Example described in the paper 'A Novel Data-Driven Boolean Model for Genetic Regulatory Networks' (Chen, L., etc., 2018)
data(Common_Genes_Clusters)An object of class 'list';
Chen et al.(2018), Front. Physiol., 25 September 2018, (Front. Physiol.)
data(Common_Genes_Clusters)
Common_Genes_Clusters
#> $`Annotation Cluster 1`
#> Category Term Count %
#> 3 UP_KEYWORDS Cell cycle 72 25.26315789
#> 4 UP_KEYWORDS Mitosis 45 15.78947368
#> 5 UP_KEYWORDS Cell division 50 17.54385965
#> 6 GOTERM_BP_DIRECT GO:0051301~cell division 43 15.0877193
#> 7 GOTERM_BP_DIRECT GO:0007067~mitotic nuclear division 36 12.63157895
#> PValue
#> 3 3.02E-45
#> 4 6.15E-36
#> 5 6.21E-34
#> 6 5.50E-26
#> 7 3.93E-24
#> Genes
#> 3 157313, 6790, 4173, 4174, 4176, 11065, 9787, 1021, 1063, 259266, 1062, 990, 2305, 672, 991, 55165, 201161, 79733, 1058, 1894, 51203, 3832, 64151, 150094, 9232, 9833, 1033, 83937, 4739, 1104, 10628, 55215, 54962, 54443, 79723, 83461, 83540, 146909, 113130, 7803, 10592, 4751, 1163, 57082, 79075, 22974, 890, 891, 144455, 332, 699, 1111, 11004, 9212, 4085, 3070, 9133, 9134, 4288, 11130, 23397, 9493, 55355, 11339, 100526739, 387103, 983, 26586, 81620, 701, 8318, 8914
#> 4 157313, 6790, 10592, 11065, 4751, 259266, 1063, 1062, 57082, 22974, 890, 990, 891, 991, 332, 55165, 201161, 1058, 699, 51203, 3832, 11004, 64151, 9212, 4085, 3070, 9232, 9133, 11130, 23397, 9493, 11339, 4739, 100526739, 1104, 983, 387103, 54962, 54443, 701, 83461, 83540, 146909, 113130, 8914
#> 5 157313, 6790, 4174, 11065, 1021, 1063, 259266, 1062, 990, 991, 55165, 201161, 1058, 1894, 51203, 3832, 64151, 9232, 4739, 1104, 54962, 54443, 83461, 83540, 146909, 113130, 10592, 4751, 1163, 57082, 22974, 890, 891, 332, 699, 11004, 9212, 4085, 3070, 9133, 9134, 11130, 23397, 9493, 11339, 100526739, 387103, 983, 701, 8914
#> 6 157313, 6790, 4174, 10592, 11065, 4751, 1021, 1163, 1063, 1062, 57082, 22974, 890, 990, 891, 991, 332, 201161, 699, 3832, 11004, 64151, 4085, 3070, 9232, 9133, 9134, 11130, 23397, 11339, 4739, 100526739, 1104, 983, 387103, 54962, 701, 83461, 83540, 9928, 146909, 113130, 8914
#> 7 157313, 6790, 4751, 259266, 1063, 57082, 22974, 890, 990, 991, 332, 55165, 201161, 56992, 699, 3832, 11004, 9212, 3070, 9232, 9133, 55872, 11339, 4739, 100526739, 1104, 983, 387103, 54962, 54443, 701, 83461, 83540, 113130, 55839, 8914
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 3 270 650 20581 8.443487179 8.22E-43 8.22E-43 7.29E-43
#> 4 270 262 20581 13.09223919 1.67E-33 8.36E-34 7.41E-34
#> 5 270 388 20581 9.822928599 1.69E-31 5.63E-32 4.99E-32
#> 6 253 350 16792 8.154217956 8.79E-23 8.79E-23 8.51E-23
#> 7 253 248 16792 9.634578605 6.28E-21 3.14E-21 3.04E-21
#>
#> $`Annotation Cluster 2`
#> Category Term Count
#> 11 UP_KEYWORDS Chromosome 35
#> 12 UP_KEYWORDS Centromere 23
#> 13 UP_KEYWORDS Kinetochore 19
#> 14 GOTERM_BP_DIRECT GO:0007062~sister chromatid cohesion 20
#> 15 GOTERM_CC_DIRECT GO:0000777~condensed chromosome kinetochore 18
#> 16 GOTERM_CC_DIRECT GO:0000776~kinetochore 15
#> 17 GOTERM_BP_DIRECT GO:0034080~CENP-A containing nucleosome assembly 11
#> % PValue
#> 11 12.28070175 3.53E-18
#> 12 8.070175439 5.72E-18
#> 13 6.666666667 6.48E-16
#> 14 7.01754386 8.52E-16
#> 15 6.315789474 6.89E-15
#> 16 5.263157895 1.03E-11
#> 17 3.859649123 6.02E-10
#> Genes
#> 11 10592, 4751, 24137, 1063, 1062, 57082, 672, 332, 201161, 1058, 699, 51203, 11004, 64151, 9212, 4085, 4288, 11130, 23397, 64105, 64946, 79682, 11339, 55355, 100526739, 387103, 79723, 701, 83540, 121504, 113130, 55839, 51514, 10721, 2956
#> 12 9212, 4085, 4751, 11130, 64105, 1063, 1062, 64946, 57082, 79682, 11339, 55355, 332, 100526739, 201161, 387103, 1058, 699, 79723, 701, 83540, 11004, 55839
#> 13 4085, 4751, 11130, 64105, 1063, 1062, 64946, 57082, 79682, 332, 100526739, 201161, 387103, 1058, 699, 701, 83540, 11004, 55839
#> 14 9212, 4085, 11130, 64105, 1063, 1062, 64946, 57082, 79682, 81930, 991, 332, 100526739, 1058, 699, 701, 83540, 113130, 11004, 55839
#> 15 4085, 4751, 11130, 64105, 1062, 64946, 57082, 79682, 55355, 332, 100526739, 201161, 387103, 699, 701, 83540, 11004, 55839
#> 16 9212, 4085, 4751, 11130, 1063, 1062, 64946, 7272, 81930, 100526739, 201161, 387103, 699, 701, 11004
#> 17 55355, 11339, 100526739, 387103, 1058, 64105, 121504, 64946, 57082, 55839, 79682
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 11 270 400 20581 6.669768519 9.60E-16 1.92E-16 1.70E-16
#> 12 270 137 20581 12.79705326 1.56E-15 2.59E-16 2.30E-16
#> 13 270 99 20581 14.62921811 1.81E-13 2.20E-14 1.95E-14
#> 14 253 103 16792 12.88767796 1.42E-12 2.72E-13 2.64E-13
#> 15 266 87 18224 14.17474721 1.87E-12 9.36E-13 8.44E-13
#> 16 266 81 18224 12.68727374 2.79E-09 4.65E-10 4.19E-10
#> 17 253 43 16792 16.97876643 9.61E-07 1.20E-07 1.16E-07
#>
#> $`Annotation Cluster 3`
#> Category
#> 21 UP_SEQ_FEATURE
#> 22 UP_KEYWORDS
#> 23 UP_KEYWORDS
#> 24 GOTERM_MF_DIRECT
#> 25 INTERPRO
#> Term Count
#> 21 nucleotide phosphate-binding region:ATP 45
#> 22 ATP-binding 53
#> 23 Nucleotide-binding 59
#> 24 GO:0005524~ATP binding 56
#> 25 IPR027417:P-loop containing nucleoside triphosphate hydrolase 34
#> % PValue
#> 21 15.78947368 2.17E-12
#> 22 18.59649123 4.57E-12
#> 23 20.70175439 6.58E-11
#> 24 19.64912281 3.27E-10
#> 25 11.92982456 1.45E-07
#> Genes
#> 21 6790, 4173, 6196, 4174, 4176, 10592, 4751, 1660, 1021, 24137, 1062, 7083, 990, 81930, 10733, 26153, 29028, 2268, 56992, 699, 1111, 83990, 9319, 10112, 5634, 3832, 11004, 9212, 150094, 7153, 3070, 9833, 4288, 9493, 7272, 55872, 3707, 983, 701, 5888, 9928, 146909, 11213, 5208, 2956
#> 22 6790, 6196, 4173, 4174, 22836, 4176, 11065, 1660, 1021, 24137, 1062, 7083, 990, 81930, 10733, 26153, 29028, 2268, 83990, 3832, 150094, 9833, 3326, 146909, 2956, 10592, 4751, 123283, 29089, 56992, 699, 1111, 9319, 10112, 5634, 11004, 9212, 7153, 3070, 4288, 9493, 7272, 55872, 3707, 983, 10606, 701, 4830, 5888, 9928, 11213, 5208, 10721
#> 23 6790, 6196, 4173, 4174, 22836, 4176, 11065, 1660, 1021, 24137, 1062, 7083, 990, 81930, 115361, 10733, 26153, 29028, 2268, 83990, 3832, 150094, 9833, 11031, 3326, 146909, 2956, 10592, 4751, 123283, 29089, 55303, 56992, 699, 387751, 1111, 9319, 10112, 5634, 11004, 9212, 7153, 3070, 7277, 4288, 9493, 7272, 55872, 3707, 983, 10606, 168537, 701, 4830, 5888, 9928, 11213, 5208, 10721
#> 24 6790, 6196, 4173, 4174, 22836, 4176, 11065, 5026, 1660, 1021, 24137, 1062, 7083, 990, 81930, 10733, 26153, 29028, 2268, 83990, 3832, 150094, 9833, 3326, 10221, 146909, 2956, 10592, 4751, 123283, 22974, 29089, 56992, 699, 1111, 9319, 10112, 5634, 11004, 9212, 7153, 3070, 4288, 9493, 7272, 55872, 3707, 983, 10606, 701, 4830, 5888, 9928, 11213, 5208, 10721
#> 25 4173, 4174, 22836, 4176, 10592, 5983, 1660, 259266, 24137, 1062, 7083, 990, 81930, 115361, 26153, 29028, 55303, 56992, 387751, 83990, 9319, 10112, 3832, 11004, 3070, 11031, 9493, 168537, 5888, 9928, 146909, 5208, 10721, 2956
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 21 269 994 20063 3.376523079 2.07E-09 2.07E-09 2.07E-09
#> 22 270 1391 20581 2.904366696 1.24E-09 1.04E-10 9.19E-11
#> 23 270 1788 20581 2.515285028 1.79E-08 1.28E-09 1.13E-09
#> 24 255 1495 16881 2.479732441 1.37E-07 6.87E-08 6.66E-08
#> 25 255 879 18559 2.815168752 8.27E-05 2.76E-05 2.73E-05
#>
#> $`Annotation Cluster 4`
#> Category
#> 29 UP_SEQ_FEATURE
#> 30 INTERPRO
#> 31 SMART
#> 32 UP_KEYWORDS
#> 33 GOTERM_CC_DIRECT
#> 34 INTERPRO
#> 35 GOTERM_MF_DIRECT
#> 36 GOTERM_BP_DIRECT
#> 37 GOTERM_CC_DIRECT
#> 38 GOTERM_MF_DIRECT
#> 39 UP_KEYWORDS
#> 40 GOTERM_MF_DIRECT
#> 41 GOTERM_BP_DIRECT
#> 42 GOTERM_BP_DIRECT
#> 43 GOTERM_BP_DIRECT
#> 44 GOTERM_MF_DIRECT
#> Term
#> 29 domain:Kinesin-motor
#> 30 IPR001752:Kinesin, motor domain
#> 31 SM00129:KISc
#> 32 Microtubule
#> 33 GO:0005871~kinesin complex
#> 34 IPR019821:Kinesin, motor region, conserved site
#> 35 GO:0003777~microtubule motor activity
#> 36 GO:0007018~microtubule-based movement
#> 37 GO:0005874~microtubule
#> 38 GO:0008574~ATP-dependent microtubule motor activity, plus-end-directed
#> 39 Motor protein
