PITA_4
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 |
|---|---|---|---|---|
| 34 | 403 | 0.50 (0.0E+00) |
-1.08 (2.8E-01) | Co-expression Survival |
| Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
|---|---|---|---|
| 1 | 18 | 20 | 1 |
Replication in independent datasets
| Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
|---|---|---|
| Gravendeel, et al. 2009 | 0.17 (2.0E-01) | -2.57 (1.0E-02) |
| Madhavan, et al. 2009 | 0.19 (1.0E+00) | -1.63 (1.0E-01) |
| Murat, et al. 2008 | 0.23 (1.0E-03) | 0.30 (7.6E-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.02.0107
- 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.06.1805
- 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.08.0346
- 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.12.0654
- 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.12.0819
- 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.12.1099
- 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.14.1454
- TCGA.14.1456
- TCGA.14.1458
- TCGA.14.1459
- TCGA.14.1827
- 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.16.0849
- TCGA.16.0850
- TCGA.16.0861
- TCGA.16.1045
- TCGA.16.1047
- TCGA.16.1055
- TCGA.16.1060
- TCGA.16.1062
- TCGA.16.1063
- TCGA.19.0955
- TCGA.19.0957
- TCGA.19.0963
- TCGA.19.0964
- TCGA.19.1390
- TCGA.19.1392
- 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.26.1438
- 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.32.1982
- 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.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 |
|---|---|---|---|
| TF | NR2F1 | Activator | No |
Causal Flows
| Mutation | Regulator | Bicluster | ||
|---|---|---|---|---|
| EGF_RECEPTOR_SIGNALING_PATHWAY | NR2F1 | PITA_4 | ||
| EPHA2_FORWARD_SIGNALING | NR2F1 | PITA_4 | ||
| EPHRIN_B_REVERSE_SIGNALING | NR2F1 | PITA_4 | ||
| ERBB1_DOWNSTREAM_SIGNALING | NR2F1 | PITA_4 | ||
| FAS_SIGNALING_PATHWAY | NR2F1 | PITA_4 | ||
| GMCSF_MEDIATED_SIGNALING_EVENTS | NR2F1 | PITA_4 | ||
| IL1_MEDIATED_SIGNALING_EVENTS | NR2F1 | PITA_4 | ||
| IL3_MEDIATED_SIGNALING_EVENTS | NR2F1 | PITA_4 | ||
| IL5_MEDIATED_SIGNALING_EVENTS | NR2F1 | PITA_4 | ||
| INSULIN_PATHWAY | NR2F1 | PITA_4 | ||
| NEPHRIN_NEPH1_SIGNALING_IN_THE_KIDNEY_PODOCYTE | NR2F1 | PITA_4 | ||
| N_CADHERIN_SIGNALING_EVENTS | NR2F1 | PITA_4 | ||
| OSTEOPONTIN_MEDIATED_EVENTS | NR2F1 | PITA_4 | ||
| PLASMA_MEMBRANE_ESTROGEN_RECEPTOR_SIGNALING | NR2F1 | PITA_4 | ||
| SIGNALING_EVENTS_MEDIATED_BY_HEPATOCYTE_GROWTH_FACTOR_RECEPTOR | NR2F1 | PITA_4 | ||
| SIGNALING_EVENTS_MEDIATED_BY_VEGFR1_AND_VEGFR2 | NR2F1 | PITA_4 | ||
| SIGNALING_EVENTS_REGULATED_BY_RET_TYROSINE_KINASE | NR2F1 | PITA_4 | ||
| TRK_RECEPTOR_SIGNALING_MEDIATED_BY_PI3K_AND_PLC_GAMMA | NR2F1 | PITA_4 |
Enriched GO Biological Processes
| GO Term | GO BP ID | Genes |
| Microtubule cytoskeleton organization | GO:0000226 | CLASP1 |
| Mitotic prometaphase | GO:0000236 | |
| Microtubule bundle formation | GO:0001578 | CLASP1 CLIP1 NAV1 |
| Chromatin organization | GO:0006325 | EP300 MLL5 MYST4 SETD2 |
| Organelle organization | GO:0006996 | CLASP1 PCM1 |
| Cytoskeleton organization | GO:0007010 | |
| Microtubule-based process | GO:0007017 | |
| Cellular component organization | GO:0016043 | |
| Chromatin modification | GO:0016568 | CABIN1 CHD6 JMJD1C |
| Interkinetic nuclear migration | GO:0022027 | HOOK3 PCM1 |
| Regulation of organelle organization | GO:0033043 | |
| Microtubule anchoring | GO:0034453 | CLASP1 PCM1 |
| Protein localization to cytoskeleton | GO:0044380 | |
| Regulation of cellular process | GO:0050794 | |
| Chromosome organization | GO:0051276 | |
| Regulation of cytoskeleton organization | GO:0051493 | TAOK1 |
| Protein localization to centrosome | GO:0071539 | HOOK3 PCM1 |
| Cellular component organization or biogenesis | GO:0071840 | |
| Cellular component organization or biogenesis at cellular level | GO:0071841 | |
| Cellular component organization at cellular level | GO:0071842 |
Enriched Hallmarks of Cancer
|
Legend: Hanahan and Weinberg, Cell 2011 |
Genome instability and mutation