GBG logo LeFE Build:8 Genomics and Bioinformatics Group
Example Output
This example output shows the ensembles that differ between cell lines with either Wildtype or Mutant copies of p53. It was generated using LeFEMiner and the following inputs:
  • Step 1: File defining samples as WildType or Mutant available here.
  • Step 2: The signature file contains classification data
  • Step 3: Gene expression of 50 NCI60 cell lines available here.
  • Step 4: Gene Symbol
  • Step 5: GO Biological Process, GO Molecular Function, GO Cellular Compartment and MSigDB Curated Gene Sets.
  • Step 6: Gene ensembles from size 2 to 50.
Number of Genes:10101
Number of Categories Within Size Range:1004
Number of Samples:50
Gene Expression File:p53.gex
Signature File:p53.cls
Customer Category File:None
Identifier Type:geneSymbol
Category Size Range:2-50 genes
Signature File Interpretation:Categorical values (Classification)
Execution Time:2007-07-20 10:54:09

You can view rest of the results at: Results Archive

Help in understanding the table below can be found at the Understanding Your Results page.

Category Rank Category Name Category Size Median Category p-Value(see note) False Discovery Rate Original Category Order Top 5 most Important Genes with Importance Scores Importance Score Distribution (click to enlarge)
1 G2/M transition of mitotic cell cycle 28 0.0080 0.0 374
1. CDKN1A 1.497
2. CDKN2D 1.201
3. CDKN2A 0.277
4. GTF2H1 0.262
5. CHEK1 0.194
Thumbnail of results for the category 1. Click for larger image.
2 G1/S transition of mitotic cell cycle 37 0.01 0.0 375
1. CDKN1A 1.365
2. CDKN2D 1.09
3. PPP6C 0.436
4. GTF2H1 0.262
5. CHEK1 0.21
Thumbnail of results for the category 2. Click for larger image.
2 regulation of cyclin dependent protein kinase activity 24 0.01 0.0 594
1. CDKN1A 1.53
2. CDKN2D 1.24
3. GTF2H1 0.365
4. CDKN2A 0.21
5. CHEK1 0.17
Thumbnail of results for the category 3. Click for larger image.
4 tyrosine metabolism 5 0.011 0.0 743
1. DCT 0.989
2. HGD 0.819
3. FAH 0.228
4. TYR 0.221
5. HPD 0.032
Thumbnail of results for the category 4. Click for larger image.
5 interphase of mitotic cell cycle 50 0.0115 0.0 208
1. CDKN1A 1.216
2. CDKN2D 1.017
3. PPP6C 0.399
4. CHES1 0.326
5. GTF2H1 0.191
Thumbnail of results for the category 5. Click for larger image.
6 interphase 50 0.014 0.0 109
1. CDKN1A 1.237
2. CDKN2D 0.994
3. PPP6C 0.419
4. CHES1 0.303
5. GTF2H1 0.251
Thumbnail of results for the category 6. Click for larger image.
6 cell cycle arrest 37 0.014 0.0 215
1. CDKN1A 1.37
2. CDKN2D 1.088
3. RASSF1 0.344
4. CDKN2A 0.22
5. INHA 0.159
Thumbnail of results for the category 7. Click for larger image.
8 myoblast fusion 3 0.016 0.031 563
1. CACNA1H 1.215
2. KCNH1 1.077
3. ADAM12 -0.252
Thumbnail of results for the category 8. Click for larger image.
9 regulation of survival gene product activity 4 0.0275 0.056 854
1. BAX 2.687
2. HRK 0.661
3. BNIP3L 0.029
4. BCL2L1 -0.235
Thumbnail of results for the category 9. Click for larger image.
10 myogenesis 16 0.0295 0.075 330
1. MYOG 0.632
2. CACNA1H 0.613
3. KCNH1 0.521
4. CACNB2 0.413
5. MYL6 0.28
Thumbnail of results for the category 10. Click for larger image.
11 RNA modification 11 0.03 0.075 489
1. PARN 1.21
2. METTL1 1.047
3. AARS 0.056
4. RARS -0.04
5. SSB -0.052
Thumbnail of results for the category 11. Click for larger image.