#> 40 GO:0008017~microtubule binding
#> 41 GO:0019886~antigen processing and presentation of exogenous peptide antigen via MHC class II
#> 42 GO:0006890~retrograde vesicle-mediated transport, Golgi to ER
#> 43 GO:0007019~microtubule depolymerization
#> 44 GO:0016887~ATPase activity
#> Count % PValue
#> 29 11 3.859649123 2.54E-10
#> 30 11 3.859649123 4.05E-10
#> 31 11 3.859649123 1.29E-09
#> 32 19 6.666666667 3.30E-08
#> 33 10 3.50877193 6.43E-08
#> 34 9 3.157894737 7.13E-08
#> 35 11 3.859649123 3.26E-07
#> 36 11 3.859649123 3.58E-07
#> 37 18 6.315789474 3.28E-06
#> 38 6 2.105263158 3.96E-06
#> 39 11 3.859649123 1.16E-05
#> 40 14 4.912280702 1.66E-05
#> 41 9 3.157894737 7.23E-05
#> 42 8 2.807017544 2.30E-04
#> 43 4 1.403508772 3.71E-04
#> 44 11 3.859649123 4.62E-04
#> Genes
#> 29 81930, 26153, 56992, 10112, 24137, 1062, 9928, 3832, 146909, 11004, 9493
#> 30 81930, 26153, 56992, 10112, 24137, 1062, 9928, 3832, 146909, 11004, 9493
#> 31 81930, 26153, 56992, 10112, 24137, 1062, 9928, 3832, 146909, 11004, 9493
#> 32 6790, 7277, 4751, 24137, 1062, 22974, 9493, 81930, 26153, 332, 56992, 26586, 51203, 6645, 10112, 9928, 3832, 146909, 11004
#> 33 81930, 26153, 10112, 24137, 1062, 9928, 3832, 146909, 11004, 9493
#> 34 81930, 10112, 24137, 1062, 9928, 3832, 146909, 11004, 9493
#> 35 81930, 26153, 56992, 10112, 24137, 1062, 9928, 3832, 146909, 11004, 9493
#> 36 81930, 26153, 56992, 10112, 24137, 1062, 9928, 3832, 146909, 11004, 9493
#> 37 6790, 7277, 4751, 24137, 1062, 22974, 9493, 81930, 26153, 332, 56992, 51203, 6645, 10112, 9928, 3832, 146909, 11004
#> 38 81930, 26153, 24137, 9928, 3832, 146909
#> 39 81930, 26153, 56992, 10112, 24137, 1062, 9928, 3832, 146909, 11004, 9493
#> 40 6279, 24137, 1062, 9493, 10018, 81930, 26153, 332, 56992, 51203, 10112, 9928, 3832, 146909
#> 41 2207, 81930, 26153, 56992, 24137, 1062, 3832, 11004, 9493
#> 42 81930, 26153, 56992, 24137, 1062, 3832, 11004, 9493
#> 43 81930, 9928, 146909, 11004
#> 44 26153, 22836, 29028, 56992, 5983, 10112, 1062, 9928, 11004, 9493, 2956
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 29 269 44 20063 18.64591078 2.43E-07 1.21E-07
#> 30 255 45 18559 17.79076253 2.31E-07 2.31E-07
#> 31 158 45 10057 15.55935302 1.80E-07 1.80E-07
#> 32 270 280 20581 5.172473545 8.97E-06 5.98E-07
#> 33 266 53 18224 12.92665626 1.75E-05 1.59E-06
#> 34 255 41 18559 15.97618364 4.06E-05 2.03E-05
#> 35 255 80 16881 9.1025 1.37E-04 4.56E-05
#> 36 253 81 16792 9.013419216 5.71E-04 4.74E-05
#> 37 266 311 18224 3.965282982 8.92E-04 6.87E-05
#> 38 255 17 16881 23.36470588 0.001660766 4.16E-04
#> 39 270 135 20581 6.211001372 0.003139354 1.75E-04
#> 40 255 208 16881 4.455769231 0.006935668 0.001159962
#> 41 253 92 16792 6.49286819 0.109115064 0.004998805
#> 42 253 82 16792 6.475272342 0.307754903 0.010816849
#> 43 253 10 16792 26.5486166 0.447058322 0.016455359
#> 44 255 183 16881 3.979234973 0.176381298 0.018126691
#> FDR
#> 29 1.21E-07
#> 30 2.28E-07
#> 31 1.80E-07
#> 32 5.30E-07
#> 33 1.43E-06
#> 34 2.01E-05
#> 35 4.42E-05
#> 36 4.59E-05
#> 37 6.19E-05
#> 38 4.03E-04
#> 39 1.55E-04
#> 40 0.001124059
#> 41 0.004839268
#> 42 0.010471631
#> 43 0.015930188
#> 44 0.017565627
#>
#> $`Annotation Cluster 5`
#> Category Term Count % PValue
#> 48 UP_KEYWORDS DNA damage 20 7.01754386 2.14E-07
#> 49 GOTERM_BP_DIRECT GO:0006281~DNA repair 15 5.263157895 1.31E-05
#> 50 UP_KEYWORDS DNA repair 15 5.263157895 3.41E-05
#> Genes
#> 48 9232, 5111, 10635, 55388, 672, 2305, 29089, 144455, 100526739, 2237, 55215, 54962, 1111, 83990, 9768, 5888, 51514, 10721, 8914, 2956
#> 49 9232, 10635, 672, 2305, 29089, 100526739, 2237, 983, 55215, 1111, 5888, 5427, 10432, 10721, 2956
#> 50 9232, 5111, 10635, 672, 2305, 29089, 100526739, 2237, 55215, 1111, 83990, 9768, 5888, 10721, 2956
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 48 270 352 20581 4.331018519 5.81E-05 3.63E-06
#> 49 253 235 16792 4.236481372 0.020678081 0.001160818
#> 50 270 293 20581 3.902351157 0.009240603 4.89E-04
#> FDR
#> 48 3.22E-06
#> 49 0.001123771
#> 50 4.33E-04
#>
#> $`Annotation Cluster 6`
#> Category Term
#> 54 UP_KEYWORDS DNA replication
#> 55 GOTERM_BP_DIRECT GO:0006270~DNA replication initiation
#> 56 KEGG_PATHWAY hsa03030:DNA replication
#> 57 BIOCARTA h_mcmPathway:CDK Regulation of DNA Replication
#> 58 INTERPRO IPR018525:Mini-chromosome maintenance, conserved site
#> 59 GOTERM_CC_DIRECT GO:0000784~nuclear chromosome, telomeric region
#> 60 UP_SEQ_FEATURE domain:MCM
#> 61 INTERPRO IPR001208:Mini-chromosome maintenance, DNA-dependent ATPase
#> 62 GOTERM_CC_DIRECT GO:0042555~MCM complex
#> 63 SMART SM00350:MCM
#> 64 UP_KEYWORDS Helicase
#> 65 GOTERM_MF_DIRECT GO:0003678~DNA helicase activity
#> 66 INTERPRO IPR012340:Nucleic acid-binding, OB-fold
#> Count % PValue
#> 54 17 5.964912281 8.56E-14
#> 55 8 2.807017544 3.85E-07
#> 56 7 2.456140351 2.87E-05
#> 57 5 1.754385965 0.001397566
#> 58 3 1.052631579 0.002698904
#> 59 8 2.807017544 0.002942532
#> 60 3 1.052631579 0.004720197
#> 61 3 1.052631579 0.00630399
#> 62 3 1.052631579 0.007089241
#> 63 3 1.052631579 0.00811233
#> 64 6 2.105263158 0.039937009
#> 65 3 1.052631579 0.050090993
#> 66 3 1.052631579 0.284195761
#> Genes
#> 54 6241, 4173, 4174, 4176, 5111, 5983, 116028, 79075, 55388, 990, 2237, 81620, 8318, 9837, 5427, 51514, 51659
#> 55 55388, 990, 4173, 4174, 9134, 4176, 8318, 5427
#> 56 4173, 4174, 2237, 4176, 5111, 5983, 5427
#> 57 990, 4173, 4174, 4176, 81620
#> 58 4173, 4174, 4176
#> 59 4173, 4174, 2237, 4176, 983, 5111, 5888, 121504
#> 60 4173, 4174, 4176
#> 61 4173, 4174, 4176
#> 62 4173, 4174, 4176
#> 63 4173, 4174, 4176
#> 64 4173, 3070, 4174, 4176, 83990, 1660
#> 65 4173, 4174, 4176
#> 66 4173, 4174, 4176
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 54 270 94 20581 13.7855398 2.33E-11 2.12E-12
#> 55 253 32 16792 16.59288538 6.16E-04 4.74E-05
#> 56 119 36 6879 11.24019608 0.00466586 0.001558904
#> 57 48 18 1625 9.403935185 0.126859448 0.135563919
#> 58 255 6 18559 36.39019608 0.785716388 0.191702812
#> 59 266 130 18224 4.216078658 0.551366261 0.032014743
#> 60 269 8 20063 27.96886617 0.988990513 0.562883509
#> 61 255 9 18559 24.26013072 0.972802989 0.326661307
#> 62 266 9 18224 22.83709273 0.855596107 0.068866915
#> 63 158 9 10057 21.21729958 0.680295459 0.283931565
#> 64 270 143 20581 3.198290598 0.999984671 0.271571663
#> 65 255 24 16881 8.275 1 0.725455766
#> 66 255 77 18559 2.835599694 1 1
#> FDR
#> 54 1.88E-12
#> 55 4.59E-05
#> 56 0.001511085
#> 57 0.132768787
#> 58 0.189684887
#> 59 0.028836809
#> 60 0.561703459
#> 61 0.323222767
#> 62 0.062030861
#> 63 0.283931565
#> 64 0.240620481
#> 65 0.703001183
#> 66 0.991212654
#>
#> $`Annotation Cluster 7`
#> Category Term Count %
#> 70 INTERPRO IPR004367:Cyclin, C-terminal domain 5 1.754385965
#> 71 SMART SM01332:SM01332 5 1.754385965
#> 72 INTERPRO IPR006671:Cyclin, N-terminal 5 1.754385965
#> 73 UP_KEYWORDS Cyclin 5 1.754385965
#> 74 SMART SM00385:CYCLIN 5 1.754385965
#> 75 INTERPRO IPR013763:Cyclin-like 5 1.754385965
#> PValue Genes List Total Pop Hits Pop Total
#> 70 9.01E-05 891, 57018, 9133, 9134, 890 255 18 18559
#> 71 1.47E-04 891, 57018, 9133, 9134, 890 158 18 10057
#> 72 0.001150566 891, 57018, 9133, 9134, 890 255 34 18559
#> 73 0.001801685 891, 57018, 9133, 9134, 890 270 40 20581
#> 74 0.002282201 891, 57018, 9133, 9134, 890 158 36 10057
#> 75 0.003026886 891, 57018, 9133, 9134, 890 255 44 18559
#> Fold Enrichment Bonferroni Benjamini FDR
#> 70 20.2167756 0.050088956 0.012846155 0.012710932
#> 71 17.68108298 0.020436091 0.010323137 0.010323137
#> 72 10.70299885 0.481181063 0.109303792 0.108153226
#> 73 9.528240741 0.387680062 0.017186149 0.015227434
#> 74 8.840541491 0.273758966 0.106502723 0.106502723
#> 75 8.270499109 0.822350322 0.191702812 0.189684887
#>
#> $`Annotation Cluster 8`
#> Category Term Count
#> 79 GOTERM_BP_DIRECT GO:0007076~mitotic chromosome condensation 5
#> 80 GOTERM_CC_DIRECT GO:0000796~condensin complex 3
#> 81 UP_KEYWORDS DNA condensation 3
#> % PValue Genes List Total
