| Antigen processing and presentation | GO:0019882 | HLA-A HLA-B HLA-G |
| Antigen processing and presentation of exogenous antigen | GO:0019884 | |
| Viral reproductive process | GO:0022415 | |
| Regulation of defense response | GO:0031347 | |
| Response to cytokine stimulus | GO:0034097 | SP100 |
| Response to type i interferon | GO:0034340 | SP100 |
| Response to interferon-gamma | GO:0034341 | SP100 TRIM21 |
| Response to chemical stimulus | GO:0042221 | |
| Antigen processing and presentation of exogenous peptide antigen via mhc class i | GO:0042590 | B2M HLA-A HLA-B HLA-E HLA-F HLA-G TAP1 |
| Interspecies interaction between organisms | GO:0044419 | |
| Innate immune response | GO:0045087 | B2M CASP1 HERC5 HLA-B HLA-E IRF7 TRIM21 |
| Antigen processing and presentation of peptide antigen | GO:0048002 | |
| Regulation of response to stimulus | GO:0048583 | |
| Regulation of defense response to virus | GO:0050688 | HERC5 |
| Regulation of immune response | GO:0050776 | B2M HLA-A HLA-B HLA-E HLA-F HLA-G IRF7 |
| Regulation of viral reproduction | GO:0050792 | |
| Defense response to virus | GO:0051607 | GBP1 GBP3 HERC5 OAS3 PLSCR1 |
| Multi-organism process | GO:0051704 | |
| Response to other organism | GO:0051707 | |
| Interferon-gamma-mediated signaling pathway | GO:0060333 | B2M GBP1 HLA-A HLA-B HLA-E HLA-F HLA-G IRF7 OAS3 SP100 TRIM21 |
| Type i interferon-mediated signaling pathway | GO:0060337 | HLA-A HLA-B HLA-E HLA-F HLA-G IRF7 OAS3 SP100 |
| Cellular response to chemical stimulus | GO:0070887 | |
| Cellular response to organic substance | GO:0071310 | CASP1 |
| Cellular response to cytokine stimulus | GO:0071345 | |
| Cellular response to interferon-gamma | GO:0071346 | |
| Cellular response to type i interferon | GO:0071357 | |
| Dendritic cell differentiation | GO:0097028 | |
| Negative regulation of reproductive process | GO:2000242 | |
| Regulation of dendritic cell differentiation | GO:2001198 | HLA-B |
Enriched Hallmarks of Cancer
|
Legend: Hanahan and Weinberg, Cell 2011 |
Tumor promoting inflammation
Evading immune detection