12 negative regulation of phosphorylation 3 0.0335 0.083 731
1. PPP2R1B 0.909
2. INHA 0.795
3. INHBA 0.189
Thumbnail of results for the category 12. Click for larger image.
13 determination of left/right symmetry 3 0.0355 0.096 348
1. KIF3B 1.089
2. ZIC3 0.523
3. PITX2 0.038
Thumbnail of results for the category 13. Click for larger image.
14 inorganic anion transport 9 0.037 0.096 645
1. PML 0.804
2. SLC17A1 0.534
3. FXYD3 0.428
4. SLC26A4 0.302
5. SLC26A2 0.211
Thumbnail of results for the category 14. Click for larger image.
15 negative regulation of survival gene product activity 4 0.038 0.096 941
1. BAX 2.684
2. HRK 0.693
3. BNIP3L -0.13
4. BCL2L1 -0.218
Thumbnail of results for the category 15. Click for larger image.
16 determination of bilateral symmetry 3 0.0415 0.125 189
1. KIF3B 1.126
2. ZIC3 0.486
3. PITX2 -0.026
Thumbnail of results for the category 16. Click for larger image.
17 actin cytoskeleton organization and biogenesis 42 0.0425 0.132 590
1. WASPIP 0.711
2. EPB49 0.678
3. CFL1 0.56
4. ADRA2A 0.52
5. WASF1 0.306
Thumbnail of results for the category 17. Click for larger image.
18 female gamete generation 10 0.044 0.132 351
1. PARN 1.305
2. MAGOH 0.784
3. AXIN1 0.102
4. DMC1 0.039
5. TOB2 0.007
Thumbnail of results for the category 18. Click for larger image.
19 determination of symmetry 3 0.05 0.138 83
1. KIF3B 0.99
2. ZIC3 0.492
3. PITX2 -0.02
Thumbnail of results for the category 19. Click for larger image.
19 regulation of B-cell activation 3 0.05 0.138 837
1. IL4 0.867
2. INHA 0.55
3. INHBA 0.037
Thumbnail of results for the category 20. Click for larger image.
21 steroid biosynthesis 19 0.055 0.143 681
1. FDXR 0.971
2. SCP2 0.581
3. CYP19A1 0.499
4. CYP11A1 0.18
5. HSD11B2 0.042
Thumbnail of results for the category 21. Click for larger image.
22 JNK cascade 28 0.057 0.143 608
1. AMBP 0.936
2. DUSP9 0.742
3. MAP3K12 0.203
4. MAP3K10 0.177
5. ADORA2B 0.133
Thumbnail of results for the category 22. Click for larger image.
23 negative regulation of signal transduction 6 0.06 0.163 222
1. AMBP 1.541
2. PPP2R1B 0.583
3. FRZB -0.059
4. BRAP -0.062
5. SMURF1 -0.272
Thumbnail of results for the category 23. Click for larger image.
24 disaccharide metabolism 3 0.062 0.167 544
1. LALBA 1.625
2. TREH 0.157
3. IDUA -0.18
Thumbnail of results for the category 24. Click for larger image.
25 melanin metabolism 2 0.063 0.167 315
1. DCT 1.528
2. TYR 0.201
Thumbnail of results for the category 25. Click for larger image.
25 apoptotic mitochondrial changes 5 0.063 0.167 678
1. BAX 2.452
2. BBC3 0.536
3. BAK1 -0.145
4. BID -0.221
5. BCL2L1 -0.227
Thumbnail of results for the category 26. Click for larger image.
27 tyrosine catabolism 3 0.064 0.167 881
1. HGD 1.021
2. FAH 0.391
3. HPD 0.072
Thumbnail of results for the category 27. Click for larger image.
27 melanin biosynthesis from tyrosine 2 0.064 0.167 883
1. DCT 1.557
2. TYR 0.036
Thumbnail of results for the category 28. Click for larger image.
29 stress-activated protein kinase signaling pathway 28 0.066 0.167 223
1. AMBP 0.909
2. DUSP9 0.738
3. MAP3K12 0.17
4. MAP3K10 0.159
5. ADORA2B 0.082
Thumbnail of results for the category 29. Click for larger image.