#> 79 1.754385965 5.94E-05 10592, 51203, 23397, 113130, 64151 253
#> 80 1.052631579 0.002046463 10592, 23397, 64151 266
#> 81 1.052631579 0.01396395 10592, 23397, 64151 270
#> Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 79 15 16792 22.12384717 0.090486674 0.004311037 0.004173451
#> 80 5 18224 41.10676692 0.427194091 0.024201652 0.021799282
#> 81 14 20581 16.33412698 0.97818075 0.105505397 0.093480885
#>
#> $`Annotation Cluster 9`
#> Category
#> 85 GOTERM_BP_DIRECT
#> 86 GOTERM_BP_DIRECT
#> 87 KEGG_PATHWAY
#> 88 UP_KEYWORDS
#> 89 GOTERM_BP_DIRECT
#> Term Count
#> 85 GO:0000731~DNA synthesis involved in DNA repair 6
#> 86 GO:0000732~strand displacement 5
#> 87 hsa03460:Fanconi anemia pathway 6
#> 88 DNA recombination 6
#> 89 GO:0000724~double-strand break repair via homologous recombination 5
#> % PValue Genes List Total
#> 85 2.105263158 1.64E-04 10635, 672, 5983, 83990, 116028, 5888 253
#> 86 1.754385965 5.71E-04 10635, 672, 83990, 116028, 5888 253
#> 87 2.105263158 0.002029646 672, 29089, 55215, 83990, 116028, 5888 119
#> 88 2.105263158 0.00419786 10635, 672, 5896, 5897, 5888, 84057 270
#> 89 1.754385965 0.025148755 10635, 672, 2237, 5888, 10721 253
#> Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 85 35 16792 11.37797854 0.231003813 0.009056817 0.008767769
#> 86 26 16792 12.76375798 0.59850689 0.02280761 0.022079707
#> 87 53 6879 6.544157286 0.28191581 0.047482463 0.046025946
#> 88 81 20581 5.646364883 0.681528174 0.035681811 0.031615134
#> 89 74 16792 4.484563615 1 0.427528834 0.413884297
#>
#> $`Annotation Cluster 10`
#> Category
#> 93 GOTERM_BP_DIRECT
#> 94 KEGG_PATHWAY
#> 95 GOTERM_BP_DIRECT
#> 96 GOTERM_BP_DIRECT
#> 97 GOTERM_BP_DIRECT
#> 98 GOTERM_BP_DIRECT
#> 99 GOTERM_CC_DIRECT
#> 100 GOTERM_BP_DIRECT
#> Term
#> 93 GO:0031145~anaphase-promoting complex-dependent catabolic process
#> 94 hsa04114:Oocyte meiosis
#> 95 GO:0042787~protein ubiquitination involved in ubiquitin-dependent protein catabolic process
#> 96 GO:0051436~negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle
#> 97 GO:0051439~regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle
#> 98 GO:0051437~positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition
#> 99 GO:0005680~anaphase-promoting complex
#> 100 GO:0043161~proteasome-mediated ubiquitin-dependent protein catabolic process
#> Count % PValue
#> 93 10 3.50877193 2.76E-06
#> 94 10 3.50877193 1.10E-04
#> 95 10 3.50877193 5.11E-04
#> 96 6 2.105263158 0.004257465
#> 97 4 1.403508772 0.00473706
#> 98 6 2.105263158 0.005687913
#> 99 3 1.052631579 0.043609458
#> 100 6 2.105263158 0.190354677
#> Genes List Total Pop Hits
#> 93 891, 9212, 4085, 6790, 991, 9232, 983, 11065, 6502, 701 253 79
#> 94 891, 6196, 4085, 6790, 991, 9232, 9133, 9134, 983, 699 119 111
#> 95 891, 9212, 4085, 6790, 991, 9232, 983, 11065, 701, 4193 253 153
#> 96 891, 4085, 991, 983, 11065, 701 253 71
#> 97 891, 991, 983, 11065 253 23
#> 98 891, 4085, 991, 983, 11065, 701 253 76
#> 99 991, 11065, 701 266 23
#> 100 4085, 991, 983, 11065, 701, 9928 253 203
#> Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 93 16792 8.40146095 0.004399379 2.94E-04 2.85E-04
#> 94 6879 5.207812855 0.01783808 0.004499526 0.004361503
#> 95 16792 4.338009248 0.558194499 0.02094043 0.020272119
#> 96 16792 5.608862662 0.998906042 0.119358398 0.115549087
#> 97 16792 11.54287678 0.99949341 0.12616369 0.12213719
#> 98 16792 5.23985854 0.999890022 0.149004666 0.144249198
#> 99 18224 8.936253678 0.999994595 0.289311526 0.260593102
#> 100 16792 1.961720438 1 1 0.968691296
#>
#> $`Annotation Cluster 11`
#> Category Term Count %
#> 104 UP_KEYWORDS Fanconi anemia 4 1.403508772
#> 105 KEGG_PATHWAY hsa03460:Fanconi anemia pathway 6 2.105263158
#> 106 GOTERM_BP_DIRECT GO:0036297~interstrand cross-link repair 5 1.754385965
#> PValue Genes List Total Pop Hits
#> 104 0.001832347 29089, 100526739, 55215, 83990 270 19
#> 105 0.002029646 672, 29089, 55215, 83990, 116028, 5888 119 53
#> 106 0.006181815 10635, 29089, 100526739, 55215, 5888 253 49
#> Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 104 20581 16.04756335 0.392774774 0.017186149 0.015227434
#> 105 6879 6.544157286 0.28191581 0.047482463 0.046025946
#> 106 16792 6.772606276 0.999950285 0.156802228 0.151797901
#>
#> $`Annotation Cluster 12`
#> Category Term
#> 110 UP_SEQ_FEATURE binding site:ATP
#> 111 UP_KEYWORDS Kinase
#> 112 UP_KEYWORDS Serine/threonine-protein kinase
#> 113 INTERPRO IPR000719:Protein kinase, catalytic domain
#> 114 UP_KEYWORDS Transferase
#> 115 UP_SEQ_FEATURE domain:Protein kinase
#> 116 INTERPRO IPR011009:Protein kinase-like domain
#> 117 INTERPRO IPR008271:Serine/threonine-protein kinase, active site
#> 118 GOTERM_MF_DIRECT GO:0004674~protein serine/threonine kinase activity
#> 119 SMART SM00220:S_TKc
#> 120 GOTERM_BP_DIRECT GO:0046777~protein autophosphorylation
#> 121 INTERPRO IPR017441:Protein kinase, ATP binding site
#> 122 GOTERM_BP_DIRECT GO:0006468~protein phosphorylation
#> 123 GOTERM_MF_DIRECT GO:0004672~protein kinase activity
#> 124 UP_SEQ_FEATURE active site:Proton acceptor
#> Count % PValue
#> 110 21 7.368421053 6.61E-05
#> 111 24 8.421052632 1.07E-04
#> 112 15 5.263157895 7.09E-04
#> 113 17 5.964912281 0.001138911
#> 114 38 13.33333333 0.001628267
#> 115 16 5.614035088 0.002041272
#> 116 17 5.964912281 0.002754012
#> 117 12 4.210526316 0.00389947
#> 118 14 4.912280702 0.004712938
#> 119 13 4.561403509 0.010454751
#> 120 8 2.807017544 0.015257259
#> 121 12 4.210526316 0.016179699
#> 122 13 4.561403509 0.042995546
#> 123 11 3.859649123 0.045909065
#> 124 15 5.263157895 0.067273768
#> Genes
#> 110 9212, 6790, 150094, 7153, 6196, 9833, 4751, 1021, 7272, 55872, 10733, 3707, 983, 2268, 699, 1111, 701, 4830, 5634, 11213, 11004
#> 111 9212, 6790, 150094, 6196, 9833, 4751, 1033, 1021, 1163, 7083, 7272, 55872, 10733, 3707, 983, 2268, 699, 1111, 6502, 701, 4830, 5634, 11213, 5208
#> 112 9212, 6790, 150094, 6196, 9833, 4751, 1021, 7272, 55872, 10733, 983, 699, 1111, 701, 11213
#> 113 9212, 6790, 150094, 6196, 9833, 4751, 1021, 7272, 55872, 10733, 983, 2268, 699, 1111, 701, 10221, 11213
#> 114 6790, 6196, 11065, 4751, 25840, 1021, 1163, 7083, 330, 672, 29089, 10733, 10678, 2268, 699, 1111, 6502, 5634, 639, 9212, 150094, 7298, 9833, 1033, 2162, 7272, 55872, 586, 3707, 983, 79723, 85465, 701, 4830, 5427, 11213, 5208, 10721
#> 115 9212, 6790, 150094, 9833, 4751, 1021, 7272, 55872, 10733, 983, 2268, 699, 1111, 701, 10221, 11213
#> 116 9212, 6790, 150094, 6196, 9833, 4751, 1021, 7272, 55872, 10733, 983, 2268, 699, 1111, 701, 10221, 11213
#> 117 55872, 9212, 6196, 6790, 150094, 983, 9833, 699, 1111, 4751, 1021, 7272
#> 118 9212, 6790, 150094, 6196, 9833, 4751, 7272, 55872, 10733, 983, 699, 1111, 701, 11213
#> 119 9212, 6790, 150094, 6196, 9833, 4751, 1021, 7272, 55872, 983, 699, 1111, 10221
#> 120 9212, 6790, 150094, 9833, 2268, 4751, 11213, 7272
#> 121 9212, 6196, 6790, 150094, 10733, 983, 9833, 2268, 699, 1111, 1021, 7272
#> 122 9212, 6790, 150094, 4751, 1021, 55872, 10733, 332, 2268, 699, 701, 10221, 11213
#> 123 55872, 9212, 6196, 6790, 983, 9833, 699, 1111, 4751, 701, 10221
#> 124 9212, 6790, 150094, 6196, 9833, 4751, 1021, 7272, 55872, 10733, 983, 2268, 699, 1111, 701
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 110 269 558 20063 2.8069113 0.061016886 0.015755441
#> 111 270 735 20581 2.489009826 0.028619121 0.001382623
#> 112 270 393 20581 2.909386486 0.175445224 0.007713732
#> 113 255 487 18559 2.540588638 0.477718765 0.109303792
#> 114 270 1708 20581 1.695892966 0.358053033 0.016403282
#> 115 269 478 20063 2.496523619 0.857344241 0.324562319
#> 116 255 531 18559 2.330069052 0.792360583 0.191702812
#> 117 255 312 18559 2.799245852 0.892153105 0.222269773
#> 118 255 376 16881 2.464893617 0.862497506 0.116437297
#> 119 158 359 10057 2.304943408 0.770389293 0.292733022
#> 120 253 172 16792 3.087048442 1 0.313407724
#> 121 255 381 18559 2.292295816 0.999908379 0.70941759
#> 122 253 456 16792 1.892171139 1 0.585736689
#> 123 255 359 16881 2.028412256 0.999999997 0.688635977
