PITA_425
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 |
|---|---|---|---|---|
| 51 | 391 | 0.36 (0.0E+00) |
-2.75 (5.9E-03) |
Co-expression Survival |
| Regulators | Causal Flows | Enriched GO BPs | Enriched Hallmarks of Cancer |
|---|---|---|---|
| 0 | 0 | 43 | 1 |
Replication in independent datasets
| Study | FPC Var. Exp. (Perm. p-value) | Survival (p-value) |
|---|---|---|
| Gravendeel, et al. 2009 | 0.21 (3.0E-03) | -3.43 (6.1E-04) |
| Madhavan, et al. 2009 | 0.22 (8.7E-01) | 0.86 (3.9E-01) |
| Murat, et al. 2008 | 0.25 (0.0E+00) | 0.39 (6.9E-01) |
Genes
- AFAR3
- ANKRD15
- ARIH2
- ASAHL
- C11ORF17
- C19ORF7
- C3ORF19
- C4ORF8
- CREBBP
- DMPK
- EAF2
- EP300
- EPC1
- EPC2
- FAM120AOS
- FBXO46
- FOXO3
- GATAD2B
- GOSR1
- JMJD1C
- JMJD2B
- KCNAB3
- KIAA1267
- KLF12
- LOC100101267
- MCM3AP
- MED13L
- MLL5
- NCOA6
- PCBP4
- PPP1R10
- PTPMT1
- RAB3IP
- SETD2
- SGK269
- SPCS1
- STOM
- SYNPO2L
- TCF4
- TMEM126B
- TNRC6A
- TTMA
- TUG1
- ZNF133
- ZNF219
- ZNF292
- ZNF500
- ZNF573
- ZNF585A
- ZNF689
- ZNF704
Patients
- TCGA.02.0001
- TCGA.02.0003
- TCGA.02.0004
- TCGA.02.0006
- TCGA.02.0009
- TCGA.02.0010
- TCGA.02.0011
- 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.02.0115
- 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.06.0206
- 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.06.0673
- 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.06.1805
- 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.06.6695
- TCGA.06.6697
- TCGA.06.6698
- TCGA.06.6699
- TCGA.08.0244
- TCGA.08.0245
- TCGA.08.0246
- TCGA.08.0346
- TCGA.08.0347
- TCGA.08.0348
- 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.08.0623
- 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.12.1099
- 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.14.0867
- 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.14.1827
- 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.19.1387
- 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.19.5951
- 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.28.1746
- 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.32.1982
- TCGA.32.1986
- TCGA.32.1987
- TCGA.32.1991
- TCGA.32.2491
- TCGA.32.2494
- TCGA.32.2495
- TCGA.32.2615
- 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.76.6657
- TCGA.76.6660
- TCGA.76.6661
- TCGA.76.6664
- TCGA.81.5910
- TCGA.81.5911
- TCGA.87.5896
Regulators
| Type | Name | Action | Prior Knowledge |
|---|---|---|---|
Causal Flows
| Mutation | Regulator | Bicluster |
|---|
Enriched GO Biological Processes
| GO Term | GO BP ID | Genes |
| Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | GO:0006139 | |
| Chromatin organization | GO:0006325 | CREBBP EP300 EPC1 KIAA1267 MLL5 SETD2 |
| Transcription, dna-dependent | GO:0006351 | EPC1 EPC2 GATAD2B JMJD1C KLF12 MED13L MLL5 PPP1R10 ZNF133 ZNF219 ZNF500 ZNF573 ZNF585A ZNF689 |
| Regulation of transcription, dna-dependent | GO:0006355 | CREBBP EP300 JMJD1C SETD2 ZNF133 ZNF219 ZNF500 ZNF573 ZNF585A ZNF689 |
| N-terminal protein amino acid acetylation | GO:0006474 | |
| Biosynthetic process | GO:0009058 | |
| Macromolecule biosynthetic process | GO:0009059 | |
| Regulation of biosynthetic process | GO:0009889 | |
| Gene expression | GO:0010467 | CREBBP EP300 SPCS1 TNRC6A |
| Regulation of gene expression | GO:0010468 | |
| Regulation of macromolecule biosynthetic process | GO:0010556 | |
| Positive regulation of macromolecule biosynthetic process | GO:0010557 | |
| Positive regulation of gene expression | GO:0010628 | |
| Rna metabolic process | GO:0016070 | |
| Chromatin modification | GO:0016568 | EPC2 JMJD1C |
| Covalent chromatin modification | GO:0016569 | |
| Histone modification | GO:0016570 | |
| N-terminal peptidyl-lysine acetylation | GO:0018076 | CREBBP EP300 |
| Peptidyl-lysine modification | GO:0018205 | |
| Regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | GO:0019219 | |
| Regulation of cellular metabolic process | GO:0031323 | |
| Regulation of cellular biosynthetic process | GO:0031326 | |
| Positive regulation of cellular biosynthetic process | GO:0031328 | |
| N-terminal protein amino acid modification | GO:0031365 | |
| Rna biosynthetic process | GO:0032774 | |
| Cellular nitrogen compound metabolic process | GO:0034641 | |
| Cellular macromolecule biosynthetic process | GO:0034645 | |
| Macromolecule metabolic process | GO:0043170 | |
| Cellular biosynthetic process | GO:0044249 | |
| Cellular macromolecule metabolic process | GO:0044260 | |
| Positive regulation of transcription, dna-dependent | GO:0045893 | CREBBP EPC1 FOXO3 MLL5 NCOA6 TCF4 |
| Positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | GO:0045935 | |
| Positive regulation of transcription from rna polymerase ii promoter | GO:0045944 | CREBBP EAF2 EP300 EPC1 FOXO3 KLF12 NCOA6 TCF4 ZNF292 |
| Regulation of nitrogen compound metabolic process | GO:0051171 | |
| Positive regulation of nitrogen compound metabolic process | GO:0051173 | |
| Regulation of rna metabolic process | GO:0051252 | |
| Positive regulation of rna metabolic process | GO:0051254 | |
| Chromosome organization | GO:0051276 | |
| Regulation of macromolecule metabolic process | GO:0060255 | |
| Regulation of primary metabolic process | GO:0080090 | |
| Nucleic acid metabolic process | GO:0090304 | |
| Regulation of cellular macromolecule biosynthetic process | GO:2000112 | |
| Regulation of rna biosynthetic process | GO:2001141 |
Enriched Hallmarks of Cancer
|
Legend: Hanahan and Weinberg, Cell 2011 |
Genome instability and mutation