30 Rho protein signal transduction 18 0.067 0.167 389
1. CFL1 0.829
2. ADRA2A 0.772
3. ARHGAP6 0.566
4. ARHGAP1 0.072
5. ARHGEF1 0.056
Thumbnail of results for the category 30. Click for larger image.
31 negative regulation of lymphocyte differentiation 3 0.068 0.167 934
1. INHA 0.692
2. SOCS5 0.617
3. INHBA 0.031
Thumbnail of results for the category 31. Click for larger image.
32 melanin biosynthesis 2 0.074 0.172 549
1. DCT 1.536
2. TYR 0.125
Thumbnail of results for the category 32. Click for larger image.
33 steroid metabolism 49 0.0745 0.172 478
1. FDXR 0.705
2. ELA3A 0.628
3. SCP2 0.352
4. IL4 0.299
5. CYP19A1 0.264
Thumbnail of results for the category 33. Click for larger image.
34 fertilization (sensu Metazoa) 18 0.08 0.2 349
1. AKAP3 0.777
2. AKAP4 0.747
3. SPAM1 0.296
4. TNP1 0.193
5. MST1R 0.087
Thumbnail of results for the category 34. Click for larger image.
34 steroid catabolism 3 0.08 0.2 697
1. CEL 0.767
2. UGT2B4 0.415
3. STS 0.087
Thumbnail of results for the category 35. Click for larger image.
36 actin filament-based process 47 0.083 0.215 363
1. WASPIP 0.668
2. CFL1 0.598
3. EPB49 0.595
4. ADRA2A 0.52
5. WASF1 0.246
Thumbnail of results for the category 36. Click for larger image.
37 drug metabolism 2 0.0845 0.224 156
1. BCHE 1.158
2. FPGS 0.141
Thumbnail of results for the category 37. Click for larger image.
37 sperm-egg recognition 2 0.0845 0.224 577
1. SPAM1 1.246
2. ZP2 0.005
Thumbnail of results for the category 38. Click for larger image.
39 neuromuscular junction development 3 0.085 0.224 562
1. CACNB2 0.647
2. COL4A4 0.353
3. NRD1 0.194
Thumbnail of results for the category 39. Click for larger image.
40 heterophilic cell adhesion 6 0.085 0.224 235
1. COLEC10 0.636
2. LGALS7 0.349
3. TNF 0.223
4. ITGB2 0.22
5. SYK 0.147
Thumbnail of results for the category 40. Click for larger image.
41 induction of apoptosis by extracellular signals 23 0.086 0.224 858
1. BAX 1.63
2. DAP 0.323
3. PTH 0.245
4. TNFRSF10B 0.223
5. FADD 0.181
Thumbnail of results for the category 41. Click for larger image.
42 anti-inflammatory response 2 0.088 0.224 129
1. AMBP 1.991
2. PROC -0.156
Thumbnail of results for the category 42. Click for larger image.
43 apoptotic program 30 0.09 0.224 473
1. BAX 1.534
2. BBC3 0.24
3. CASP8 0.176
4. COL4A3 0.134
5. PSEN2 0.125
Thumbnail of results for the category 43. Click for larger image.
44 base-excision repair, DNA ligation 2 0.0925 0.224 721
1. HMGB1 1.054
2. HMGB2 -0.019
Thumbnail of results for the category 44. Click for larger image.
45 clustering of voltage-gated sodium channels 2 0.096 0.224 568
1. NRCAM 1.339
2. AGRN -0.097
Thumbnail of results for the category 45. Click for larger image.
46 germ cell development 4 0.097 0.224 352
1. BAX 2.735
2. DEAF1 -0.046
3. DAZL -0.201
4. TPX2 -0.316
Thumbnail of results for the category 46. Click for larger image.
47 actin filament bundle formation 3 0.099 0.224 810
1. EPB49 1.538
2. FSCN2 0.006
3. FSCN1 -0.023
Thumbnail of results for the category 47. Click for larger image.