#> 124 269 672 20063 1.664813463 1 1
#> FDR
#> 110 0.015722411
#> 111 0.001225045
#> 112 0.006834594
#> 113 0.108153226
#> 114 0.014533791
#> 115 0.323881895
#> 116 0.189684887
#> 117 0.219930091
#> 118 0.112833285
#> 119 0.292733022
#> 120 0.30340535
#> 121 0.701950037
#> 122 0.567042965
#> 123 0.667321054
#> 124 0.998950682
#>
#> $`Annotation Cluster 13`
#> Category Term Count
#> 128 KEGG_PATHWAY hsa03030:DNA replication 7
#> 129 GOTERM_BP_DIRECT GO:0000722~telomere maintenance via recombination 5
#> 130 GOTERM_BP_DIRECT GO:0042276~error-prone translesion synthesis 3
#> 131 KEGG_PATHWAY hsa03410:Base excision repair 3
#> 132 KEGG_PATHWAY hsa03420:Nucleotide excision repair 3
#> % PValue Genes List Total
#> 128 2.456140351 2.87E-05 4173, 4174, 2237, 4176, 5111, 5983, 5427 119
#> 129 1.754385965 0.001279731 2237, 5111, 5983, 5888, 5427 253
#> 130 1.052631579 0.032431072 5111, 5983, 5427 253
#> 131 1.052631579 0.109285166 2237, 5111, 5427 119
#> 132 1.052631579 0.192564654 5111, 5983, 5427 119
#> Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 128 36 6879 11.24019608 0.00466586 0.001558904 0.001511085
#> 129 32 16792 10.37055336 0.870790388 0.045207345 0.043764558
#> 130 19 16792 10.47971708 1 0.498315891 0.482412193
#> 131 33 6879 5.255156608 0.999999994 0.890674102 0.863352811
#> 132 47 6879 3.68979081 1 1 0.975308642
#>
#> $`Annotation Cluster 14`
#> Category
#> 136 KEGG_PATHWAY
#> 137 BIOCARTA
#> 138 GOTERM_MF_DIRECT
#> 139 GOTERM_BP_DIRECT
#> 140 BIOCARTA
#> Term
#> 136 hsa04115:p53 signaling pathway
#> 137 h_EfpPathway:Estrogen-responsive protein Efp controls cell cycle and breast tumors growth
#> 138 GO:0004693~cyclin-dependent protein serine/threonine kinase activity
#> 139 GO:0007077~mitotic nuclear envelope disassembly
#> 140 h_cellcyclePathway:Cyclins and Cell Cycle Regulation
#> Count % PValue
#> 136 9 3.157894737 1.66E-05
#> 137 4 1.403508772 0.009752169
#> 138 4 1.403508772 0.014284784
#> 139 3 1.052631579 0.141085171
#> 140 3 1.052631579 0.161543243
#> Genes List Total Pop Hits
#> 136 6241, 891, 9133, 9134, 983, 1111, 27244, 1021, 4193 119 67
#> 137 891, 9133, 983, 1021 48 16
#> 138 891, 9133, 983, 1021 255 34
#> 139 891, 9133, 983 253 44
#> 140 891, 983, 1021 48 25
#> Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 136 6879 7.765082152 0.002695955 0.001349787 0.001308382
#> 137 1625 8.463541667 0.61349218 0.236490097 0.231614012
#> 138 16881 7.788235294 0.997625275 0.260852584 0.252778575
#> 139 16792 4.525332375 1 1 0.968691296
#> 140 1625 4.0625 0.999999962 1 0.989583333
#>
#> $`Annotation Cluster 15`
#> Category
#> 144 GOTERM_BP_DIRECT
#> 145 GOTERM_BP_DIRECT
#> 146 UP_SEQ_FEATURE
#> Term
#> 144 GO:0032464~positive regulation of protein homooligomerization
#> 145 GO:0090200~positive regulation of release of cytochrome c from mitochondria
#> 146 short sequence motif:BH3
#> Count % PValue Genes List Total Pop Hits
#> 144 3 1.052631579 0.00753322 10018, 90427, 8739 253 9
#> 145 4 1.403508772 0.008293423 10018, 90427, 10105, 8739 253 28
#> 146 3 1.052631579 0.021184358 10018, 90427, 8739 269 17
#> Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 144 16792 22.12384717 0.999994349 0.174465006 0.168896974
#> 145 16792 9.481648786 0.999998339 0.186660412 0.180703165
#> 146 20063 13.16181937 0.999999999 1 0.998950682
#>
#> $`Annotation Cluster 16`
#> Category
#> 150 GOTERM_CC_DIRECT
#> 151 BIOCARTA
#> 152 BIOCARTA
#> Term
#> 150 GO:0000794~condensed nuclear chromosome
#> 151 h_atmPathway:ATM Signaling Pathway
#> 152 h_atrbrcaPathway:Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility
#> Count % PValue Genes List Total
#> 150 5 1.754385965 6.80E-04 672, 1104, 1111, 4751, 5888 266
#> 151 4 1.403508772 0.020930517 672, 1111, 5888, 4193 48
#> 152 3 1.052631579 0.131233005 672, 1111, 5888 48
#> Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 150 28 18224 12.23415682 0.168870088 0.00973191 0.008765875
#> 151 21 1625 6.448412698 0.871497711 0.40605203 0.397679823
#> 152 22 1625 4.616477273 0.999998815 1 0.989583333
#>
#> $`Annotation Cluster 17`
#> Category
#> 156 GOTERM_BP_DIRECT
#> 157 BIOCARTA
#> 158 GOTERM_BP_DIRECT
#> 159 GOTERM_BP_DIRECT
#> Term
#> 156 GO:0006977~DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest
#> 157 h_g2Pathway:Cell Cycle: G2/M Checkpoint
#> 158 GO:0045931~positive regulation of mitotic cell cycle
#> 159 GO:0006461~protein complex assembly
#> Count % PValue Genes List Total
#> 156 6 2.105263158 0.002359108 891, 144455, 6790, 983, 5111, 4193 253
#> 157 5 1.754385965 0.004977693 891, 672, 983, 1111, 4193 48
#> 158 4 1.403508772 0.008293423 891, 332, 983, 4193 253
#> 159 4 1.403508772 0.252807368 891, 983, 8936, 4193 253
#> Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 156 62 16792 6.423052403 0.977047032 0.073918711 0.071559603
#> 157 25 1625 6.770833333 0.383712655 0.160945416 0.157626953
#> 158 28 16792 9.481648786 0.999998339 0.186660412 0.180703165
#> 159 116 16792 2.288673845 1 1 0.968691296
#>
#> $`Annotation Cluster 18`
#> Category Term Count %
#> 163 SMART SM00240:FHA 3 1.052631579
#> 164 UP_SEQ_FEATURE domain:FHA 3 1.052631579
#> 165 INTERPRO IPR000253:Forkhead-associated (FHA) domain 3 1.052631579
#> 166 INTERPRO IPR008984:SMAD/FHA domain 3 1.052631579
#> PValue Genes List Total Pop Hits Pop Total Fold Enrichment
#> 163 0.049455762 4288, 6941, 9928 158 23 10057 8.302421574
#> 164 0.079321273 4288, 6941, 9928 269 35 20063 6.392883696
#> 165 0.090941721 4288, 6941, 9928 255 37 18559 5.901112878
#> 166 0.163847064 4288, 6941, 9928 255 53 18559 4.119644839
#> Bonferroni Benjamini FDR
#> 163 0.999175621 0.989115234 0.989115234
#> 164 1 1 0.998950682
#> 165 1 1 0.991212654
#> 166 1 1 0.991212654
#>
#> $`Annotation Cluster 19`
#> Category Term Count %
#> 170 GOTERM_BP_DIRECT GO:0002250~adaptive immune response 6 2.105263158
#> 171 UP_KEYWORDS Immunity 10 3.50877193
#> 172 UP_KEYWORDS Adaptive immunity 4 1.403508772
#> PValue Genes
#> 170 0.072444748 27242, 5896, 10288, 11024, 639, 8915
#> 171 0.209392094 3958, 27242, 2268, 6279, 10288, 11024, 23643, 639, 3669, 8915
#> 172 0.398019992 27242, 10288, 11024, 639
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 170 253 148 16792 2.690738169 1 0.765626468
#> 171 270 500 20581 1.524518519 1 0.956269043
#> 172 270 174 20581 1.752320136 1 1
#> FDR
#> 170 0.74119158
#> 171 0.847282497
#> 172 0.889298893
#>
#> $`Annotation Cluster 20`
#> Category Term Count %
#> 176 GOTERM_BP_DIRECT GO:0045087~innate immune response 10 3.50877193
#> 177 UP_KEYWORDS Immunity 10 3.50877193
#> 178 UP_KEYWORDS Innate immunity 6 2.105263158
#> PValue Genes
#> 176 0.198745711 2207, 3537, 1667, 3958, 2268, 3543, 6279, 23643, 639, 8915
#> 177 0.209392094 3958, 27242, 2268, 6279, 10288, 11024, 23643, 639, 3669, 8915
#> 178 0.256164931 3958, 2268, 6279, 23643, 639, 3669
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 176 253 430 16792 1.543524221 1 1
#> 177 270 500 20581 1.524518519 1 0.956269043
#> 178 270 261 20581 1.752320136 1 1
#> FDR
#> 176 0.968691296
#> 177 0.847282497
#> 178 0.889298893
#>
#> $`Annotation Cluster 21`
#> Category Term
#> 182 UP_KEYWORDS Helicase
#> 183 INTERPRO IPR014001:Helicase, superfamily 1/2, ATP-binding domain
#> 184 SMART SM00487:DEXDc
#> 185 INTERPRO IPR001650:Helicase, C-terminal
#> 186 UP_SEQ_FEATURE domain:Helicase ATP-binding
#> 187 SMART SM00490:HELICc
#> Count % PValue Genes
#> 182 6 2.105263158 0.039937009 4173, 3070, 4174, 4176, 83990, 1660
#> 183 4 1.403508772 0.191279591 3070, 83990, 1660, 10721
#> 184 4 1.403508772 0.242111971 3070, 83990, 1660, 10721
#> 185 3 1.052631579 0.436387325 3070, 1660, 10721
#> 186 3 1.052631579 0.451430267 3070, 83990, 1660
#> 187 3 1.052631579 0.500267741 3070, 1660, 10721
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 182 270 143 20581 3.198290598 0.999984671 0.271571663
#> 183 255 110 18559 2.646559715 1 1
#> 184 158 109 10057 2.335849495 1 1
#> 185 255 108 18559 2.02167756 1 1
#> 186 269 114 20063 1.962727451 1 1
#> 187 158 107 10057 1.784632675 1 1
#> FDR
#> 182 0.240620481
#> 183 0.991212654
#> 184 1
#> 185 0.991212654
#> 186 0.998950682
#> 187 1
#>
#> $`Annotation Cluster 22`
#> Category
#> 191 GOTERM_BP_DIRECT
#> 192 UP_KEYWORDS
#> 193 UP_KEYWORDS
#> 194 UP_KEYWORDS
#> 195 GOTERM_BP_DIRECT
#> Term
#> 191 GO:0000122~negative regulation of transcription from RNA polymerase II promoter
#> 192 Repressor
#> 193 Transcription regulation
#> 194 Transcription
#> 195 GO:0006351~transcription, DNA-templated
#> Count % PValue
#> 191 18 6.315789474 0.044041799
#> 192 14 4.912280702 0.048637928
#> 193 29 10.1754386 0.712423233
#> 194 29 10.1754386 0.765476924
#> 195 25 8.771929825 0.878115211
#> Genes
#> 191 9212, 7466, 3398, 26147, 4193, 2305, 144455, 10628, 10507, 79733, 51176, 3399, 79723, 5457, 1958, 639, 7704, 8914
#> 192 4332, 3398, 26147, 256380, 79682, 144455, 10659, 332, 79733, 3399, 79723, 55635, 639, 10432
#> 193 22936, 4332, 195828, 2305, 144455, 672, 332, 29028, 79733, 3399, 5457, 6941, 55723, 1958, 639, 10432, 3070, 3398, 26147, 256380, 79682, 57018, 10628, 51176, 687, 79723, 55635, 7704, 8914
#> 194 22936, 4332, 195828, 2305, 144455, 672, 332, 29028, 79733, 3399, 5457, 6941, 55723, 1958, 639, 10432, 3070, 3398, 26147, 256380, 79682, 57018, 10628, 51176, 687, 79723, 55635, 7704, 8914
#> 195 4332, 195828, 2305, 144455, 672, 332, 29028, 79733, 3399, 6941, 55723, 639, 10432, 3070, 3398, 26147, 256380, 79682, 57018, 10628, 687, 79723, 55635, 7704, 8914
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 191 253 720 16792 1.659288538 1 0.585736689
#> 192 270 592 20581 1.80264014 0.999998712 0.322671132
#> 193 270 2332 20581 0.947921034 1 1
#> 194 270 2398 20581 0.921831464 1 1
#> 195 253 1955 16792 0.84874094 1 1
#> FDR
#> 191 0.567042965
#> 192 0.285896113
#> 193 0.889298893
#> 194 0.889298893
#> 195 0.968691296
#>
#> $`Annotation Cluster 23`
#> Category Term Count
#> 199 KEGG_PATHWAY hsa04120:Ubiquitin mediated proteolysis 7
#> 200 GOTERM_BP_DIRECT GO:0051865~protein autoubiquitination 4
#> 201 GOTERM_MF_DIRECT GO:0004842~ubiquitin-protein transferase activity 9
#> 202 GOTERM_BP_DIRECT GO:0016567~protein ubiquitination 9
#> 203 UP_KEYWORDS Ubl conjugation pathway 12
#> 204 INTERPRO IPR013083:Zinc finger, RING/FYVE/PHD-type 7
#> 205 UP_SEQ_FEATURE zinc finger region:RING-type 4
#> 206 UP_KEYWORDS Ligase 5
#> 207 INTERPRO IPR001841:Zinc finger, RING-type 4
#> 208 GOTERM_MF_DIRECT GO:0016874~ligase activity 4
#> 209 SMART SM00184:RING 3
#> % PValue
#> 199 2.456140351 0.029969696
#> 200 1.403508772 0.039047317
#> 201 3.157894737 0.124642452
#> 202 3.157894737 0.175160351
#> 203 4.210526316 0.273069247
#> 204 2.456140351 0.589426788
#> 205 1.403508772 0.595736522
#> 206 1.754385965 0.667495486
#> 207 1.403508772 0.771676626
#> 208 1.403508772 0.775484865
#> 209 1.052631579 0.898110592
#> Genes
#> 199 330, 8651, 672, 991, 11065, 6502, 4193
#> 200 672, 29089, 5896, 4193
#> 201 330, 672, 29089, 332, 11065, 6502, 5896, 51514, 4193
#> 202 330, 8651, 672, 332, 11065, 83461, 5897, 7704, 4193
#> 203 330, 8651, 672, 29089, 991, 11065, 6502, 5896, 83461, 7704, 51514, 4193
#> 204 672, 25924, 221472, 5896, 26147, 6941, 4193
#> 205 330, 672, 5896, 4193
#> 206 672, 10606, 5896, 123283, 4193
#> 207 330, 672, 5896, 4193
#> 208 330, 672, 5896, 4193
#> 209 330, 672, 5896
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 199 119 137 6879 2.953628167 0.992985378 0.444096397
#> 200 253 50 16792 5.30972332 1 0.557121541
#> 201 255 329 16881 1.810942249 1 1
#> 202 253 359 16792 1.663910511 1 1
#> 203 270 680 20581 1.345163399 1 1
#> 204 255 453 18559 1.124641821 1 1
#> 205 269 230 20063 1.297106837 1 1
#> 206 270 347 20581 1.098356281 1 1
#> 207 255 295 18559 0.986852775 1 1
#> 208 255 270 16881 0.980740741 1 1
#> 209 158 244 10057 0.782605312 1 1
#> FDR
#> 199 0.430473808
#> 200 0.539341066
#> 201 0.971360382
#> 202 0.968691296
#> 203 0.889298893
#> 204 0.991212654
#> 205 0.998950682
#> 206 0.889298893
#> 207 0.991212654
#> 208 0.971360382
#> 209 1
#>
#> $`Annotation Cluster 24`
#> Category Term Count %
#> 213 GOTERM_BP_DIRECT GO:0006955~immune response 16 5.614035088
#> 214 KEGG_PATHWAY hsa04380:Osteoclast differentiation 6 2.105263158
#> 215 UP_KEYWORDS Immunoglobulin domain 11 3.859649123
#> 216 UP_SEQ_FEATURE domain:Ig-like C2-type 1 5 1.754385965
#> 217 UP_SEQ_FEATURE domain:Ig-like C2-type 2 5 1.754385965
#> 218 UP_SEQ_FEATURE domain:Ig-like C2-type 3 3 1.052631579
#> 219 GOTERM_MF_DIRECT GO:0004872~receptor activity 4 1.403508772
#> 220 INTERPRO IPR013783:Immunoglobulin-like fold 13 4.561403509
#> 221 INTERPRO IPR003599:Immunoglobulin subtype 7 2.456140351
#> 222 INTERPRO IPR007110:Immunoglobulin-like domain 10 3.50877193
#> 223 SMART SM00409:IG 7 2.456140351
#> 224 INTERPRO IPR003598:Immunoglobulin subtype 2 3 1.052631579
#> 225 SMART SM00408:IGc2 3 1.052631579
#> PValue
#> 213 0.001789286
#> 214 0.074088477
#> 215 0.182927711
#> 216 0.284356852
#> 217 0.286999328
#> 218 0.511967139
#> 219 0.637125307
#> 220 0.655196914
#> 221 0.678261027
#> 222 0.732946339
#> 223 0.794765015
#> 224 0.859257249
#> 225 0.905647329
#> Genes
#> 213 5272, 9466, 5473, 1230, 1667, 27242, 3537, 2215, 8809, 10507, 3543, 3553, 5896, 944, 10288, 8807
#> 214 8651, 3459, 2215, 3553, 10288, 11024
#> 215 3537, 3459, 2215, 8809, 10507, 3543, 153579, 10288, 3572, 11024, 8807
#> 216 2215, 8809, 10288, 11024, 8807
#> 217 2215, 8809, 10288, 11024, 8807
#> 218 8809, 10288, 11024
#> 219 8809, 10507, 10288, 8807
#> 220 9466, 153579, 3572, 2162, 3537, 3459, 2215, 8809, 10507, 3543, 10288, 11024, 8807
#> 221 2215, 8809, 10507, 153579, 10288, 11024, 8807
#> 222 3537, 2215, 8809, 10507, 3543, 153579, 10288, 3572, 11024, 8807
#> 223 2215, 8809, 10507, 153579, 10288, 11024, 8807
#> 224 10507, 10288, 11024
#> 225 10507, 10288, 11024
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 213 253 421 16792 2.522433881 0.942836502 0.058352625
#> 214 119 131 6879 2.647636154 0.999996445 0.710377746
#> 215 270 546 20581 1.535687152 1 0.888506025
#> 216 269 202 20063 1.84612978 1 1
#> 217 269 203 20063 1.837035545 1 1
#> 218 269 128 20063 1.748054136 1 1
#> 219 255 217 16881 1.220276498 1 1
#> 220 255 951 18559 0.994894951 1 1
#> 221 255 497 18559 1.025075946 1 1
#> 222 255 771 18559 0.943973958 1 1
#> 223 158 497 10057 0.896505616 1 1
#> 224 255 250 18559 0.873364706 1 1
#> 225 158 250 10057 0.763822785 1 1
#> FDR
#> 213 0.056490308
#> 214 0.688587018
#> 215 0.78724247
#> 216 0.998950682
#> 217 0.998950682
#> 218 0.998950682
#> 219 0.971360382
#> 220 0.991212654
#> 221 0.991212654
#> 222 0.991212654
#> 223 1
#> 224 0.991212654
#> 225 1
#>
#> $`Annotation Cluster 25`
#> Category
#> 229 UP_KEYWORDS
#> 230 UP_SEQ_FEATURE
#> 231 INTERPRO
#> 232 GOTERM_MF_DIRECT
#> 233 SMART
#> 234 GOTERM_MF_DIRECT
#> 235 GOTERM_BP_DIRECT
#> 236 GOTERM_BP_DIRECT
#> 237 GOTERM_BP_DIRECT
#> 238 GOTERM_MF_DIRECT
#> 239 INTERPRO
#> Term Count
#> 229 Guanine-nucleotide releasing factor 5
#> 230 domain:DH 3
#> 231 IPR000219:Dbl homology (DH) domain 3
#> 232 GO:0005085~guanyl-nucleotide exchange factor activity 4
#> 233 SM00325:RhoGEF 3
#> 234 GO:0005089~Rho guanyl-nucleotide exchange factor activity 3
#> 235 GO:0051056~regulation of small GTPase mediated signal transduction 4
#> 236 GO:0035023~regulation of Rho protein signal transduction 3
#> 237 GO:0043547~positive regulation of GTPase activity 11
#> 238 GO:0005096~GTPase activator activity 6
#> 239 IPR011993:Pleckstrin homology-like domain 5
#> % PValue
#> 229 1.754385965 0.131622205
#> 230 1.052631579 0.230271568
#> 231 1.052631579 0.253727716
#> 232 1.403508772 0.262134809
#> 233 1.052631579 0.287097785
#> 234 1.052631579 0.322906369
#> 235 1.403508772 0.326300992
#> 236 1.052631579 0.343755797
#> 237 3.859649123 0.34391913
#> 238 2.105263158 0.410378231
#> 239 1.754385965 0.839367512
#> Genes
#> 229 1104, 1894, 6654, 221472, 22898
#> 230 1894, 6654, 221472
#> 231 1894, 6654, 221472
#> 232 1894, 6654, 221472, 6915
#> 233 1894, 6654, 221472
#> 234 1894, 6654, 221472
#> 235 1894, 6654, 221472, 55789