48 protein ubiquitination during ubiquitin-dependent protein catabolism 3 0.1 0.224 973
1. RNF11 0.844
2. UBE4B 0.592
3. SMURF1 -0.211
Thumbnail of results for the category 48. Click for larger image.
49 L-phenylalanine catabolism 2 0.101 0.224 882
1. HGD 1.123
2. GSTZ1 -0.032
Thumbnail of results for the category 49. Click for larger image.
50 fertilization 19 0.103 0.224 190
1. AKAP3 0.723
2. AKAP4 0.576
3. SPAM1 0.411
4. TNP1 0.204
5. MST1R 0.113
Thumbnail of results for the category 50. Click for larger image.
50 tubulin folding 7 0.103 0.224 812
1. RP2 1.181
2. ARL2 0.264
3. TBCC 0.188
4. TBCA -0.154
5. TBCD -0.189
Thumbnail of results for the category 51. Click for larger image.
52 response to bacteria 27 0.1055 0.224 257
1. LALBA 0.782
2. LY96 0.441
3. C5 0.266
4. CD1D 0.264
5. SLC11A1 0.259
Thumbnail of results for the category 52. Click for larger image.
53 beta-tubulin folding 5 0.1085 0.224 913
1. RP2 1.231
2. TBCC 0.24
3. TBCA -0.114
4. TBCE -0.142
5. TBCD -0.222
Thumbnail of results for the category 53. Click for larger image.
54 water transport 7 0.111 0.236 424
1. AQP8 0.911
2. AQP2 0.628
3. AQP1 0.165
4. AVP -0.034
5. AQP9 -0.102
Thumbnail of results for the category 54. Click for larger image.
54 acrosome reaction 2 0.111 0.236 579
1. AKAP3 1.687
2. ACR -0.239
Thumbnail of results for the category 55. Click for larger image.
56 Ras protein signal transduction 18 0.112 0.237 390
1. ADRA2A 0.768
2. RASSF1 0.467
3. PLCE1 0.416
4. IGF1 0.206
5. RASGRP1 0.11
Thumbnail of results for the category 56. Click for larger image.
57 induction of apoptosis by intracellular signals 9 0.115 0.246 857
1. CDKN1A 2.055
2. CUL1 0.25
3. TP53 0.24
4. CUL5 -0.024
5. CUL4A -0.058
Thumbnail of results for the category 57. Click for larger image.
58 anterograde axon cargo transport 3 0.118 0.259 826
1. KIF3B 0.828
2. KIF1A 0.388
3. KIF1B -0.208
Thumbnail of results for the category 58. Click for larger image.
59 defense response to bacteria 11 0.1185 0.259 440
1. LALBA 1.1
2. LY96 0.673
3. DMBT1 0.076
4. PFC 0.073
5. STAB1 0.066
Thumbnail of results for the category 59. Click for larger image.
60 negative regulation of enzyme activity 18 0.121 0.259 30
1. TARBP2 0.877
2. ADRA2A 0.732
3. CCR2 0.292
4. TP53 0.13
5. GNAI3 0.057
Thumbnail of results for the category 60. Click for larger image.
60 response to radiation 24 0.121 0.259 258
1. PPM1D 0.95
2. CLOCK 0.464
3. PDC 0.236
4. SMC1L1 0.219
5. ABCA4 0.192
Thumbnail of results for the category 61. Click for larger image.
62 negative regulation of cell differentiation 5 0.123 0.262 112
1. INHA 0.515
2. SOCS5 0.44
3. NOTCH4 0.141
4. INHBA 0.07
5. PF4 0.021
Thumbnail of results for the category 62. Click for larger image.
62 regulation of phosphate metabolism 8 0.123 0.262 517
1. INHA 0.575
2. PPP2R1B 0.57
3. ITGB2 0.226
4. GLMN 0.087
5. INHBA 0.026
Thumbnail of results for the category 63. Click for larger image.
64 monocarboxylic acid transport 9 0.1235 0.266 639
1. SLC16A4 1.002
2. SLC16A1 0.695
3. SLC16A2 0.437
4. AKR1C4 0.109
5. SLC16A5 0.008
Thumbnail of results for the category 64. Click for larger image.