#> 236 1894, 6654, 221472
#> 237 10602, 1104, 10507, 1894, 6654, 221472, 64744, 55635, 55789, 6915, 22898
#> 238 10602, 1894, 6654, 64744, 55635, 55789
#> 239 1894, 6654, 221472, 54443, 6645
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 229 270 149 20581 2.557916977 1 0.730637547
#> 230 269 68 20063 3.290454844 1 1
#> 231 255 71 18559 3.075227838 1 1
#> 232 255 118 16881 2.244067797 1 1
#> 233 158 68 10057 2.808172003 1 1
#> 234 255 77 16881 2.579220779 1 1
#> 235 253 134 16792 1.981240045 1 1
#> 236 253 81 16792 2.458205241 1 1
#> 237 253 565 16792 1.292189304 1 1
#> 238 255 279 16881 1.423655914 1 1
#> 239 255 427 18559 0.852229416 1 1
#> FDR
#> 229 0.647366356
#> 230 0.998950682
#> 231 0.991212654
#> 232 0.971360382
#> 233 1
#> 234 0.971360382
#> 235 0.968691296
#> 236 0.968691296
#> 237 0.968691296
#> 238 0.971360382
#> 239 0.991212654
#>
#> $`Annotation Cluster 26`
#> Category Term Count %
#> 243 KEGG_PATHWAY hsa05214:Glioma 3 1.052631579
#> 244 KEGG_PATHWAY hsa05220:Chronic myeloid leukemia 3 1.052631579
#> 245 KEGG_PATHWAY hsa04151:PI3K-Akt signaling pathway 8 2.807017544
#> PValue Genes List Total
#> 243 0.306981111 6654, 1021, 4193 119
#> 244 0.351147227 6654, 1021, 4193 119
#> 245 0.379958696 54541, 672, 10018, 3326, 9134, 6654, 1021, 4193 119
#> Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 243 65 6879 2.668002586 1 1 0.975308642
#> 244 72 6879 2.408613445 1 1 0.975308642
#> 245 345 6879 1.340445744 1 1 0.975308642
#>
#> $`Annotation Cluster 27`
#> Category Term Count %
#> 249 GOTERM_MF_DIRECT GO:0005525~GTP binding 10 3.50877193
#> 250 UP_SEQ_FEATURE nucleotide phosphate-binding region:GTP 6 2.105263158
#> 251 UP_KEYWORDS GTP-binding 6 2.105263158
#> 252 GOTERM_MF_DIRECT GO:0003924~GTPase activity 4 1.403508772
#> PValue
#> 249 0.126907746
#> 250 0.404992485
#> 251 0.475379516
#> 252 0.687048128
#> Genes
#> 249 115361, 7277, 22836, 3326, 55303, 168537, 387751, 11031, 4830, 22974
#> 250 115361, 7277, 55303, 168537, 387751, 11031
#> 251 115361, 7277, 55303, 168537, 387751, 11031
#> 252 115361, 7277, 168537, 11031
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 249 255 384 16881 1.723958333 1 1
#> 250 269 310 20063 1.443554383 1 1
#> 251 270 343 20581 1.333398121 1 1
#> 252 255 234 16881 1.131623932 1 1
#> FDR
#> 249 0.971360382
#> 250 0.998950682
#> 251 0.889298893
#> 252 0.971360382
#>
#> $`Annotation Cluster 28`
#> Category Term Count % PValue
#> 256 UP_KEYWORDS Actin-binding 6 2.105263158 0.28891487
#> 257 GOTERM_MF_DIRECT GO:0003779~actin binding 6 2.105263158 0.406108673
#> 258 GOTERM_CC_DIRECT GO:0045202~synapse 4 1.403508772 0.491555566
#> Genes List Total Pop Hits Pop Total
#> 256 25924, 9788, 54443, 6645, 8936, 2934 270 274 20581
#> 257 25924, 81930, 54443, 6645, 8936, 2934 255 278 16881
#> 258 25924, 6645, 8936, 4193 266 181 18224
#> Fold Enrichment Bonferroni Benjamini FDR
#> 256 1.66918086 1 1 0.889298893
#> 257 1.428776978 1 1 0.971360382
#> 258 1.514061397 1 1 0.904059041
#>
#> $`Annotation Cluster 29`
#> Category Term Count % PValue
#> 262 UP_SEQ_FEATURE domain:SH2 3 1.052631579 0.367818941
#> 263 UP_KEYWORDS SH2 domain 3 1.052631579 0.413456872
#> 264 INTERPRO IPR000980:SH2 domain 3 1.052631579 0.459404645
#> 265 SMART SM00252:SH2 3 1.052631579 0.480159332
#> Genes List Total Pop Hits Pop Total Fold Enrichment Bonferroni
#> 262 8651, 2268, 6503 269 96 20063 2.330738848 1
#> 263 8651, 2268, 6503 270 108 20581 2.117386831 1
#> 264 8651, 2268, 6503 255 113 18559 1.932222801 1
#> 265 8651, 2268, 6503 158 103 10057 1.853938798 1
#> Benjamini FDR
#> 262 1 0.998950682
#> 263 1 0.889298893
#> 264 1 0.991212654
#> 265 1 1
#>
#> $`Annotation Cluster 30`
#> Category Term
#> 269 UP_SEQ_FEATURE lipid moiety-binding region:GPI-anchor amidated serine
#> 270 GOTERM_CC_DIRECT GO:0031225~anchored component of membrane
#> 271 UP_KEYWORDS GPI-anchor
#> 272 UP_SEQ_FEATURE propeptide:Removed in mature form
#> Count % PValue Genes List Total Pop Hits
#> 269 3 1.052631579 0.16717354 1800, 2215, 1368 269 55
#> 270 3 1.052631579 0.491021258 1800, 2215, 1368 266 113
#> 271 3 1.052631579 0.53670556 1800, 2215, 1368 270 137
#> 272 3 1.052631579 0.827933884 1800, 2215, 1368 269 237
#> Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 269 20063 4.068198716 1 1 0.998950682
#> 270 18224 1.818883492 1 1 0.904059041
#> 271 20581 1.66918086 1 1 0.889298893
#> 272 20063 0.944096748 1 1 0.998950682
#>
#> $`Annotation Cluster 31`
#> Category Term
#> 276 GOTERM_BP_DIRECT GO:0098609~cell-cell adhesion
#> 277 GOTERM_MF_DIRECT GO:0098641~cadherin binding involved in cell-cell adhesion
#> 278 GOTERM_CC_DIRECT GO:0005913~cell-cell adherens junction
#> Count % PValue Genes
#> 276 6 2.105263158 0.383827889 9133, 3326, 10606, 23670, 54443, 6282
#> 277 6 2.105263158 0.44244857 9133, 3326, 10606, 23670, 54443, 6282
#> 278 6 2.105263158 0.4956301 9133, 3326, 10606, 23670, 54443, 6282
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 276 253 271 16792 1.469480624 1 1
#> 277 255 290 16881 1.369655172 1 1
#> 278 266 323 18224 1.272655323 1 1
#> FDR
#> 276 0.968691296
#> 277 0.971360382
#> 278 0.904059041
#>
#> $`Annotation Cluster 32`
#> Category Term Count
#> 282 UP_SEQ_FEATURE repeat:WD 7 4
#> 283 INTERPRO IPR019775:WD40 repeat, conserved site 4
#> 284 UP_SEQ_FEATURE repeat:WD 6 4
#> 285 UP_SEQ_FEATURE repeat:WD 3 5
#> 286 INTERPRO IPR015943:WD40/YVTN repeat-like-containing domain 6
#> 287 INTERPRO IPR001680:WD40 repeat 5
#> 288 UP_KEYWORDS WD repeat 5
#> 289 UP_SEQ_FEATURE repeat:WD 1 5
#> 290 UP_SEQ_FEATURE repeat:WD 2 5
#> 291 SMART SM00320:WD40 5
#> 292 INTERPRO IPR017986:WD40-repeat-containing domain 5
#> 293 UP_SEQ_FEATURE repeat:WD 5 4
#> 294 UP_SEQ_FEATURE repeat:WD 4 4
#> % PValue Genes List Total
#> 282 1.403508772 0.32796704 991, 79968, 11169, 51514 269
#> 283 1.403508772 0.393283056 991, 11169, 51514, 22898 255
#> 284 1.403508772 0.486636022 991, 79968, 11169, 51514 269
#> 285 1.754385965 0.486977255 991, 79968, 11169, 51514, 22898 269
#> 286 2.105263158 0.491324742 991, 10507, 79968, 11169, 51514, 22898 255
#> 287 1.754385965 0.501565199 991, 79968, 11169, 51514, 22898 255
#> 288 1.754385965 0.502279153 991, 79968, 11169, 51514, 22898 270
#> 289 1.754385965 0.51273792 991, 79968, 11169, 51514, 22898 269
#> 290 1.754385965 0.51273792 991, 79968, 11169, 51514, 22898 269
#> 291 1.754385965 0.603311395 991, 79968, 11169, 51514, 22898 158
#> 292 1.754385965 0.605708457 991, 79968, 11169, 51514, 22898 255
#> 293 1.403508772 0.6160331 991, 79968, 11169, 51514 269
#> 294 1.403508772 0.665011022 991, 79968, 11169, 51514 269
#> Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 282 151 20063 1.975725646 1 1 0.998950682
#> 283 166 18559 1.753744389 1 1 0.991212654
#> 284 196 20063 1.522115166 1 1 0.998950682
#> 285 269 20063 1.386313069 1 1 0.998950682
#> 286 331 18559 1.319282033 1 1 0.991212654
#> 287 268 18559 1.357843137 1 1 0.991212654
#> 288 281 20581 1.356333202 1 1 0.889298893
#> 289 278 20063 1.34143243 1 1 0.998950682
#> 290 278 20063 1.34143243 1 1 0.998950682
#> 291 267 10057 1.191983122 1 1 1
#> 292 306 18559 1.189222094 1 1 0.991212654
#> 293 237 20063 1.258795665 1 1 0.998950682
#> 294 255 20063 1.1699395 1 1 0.998950682
#>
#> $`Annotation Cluster 33`
#> Category Term Count
#> 298 GOTERM_MF_DIRECT GO:0000166~nucleotide binding 7
#> 299 UP_SEQ_FEATURE domain:RRM 1 3
#> 300 UP_SEQ_FEATURE domain:RRM 2 3
#> 301 INTERPRO IPR000504:RNA recognition motif domain 4
#> 302 UP_KEYWORDS RNA-binding 9
#> 303 SMART SM00360:RRM 4
#> 304 INTERPRO IPR012677:Nucleotide-binding, alpha-beta plait 4
#> 305 GOTERM_MF_DIRECT GO:0003723~RNA binding 8
#> % PValue
#> 298 2.456140351 0.421121371
#> 299 1.052631579 0.4993644
#> 300 1.052631579 0.4993644
#> 301 1.403508772 0.600411338
#> 302 3.157894737 0.643652549
#> 303 1.403508772 0.647324045
#> 304 1.403508772 0.703552456
#> 305 2.807017544 0.72011974
#> Genes List Total Pop Hits
#> 298 990, 10659, 7298, 2521, 5888, 27303, 10432 255 348
#> 299 10659, 27303, 10432 269 125
#> 300 10659, 27303, 10432 269 125
#> 301 10659, 2521, 27303, 10432 255 226
#> 302 10635, 10659, 2521, 678, 1660, 1719, 27303, 10432, 3669 270 665
#> 303 10659, 2521, 27303, 10432 158 212
#> 304 10659, 2521, 27303, 10432 255 264
#> 305 10635, 672, 10659, 2521, 8635, 27303, 10432, 123283 255 547
#> Pop Total Fold Enrichment Bonferroni Benjamini FDR
#> 298 16881 1.331609195 1 1 0.971360382
#> 299 20063 1.790007435 1 1 0.998950682
#> 300 20063 1.790007435 1 1 0.998950682
#> 301 18559 1.288148534 1 1 0.991212654
#> 302 20581 1.031629073 1 1 0.889298893
#> 303 10057 1.200979221 1 1 1
#> 304 18559 1.102733214 1 1 0.991212654
#> 305 16881 0.968190128 1 1 0.971360382
#>
#> $`Annotation Cluster 34`
#> Category Term Count % PValue
#> 309 UP_SEQ_FEATURE repeat:5 3 1.052631579 0.636322058
#> 310 UP_SEQ_FEATURE repeat:1 4 1.403508772 0.670164008
#> 311 UP_SEQ_FEATURE repeat:2 4 1.403508772 0.677784789
#> 312 UP_SEQ_FEATURE repeat:3 3 1.052631579 0.805350956
#> Genes List Total Pop Hits Pop Total Fold Enrichment
#> 309 3958, 4288, 2055 269 161 20063 1.389757325
#> 310 3958, 4288, 2055, 57082 269 257 20063 1.160834912
#> 311 3958, 4288, 2055, 57082 269 260 20063 1.147440663
#> 312 3958, 4288, 2055 269 225 20063 0.994448575
#> Bonferroni Benjamini FDR
#> 309 1 1 0.998950682
#> 310 1 1 0.998950682
#> 311 1 1 0.998950682
#> 312 1 1 0.998950682
#>
#> $`Annotation Cluster 35`
#> Category Term Count %
#> 316 UP_SEQ_FEATURE domain:SH3 3 1.052631579
#> 317 UP_KEYWORDS SH3 domain 3 1.052631579
#> 318 INTERPRO IPR001452:Src homology-3 domain 3 1.052631579
#> 319 SMART SM00326:SH3 3 1.052631579
#> PValue Genes List Total Pop Hits Pop Total Fold Enrichment
#> 316 0.681077454 4739, 2268, 6503 269 175 20063 1.278576739
#> 317 0.774248546 4739, 2268, 6503 270 215 20581 1.063617571
#> 318 0.802200915 4739, 2268, 6503 255 218 18559 1.00156503
#> 319 0.836027319 4739, 2268, 6503 158 206 10057 0.926969399
#> Bonferroni Benjamini FDR
#> 316 1 1 0.998950682
#> 317 1 1 0.889298893
#> 318 1 1 0.991212654
#> 319 1 1 1
#>
#> $`Annotation Cluster 36`
#> Category Term Count %
#> 323 INTERPRO IPR001849:Pleckstrin homology domain 4 1.403508772
#> 324 SMART SM00233:PH 4 1.403508772
#> 325 INTERPRO IPR011993:Pleckstrin homology-like domain 5 1.754385965
#> PValue Genes List Total Pop Hits Pop Total
#> 323 0.72016821 6654, 221472, 54443, 6645 255 271 18559
#> 324 0.785294139 6654, 221472, 54443, 6645 158 264 10057
#> 325 0.839367512 1894, 6654, 221472, 54443, 6645 255 427 18559
#> Fold Enrichment Bonferroni Benjamini FDR
#> 323 1.074249331 1 1 0.991212654
#> 324 0.964422708 1 1 1
#> 325 0.852229416 1 1 0.991212654
#>
#> $`Annotation Cluster 37`
#> Category Term Count
#> 329 INTERPRO IPR013083:Zinc finger, RING/FYVE/PHD-type 7
#> 330 UP_KEYWORDS Metal-binding 45
#> 331 GOTERM_MF_DIRECT GO:0008270~zinc ion binding 16
#> 332 UP_KEYWORDS Zinc 25
#> 333 UP_KEYWORDS Zinc-finger 18
#> 334 GOTERM_MF_DIRECT GO:0046872~metal ion binding 22
#> % PValue
#> 329 2.456140351 0.589426788
#> 330 15.78947368 0.740808892
#> 331 5.614035088 0.774954644
#> 332 8.771929825 0.921349167
#> 333 6.315789474 0.935974703
#> 334 7.719298246 0.983865498
#> Genes
#> 329 672, 25924, 221472, 5896, 26147, 6941, 4193
#> 330 25924, 6196, 5142, 6279, 4751, 3684, 195828, 3043, 7083, 4193, 330, 55388, 672, 332, 2521, 221472, 678, 5896, 83990, 5897, 6941, 5634, 1958, 639, 6241, 9212, 150094, 7153, 64744, 26147, 2162, 6282, 1800, 11339, 1368, 2237, 687, 3047, 79723, 85465, 4830, 5723, 7704, 3669, 2934
#> 331 25924, 6279, 26147, 7083, 4193, 1800, 330, 672, 332, 1368, 2521, 79723, 5896, 5897, 6941, 1958
#> 332 25924, 6279, 195828, 7083, 4193, 330, 55388, 672, 332, 2521, 221472, 678, 5896, 5897, 6941, 1958, 639, 64744, 26147, 1800, 11339, 1368, 687, 79723, 7704
#> 333 25924, 64744, 195828, 26147, 4193, 330, 55388, 672, 687, 2521, 221472, 678, 5896, 5897, 6941, 1958, 639, 7704
#> 334 6241, 9212, 5142, 3684, 4751, 64744, 195828, 2162, 1800, 11339, 55388, 332, 687, 221472, 678, 5896, 83990, 85465, 1958, 639, 7704, 3669
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 329 255 453 18559 1.124641821 1 1
#> 330 270 3640 20581 0.94235348 1 1
#> 331 255 1169 16881 0.906073567 1 1
#> 332 270 2348 20581 0.811604833 1 1
#> 333 270 1781 20581 0.770391166 1 1
#> 334 255 2069 16881 0.703914935 1 1
#> FDR
#> 329 0.991212654
#> 330 0.889298893
#> 331 0.971360382
#> 332 0.921349167
#> 333 0.935974703
#> 334 0.983865498
#>
#> $`Annotation Cluster 38`
#> Category Term Count %
#> 338 GOTERM_CC_DIRECT GO:0005759~mitochondrial matrix 5 1.754385965
#> 339 UP_SEQ_FEATURE transit peptide:Mitochondrion 3 1.052631579
#> 340 UP_KEYWORDS Transit peptide 3 1.052631579
#> PValue Genes List Total Pop Hits Pop Total
#> 338 0.70331121 7298, 5888, 2271, 10105, 10797 266 327 18224
#> 339 0.989129788 2271, 10105, 10797 269 482 20063
#> 340 0.99346555 2271, 10105, 10797 270 536 20581
#> Fold Enrichment Bonferroni Benjamini FDR
#> 338 1.047573061 1 1 0.904059041
#> 339 0.464213546 1 1 0.998950682
#> 340 0.426637645 1 1 0.99346555
#>
#> $`Annotation Cluster 39`
#> Category
#> 344 GOTERM_MF_DIRECT
#> 345 GOTERM_BP_DIRECT
#> 346 GOTERM_MF_DIRECT
#> Term
#> 344 GO:0001077~transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
#> 345 GO:0006366~transcription from RNA polymerase II promoter
#> 346 GO:0043565~sequence-specific DNA binding
#> Count % PValue Genes
#> 344 3 1.052631579 0.873174215 51176, 5457, 1958
#> 345 6 2.105263158 0.887368565 2305, 9232, 51176, 9319, 5457, 1958
#> 346 5 1.754385965 0.95485967 2305, 51176, 5896, 5457, 1958
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 344 255 236 16881 0.841525424 1 1
#> 345 253 513 16792 0.776275339 1 1
#> 346 255 518 16881 0.638996139 1 1
#> FDR
#> 344 0.971360382
#> 345 0.968691296
#> 346 0.971360382
#>
#> $`Annotation Cluster 40`
#> Category Term Count % PValue Genes
#> 350 UP_SEQ_FEATURE repeat:LRR 4 3 1.052631579 0.857412313 81611, 6502, 1062
#> 351 UP_SEQ_FEATURE repeat:LRR 3 3 1.052631579 0.913957001 81611, 6502, 1062
#> 352 UP_SEQ_FEATURE repeat:LRR 1 3 1.052631579 0.930206624 81611, 6502, 1062
#> 353 UP_SEQ_FEATURE repeat:LRR 2 3 1.052631579 0.930976302 81611, 6502, 1062
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 350 269 255 20063 0.877454625 1 1
#> 351 269 302 20063 0.740897117 1 1
#> 352 269 321 20063 0.697043394 1 1
#> 353 269 322 20063 0.694878663 1 1
#> FDR
#> 350 0.998950682
#> 351 0.998950682
#> 352 0.998950682
#> 353 0.998950682
#>
#> $`Annotation Cluster 41`
#> Category Term Count
#> 357 UP_SEQ_FEATURE disulfide bond 38
#> 358 UP_KEYWORDS Receptor 20
#> 359 GOTERM_CC_DIRECT GO:0005887~integral component of plasma membrane 18
#> 360 UP_KEYWORDS Disulfide bond 40
#> 361 UP_SEQ_FEATURE signal peptide 31
#> 362 UP_SEQ_FEATURE topological domain:Extracellular 24
#> 363 UP_KEYWORDS Glycoprotein 41
#> 364 UP_SEQ_FEATURE topological domain:Cytoplasmic 29
#> 365 UP_SEQ_FEATURE glycosylation site:N-linked (GlcNAc...) 36
#> 366 UP_KEYWORDS Signal 33
#> 367 UP_KEYWORDS Transmembrane helix 45
#> 368 UP_KEYWORDS Transmembrane 45
#> 369 UP_KEYWORDS Membrane 64
#> 370 UP_SEQ_FEATURE transmembrane region 38
#> 371 GOTERM_CC_DIRECT GO:0016021~integral component of membrane 39
#> % PValue
#> 357 13.33333333 0.660347854
#> 358 7.01754386 0.748870081
#> 359 6.315789474 0.826387962
#> 360 14.03508772 0.853885736
#> 361 10.87719298 0.995614066
#> 362 8.421052632 0.997206533
#> 363 14.38596491 0.998968662
#> 364 10.1754386 0.999356941
#> 365 12.63157895 0.999769461
#> 366 11.57894737 0.999895186
#> 367 15.78947368 0.999993549
#> 368 15.78947368 0.999994352
#> 369 22.45614035 0.999998504
#> 370 13.33333333 0.999998531
#> 371 13.68421053 0.999999982
#> Genes
#> 357 3684, 153579, 23166, 23643, 4192, 2171, 2207, 3537, 27242, 3958, 3459, 8809, 26011, 931, 9934, 11024, 8807, 10875, 5473, 9976, 4069, 1230, 3572, 3492, 6282, 1800, 1667, 1368, 2215, 10507, 3543, 944, 10288, 8635, 113791, 7803, 6915, 2934
#> 358 9466, 5026, 3684, 23166, 1230, 58475, 3572, 3161, 2207, 27242, 3459, 2215, 8809, 10507, 10288, 9934, 11024, 8807, 51338, 6915