65 DNA damage checkpoint 7 0.124 0.266 439
1. CHES1 0.87
2. CHEK1 0.429
3. RAD9A 0.109
4. CHEK2 0.053
5. HUS1 -0.168
Thumbnail of results for the category 65. Click for larger image.
66 chromosome segregation 12 0.126 0.269 36
1. KNTC2 0.879
2. SMC1L1 0.245
3. SMC4L1 0.199
4. PSEN2 0.183
5. RIOK3 0.059
Thumbnail of results for the category 66. Click for larger image.
67 antigen presentation, endogenous antigen 2 0.127 0.272 657
1. CD1D 1.018
2. TAP2 0.021
Thumbnail of results for the category 67. Click for larger image.
68 regulation of viral genome replication 5 0.128 0.272 99
1. TARBP2 1.257
2. TNIP1 0.157
3. IL8 -0.14
4. PPIA -0.342
5. CD28 -0.42
Thumbnail of results for the category 68. Click for larger image.
68 transmembrane receptor protein tyrosine phosphatase signaling pathway 6 0.128 0.272 402
1. PTPRS 0.665
2. PTPRF 0.602
3. PTPRD 0.319
4. PTN 0.242
5. PTPRU -0.119
Thumbnail of results for the category 69. Click for larger image.
68 glycine metabolism 5 0.128 0.272 747
1. BAAT 0.556
2. AMT 0.414
3. GCSH 0.195
4. GLDC 0.194
5. FPGS 0.14
Thumbnail of results for the category 70. Click for larger image.
68 glycine catabolism 3 0.128 0.272 884
1. AMT 0.613
2. GLDC 0.31
3. GCSH -0.022
Thumbnail of results for the category 71. Click for larger image.
72 respiratory gaseous exchange 12 0.129 0.272 56
1. SPAR 1.196
2. COX5B 0.233
3. CSF2RB 0.203
4. BPGM 0.043
5. EDNRA 0.014
Thumbnail of results for the category 72. Click for larger image.
73 gliogenesis 2 0.1295 0.272 334
1. SLIT2 1.15
2. AZU1 -0.322
Thumbnail of results for the category 73. Click for larger image.
74 inactivation of MAPK 8 0.13 0.272 609
1. DUSP9 1.214
2. PPP2R1B 0.402
3. DUSP8 -0.139
4. SPRED2 -0.155
5. RGS3 -0.162
Thumbnail of results for the category 74. Click for larger image.
75 neuronal cell recognition 2 0.131 0.272 237
1. SLIT2 0.965
2. OPCML 0.461
Thumbnail of results for the category 75. Click for larger image.
76 G2 phase 2 0.132 0.272 210
1. CHES1 1.208
2. KPNA2 -0.312
Thumbnail of results for the category 76. Click for larger image.
76 G2 phase of mitotic cell cycle 2 0.132 0.272 377
1. CHES1 1.191
2. KPNA2 -0.454
Thumbnail of results for the category 77. Click for larger image.
78 hemoglobin metabolism 2 0.133 0.272 537
1. INHA 0.963
2. INHBA 0.088
Thumbnail of results for the category 78. Click for larger image.
79 detection of bacteria 4 0.135 0.272 462
1. CD1D 0.727
2. TLR1 0.53
3. TLR6 -0.187
4. PGLYRP1 -0.259
Thumbnail of results for the category 79. Click for larger image.
79 L-phenylalanine metabolism 2 0.135 0.272 744
1. HGD 1.131
2. GSTZ1 -0.114
Thumbnail of results for the category 80. Click for larger image.
81 serine family amino acid catabolism 3 0.1365 0.272 745
1. AMT 0.465
2. GLDC 0.264
3. GCSH 0.237
Thumbnail of results for the category 81. Click for larger image.
82 regulation of RNA metabolism 2 0.138 0.272 353
1. CDC2L2 0.603
2. FUSIP1 0.386
Thumbnail of results for the category 82. Click for larger image.
83 fluid transport 7 0.139 0.272 245
1. AQP8 1.001
2. AQP2 0.564
3. AQP1 0.14
4. AVP -0.018
5. AQP9 -0.051
Thumbnail of results for the category 83. Click for larger image.