#> 359 9466, 9976, 5026, 63027, 23166, 1230, 56660, 2207, 27242, 3459, 10507, 26011, 963, 931, 944, 10288, 9934, 6915
#> 360 5026, 3684, 153579, 23166, 23643, 4192, 2171, 2207, 3537, 27242, 3958, 3459, 8809, 26011, 931, 9934, 11024, 8807, 10875, 5473, 9976, 4069, 1230, 3572, 6282, 1800, 1667, 1687, 1368, 2215, 10628, 10507, 3543, 944, 10288, 8635, 113791, 7803, 6915, 2934
#> 361 9466, 5265, 3684, 153579, 25840, 23166, 23643, 4192, 2207, 27242, 3459, 8809, 51104, 11024, 8807, 10875, 5473, 4069, 3572, 3492, 1800, 1667, 1368, 2215, 10507, 3543, 8836, 10288, 8635, 113791, 2934
#> 362 9466, 9976, 5026, 3684, 153579, 23166, 1230, 27346, 3572, 2207, 27242, 3459, 8809, 10507, 26011, 963, 944, 10288, 9934, 11024, 113791, 8807, 51338, 6915
#> 363 9466, 4176, 5265, 7466, 5026, 3684, 2012, 153579, 63027, 23166, 3043, 23643, 3161, 81930, 27242, 10678, 3459, 8809, 26011, 9934, 11024, 8807, 10875, 9976, 1230, 3572, 56660, 2162, 1800, 1368, 2215, 3326, 10507, 963, 23670, 8836, 944, 10288, 8635, 113791, 6915
#> 364 9466, 5026, 3684, 153579, 23166, 27346, 58475, 2207, 27242, 10678, 3459, 8809, 26011, 931, 9934, 11024, 8807, 9976, 1230, 3572, 56660, 10507, 963, 255027, 944, 10288, 113791, 51338, 6915
#> 365 9466, 5265, 5026, 3684, 2012, 153579, 63027, 23166, 23643, 3161, 27242, 10678, 3459, 8809, 26011, 9934, 11024, 8807, 10875, 9976, 1230, 3572, 56660, 2162, 3492, 1800, 1368, 2215, 10507, 963, 23670, 8836, 944, 10288, 8635, 6915
#> 366 9466, 5265, 3684, 153579, 25840, 23166, 23643, 4192, 2207, 27242, 3459, 8809, 51104, 11024, 8807, 10875, 5473, 4069, 3572, 1800, 1667, 1687, 1368, 2215, 10507, 3543, 8318, 8836, 10288, 8635, 113791, 11213, 2934
#> 367 9466, 7466, 5026, 3684, 2012, 153579, 25840, 63027, 23166, 2055, 27346, 58475, 3043, 2207, 672, 27242, 10678, 3459, 8809, 26011, 931, 5897, 9934, 11024, 8807, 9976, 1230, 3572, 56660, 55273, 1368, 2215, 10507, 85027, 963, 255027, 23670, 85465, 944, 10288, 6713, 113791, 51338, 6915, 8739
#> 368 9466, 7466, 5026, 3684, 2012, 153579, 25840, 63027, 23166, 2055, 27346, 58475, 3043, 2207, 672, 27242, 10678, 3459, 8809, 26011, 931, 5897, 9934, 11024, 8807, 9976, 1230, 3572, 56660, 55273, 1368, 2215, 10507, 85027, 963, 255027, 23670, 85465, 944, 10288, 6713, 113791, 51338, 6915, 8739
#> 369 9466, 6279, 5026, 3684, 63027, 23166, 58475, 3043, 672, 115361, 10018, 27242, 8809, 2268, 5897, 11024, 9934, 8807, 7298, 9833, 11031, 1230, 9590, 3572, 56660, 10507, 255027, 963, 6713, 51338, 7803, 6915, 8739, 7466, 2012, 153579, 25840, 2055, 27346, 57561, 29887, 2207, 10678, 26051, 3459, 26011, 221472, 931, 6645, 9976, 55273, 1800, 10602, 1687, 2215, 1368, 85027, 23670, 85465, 944, 10288, 113791, 51514, 8915
#> 370 9466, 7466, 5026, 3684, 2012, 153579, 63027, 23166, 2055, 27346, 58475, 2207, 27242, 10678, 3459, 8809, 26011, 931, 9934, 11024, 8807, 9976, 1230, 3572, 56660, 55273, 10507, 85027, 963, 255027, 23670, 85465, 944, 10288, 6713, 113791, 51338, 6915
#> 371 9466, 7466, 3684, 2012, 153579, 25840, 63027, 23166, 2055, 27346, 58475, 3043, 2207, 672, 27242, 10678, 3459, 8809, 5897, 9934, 11024, 8807, 1230, 3572, 55273, 1368, 2215, 85027, 963, 255027, 23670, 85465, 944, 10288, 6713, 113791, 51338, 6915, 8739
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 357 269 2917 20063 0.971607281 1 1
#> 358 270 1648 20581 0.925071917 1 1
#> 359 266 1415 18224 0.87152156 1 1
#> 360 270 3434 20581 0.887896633 1 1
#> 361 269 3346 20063 0.691002073 1 1
#> 362 269 2787 20063 0.642270339 1 1
#> 363 270 4551 20581 0.686720053 1 1
#> 364 269 3456 20063 0.625846542 1 1
#> 365 269 4234 20063 0.634154736 1 1
#> 366 270 4160 20581 0.604676816 1 1
#> 367 270 5634 20581 0.608833274 1 1
#> 368 270 5651 20581 0.607001711 1 1
#> 369 270 7494 20581 0.65098202 1 1
#> 370 269 5056 20063 0.560557444 1 1
#> 371 266 5163 18224 0.517516918 1 1
#> FDR
#> 357 0.998950682
#> 358 0.889298893
#> 359 0.904059041
#> 360 0.889298893
#> 361 0.998950682
#> 362 0.998950682
#> 363 0.998968662
#> 364 0.999356941
#> 365 0.999769461
#> 366 0.999895186
#> 367 0.999993549
#> 368 0.999994352
#> 369 0.999998504
#> 370 0.999998531
#> 371 0.999999982
#>
#> $`Annotation Cluster 42`
#> Category
#> 375 GOTERM_MF_DIRECT
#> 376 UP_SEQ_FEATURE
#> 377 UP_SEQ_FEATURE
#> 378 INTERPRO
#> 379 UP_SEQ_FEATURE
#> 380 INTERPRO
#> 381 INTERPRO
#> 382 SMART
#> Term
#> 375 GO:0003700~transcription factor activity, sequence-specific DNA binding
#> 376 zinc finger region:C2H2-type 1
#> 377 zinc finger region:C2H2-type 2
#> 378 IPR013087:Zinc finger C2H2-type/integrase DNA-binding domain
#> 379 zinc finger region:C2H2-type 3
#> 380 IPR015880:Zinc finger, C2H2-like
#> 381 IPR007087:Zinc finger, C2H2
#> 382 SM00355:ZnF_C2H2
#> Count % PValue
#> 375 13 4.561403509 0.786501474
#> 376 5 1.754385965 0.940556728
#> 377 5 1.754385965 0.966210186
#> 378 6 2.105263158 0.968764809
#> 379 4 1.403508772 0.991730098
#> 380 5 1.754385965 0.993553747
#> 381 5 1.754385965 0.995669424
#> 382 5 1.754385965 0.998219364
#> Genes
#> 375 9232, 195828, 2305, 144455, 79733, 51176, 687, 678, 3399, 6941, 1958, 639, 7704
#> 376 687, 195828, 1958, 639, 7704
#> 377 687, 195828, 1958, 639, 7704
#> 378 687, 195828, 5896, 1958, 639, 7704
#> 379 687, 1958, 639, 7704
#> 380 687, 195828, 1958, 639, 7704
#> 381 687, 195828, 1958, 639, 7704
#> 382 687, 195828, 1958, 639, 7704
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 375 255 961 16881 0.895525494 1 1
#> 376 269 554 20063 0.673137573 1 1
#> 377 269 615 20063 0.606371082 1 1
#> 378 255 712 18559 0.613317911 1 1
#> 379 269 636 20063 0.469079516 1 1
#> 380 255 762 18559 0.477561628 1 1
#> 381 255 799 18559 0.455446759 1 1
#> 382 158 762 10057 0.417663378 1 1
#> FDR
#> 375 0.971360382
#> 376 0.998950682
#> 377 0.998950682
#> 378 0.991212654
#> 379 0.998950682
#> 380 0.993553747
#> 381 0.995669424
#> 382 1
#>
#> $`Annotation Cluster 43`
#> Category Term Count % PValue
#> 386 GOTERM_CC_DIRECT GO:0005886~plasma membrane 50 17.54385965 0.95704674
#> 387 UP_KEYWORDS Cell membrane 25 8.771929825 0.99944583
#> 388 UP_KEYWORDS Membrane 64 22.45614035 0.999998504
#> Genes
#> 386 9466, 6279, 5026, 3684, 23166, 23643, 3161, 672, 27242, 3958, 8809, 2268, 11024, 9934, 8807, 9833, 1230, 9590, 3572, 2237, 10507, 687, 963, 90427, 113130, 6915, 2956, 6654, 2012, 27346, 57561, 4193, 2207, 26051, 3537, 3459, 26011, 9976, 55273, 1800, 10602, 1687, 2215, 1368, 10288, 113791, 9928, 7704, 8915, 2934
#> 387 6279, 27346, 57561, 2207, 26051, 27242, 3459, 26011, 2268, 221472, 931, 9934, 9833, 1230, 3572, 55273, 1800, 1687, 1368, 2215, 10507, 963, 113791, 7803, 6915
#> 388 9466, 6279, 5026, 3684, 63027, 23166, 58475, 3043, 672, 115361, 10018, 27242, 8809, 2268, 5897, 11024, 9934, 8807, 7298, 9833, 11031, 1230, 9590, 3572, 56660, 10507, 255027, 963, 6713, 51338, 7803, 6915, 8739, 7466, 2012, 153579, 25840, 2055, 27346, 57561, 29887, 2207, 10678, 26051, 3459, 26011, 221472, 931, 6645, 9976, 55273, 1800, 10602, 1687, 2215, 1368, 85027, 23670, 85465, 944, 10288, 113791, 51514, 8915
#> List Total Pop Hits Pop Total Fold Enrichment Bonferroni Benjamini
#> 386 266 4121 18224 0.831245792 1 1
#> 387 270 3175 20581 0.600204141 1 1
#> 388 270 7494 20581 0.65098202 1 1
#> FDR
#> 386 0.95704674
#> 387 0.99944583
#> 388 0.999998504
#>
#> $`Annotation Cluster 44`
#> Category Term Count
#> 392 INTERPRO IPR000276:G protein-coupled receptor, rhodopsin-like 3
#> 393 INTERPRO IPR017452:GPCR, rhodopsin-like, 7TM 3
#> 394 UP_KEYWORDS G-protein coupled receptor 3
#> 395 UP_KEYWORDS Transducer 3
#> % PValue Genes List Total Pop Hits Pop Total
#> 392 1.052631579 0.999535331 1230, 9934, 6915 255 719 18559
#> 393 1.052631579 0.999627716 1230, 9934, 6915 255 736 18559
#> 394 1.052631579 0.999845568 1230, 9934, 6915 270 842 20581
#> 395 1.052631579 0.999924834 1230, 9934, 6915 270 899 20581
#> Fold Enrichment Bonferroni Benjamini FDR
#> 392 0.303673403 1 1 0.999535331
#> 393 0.296659207 1 1 0.999627716
#> 394 0.27158881 1 1 0.999845568
#> 395 0.254369052 1 1 0.999924834
#>