83 antigen presentation 2 0.139 0.272 448
1. CD1D 0.91
2. TAP2 0.035
Thumbnail of results for the category 84. Click for larger image.
85 tetrahydrobiopterin metabolism 2 0.1405 0.272 520
1. PTS 0.805
2. SPR -0.081
Thumbnail of results for the category 85. Click for larger image.
86 tRNA metabolism 11 0.141 0.272 490
1. METTL1 1.155
2. SARS 0.309
3. AARS 0.05
4. RARS -0.013
5. YARS -0.033
Thumbnail of results for the category 86. Click for larger image.
87 estrogen receptor signaling pathway 2 0.1415 0.272 606
1. ESR2 1.187
2. RBM9 -0.4
Thumbnail of results for the category 87. Click for larger image.
88 regulation of Wnt receptor signaling pathway 2 0.142 0.272 393
1. PPP2R1B 1
2. FRZB -0.026
Thumbnail of results for the category 88. Click for larger image.
89 positive regulation of viral genome replication 2 0.142 0.272 195
1. TARBP2 1.69
2. CD28 -0.55
Thumbnail of results for the category 89. Click for larger image.
90 coenzyme biosynthesis 2 0.1435 0.272 509
1. COQ7 0.485
2. FPGS 0.461
Thumbnail of results for the category 90. Click for larger image.
91 mitotic spindle checkpoint 2 0.145 0.272 813
1. TTK 0.971
2. BUB1 -0.153
Thumbnail of results for the category 91. Click for larger image.
92 protein secretion 12 0.146 0.272 61
1. SPAR 1.128
2. ACHE 0.179
3. CANX 0.162
4. GLMN 0.123
5. ARFGAP3 0.109
Thumbnail of results for the category 92. Click for larger image.
92 aromatic amino acid family catabolism 5 0.146 0.272 742
1. HGD 0.735
2. FAH 0.313
3. GSTZ1 0.143
4. HPD -0.031
5. INDO -0.382
Thumbnail of results for the category 93. Click for larger image.
94 regulation of protein amino acid phosphorylation 4 0.1465 0.272 732
1. PPP2R1B 0.932
2. ITGB2 0.447
3. CD80 -0.105
4. TDGF1 -0.399
Thumbnail of results for the category 94. Click for larger image.
95 negative regulation of protein kinase activity 5 0.147 0.274 191
1. TARBP2 1.269
2. PAK2 0.164
3. RB1 -0.137
4. SFN -0.27
5. YWHAH -0.341
Thumbnail of results for the category 95. Click for larger image.
96 aromatic compound biosynthesis 2 0.148 0.276 302
1. PTS 0.843
2. SPR -0.062
Thumbnail of results for the category 96. Click for larger image.
97 regulation of phosphorus metabolism 8 0.1495 0.276 294
1. PPP2R1B 0.547
2. INHA 0.392
3. ITGB2 0.165
4. GLMN 0.15
5. INHBA 0.071
Thumbnail of results for the category 97. Click for larger image.
98 aromatic compound metabolism 16 0.151 0.276 161
1. DCT 0.659
2. HGD 0.545
3. PTS 0.364
4. PAICS 0.216
5. FAH 0.057
Thumbnail of results for the category 98. Click for larger image.
98 regulation of peptidyl-tyrosine phosphorylation 4 0.151 0.276 967
1. PPP2R1B 0.809
2. ITGB2 0.378
3. CD80 -0.068
4. TDGF1 -0.442
Thumbnail of results for the category 99. Click for larger image.
100 sterol metabolism 17 0.1515 0.276 683
1. ELA3A 0.952
2. IL4 0.471
3. CEL 0.419
4. APOF 0.194
5. DHCR7 0.153
Thumbnail of results for the category 100. Click for larger image.

You can view rest of the results at: Results Archive

LeFE™ is a development of the Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology (LMP), Center for Cancer Research (CCR), National Cancer Institute (NCI). Please email us with any problems, questions or feedback on the tool.

Notice and Disclaimer