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Coexpression cluster:C2674: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000467!4.41e-16!625;UBERON:0000480!6.66e-16!626;UBERON:0000468!5.46e-14!659;UBERON:0002050!1.79e-12!605;UBERON:0005423!1.79e-12!605;UBERON:0000062!1.80e-12!511;UBERON:0000922!2.06e-12!612;UBERON:0000923!3.03e-12!604;UBERON:0005291!3.03e-12!604;UBERON:0006598!3.03e-12!604;UBERON:0002532!3.03e-12!604;UBERON:0000477!2.05e-10!286;UBERON:0004111!4.58e-08!241;UBERON:0001986!2.92e-07!18;UBERON:0004638!2.92e-07!18;UBERON:0004852!2.92e-07!18;UBERON:0000033!6.09e-07!123;UBERON:0004121!9.44e-07!169
|ontology_enrichment_uberon=UBERON:0000467!4.41e-16!625;UBERON:0000480!6.66e-16!626;UBERON:0000468!5.46e-14!659;UBERON:0002050!1.79e-12!605;UBERON:0005423!1.79e-12!605;UBERON:0000062!1.80e-12!511;UBERON:0000922!2.06e-12!612;UBERON:0000923!3.03e-12!604;UBERON:0005291!3.03e-12!604;UBERON:0006598!3.03e-12!604;UBERON:0002532!3.03e-12!604;UBERON:0000477!2.05e-10!286;UBERON:0004111!4.58e-08!241;UBERON:0001986!2.92e-07!18;UBERON:0004638!2.92e-07!18;UBERON:0004852!2.92e-07!18;UBERON:0000033!6.09e-07!123;UBERON:0004121!9.44e-07!169
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00818445891384525!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106617225829292!E2F4#1874;4:12.6680603152844:3.88145892637771e-05:0.000727914686320635!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00997923299069506!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161098432175995!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.0039054989532757!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00248351905860039!SPI1#6688;4:8.20432350852273:0.00022066188152768:0.00249628533848238!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322732711759564!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115571918193277!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249317052120137
|tfbs_overrepresentation=0.191353,0.0774498,3.28468e-14,0.0631091,0.257053,0.0761719,0.0569281,6.99333e-08,0.043387,0.0341265,0.0175562,0.00510754,0.243414,0.164339,0.193153,0.0816702,0.0179544,0.128744,0.0698403,0.141416,1.11198e-05,0.172742,0.107781,0.124486,0.0550418,0.276459,0.268949,0.000309089,0.186914,0.122514,0.26347,0.149094,0.0239693,0.267529,0.0877018,0.111013,1.29234e-09,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.00116753,0.2375,0.157881,0.0480278,0.0503649,0.234372,0.145553,0.158244,0.19996,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.0412226,0.103044,0.138225,0.0390464,0.194086,0.142115,0.00517131,0.0720888,0.0667453,0.0210971,0.0792005,0.113084,0.216289,0.0267205,0.0892037,0.116917,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.150119,0.0780785,0.320801,0.0848546,0.268505,0.00032273,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.112199,0.150351,0.000218357,0.199405,0.121709,0.347653,0.0759036,0.350158,0.184542,0.0491142,0.280878,0.0541957,0.0883058,0.000266423,0.187509,0.34189,0.0302681,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.215858,0.275495,0.182323,0.112709,0.134107,0.228632,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.000279662,0.202388,3.92416e-05,0.0913381,0.129544,0.110696,0.0515825,0.157774,0.258146,0.186826,0.000168201,0.0352845,0.0565357,0.153577,0.0984158,0.0476129,0.0683304,0.0447121,0.291455,0.124982,0.152417,0.192028,0.346873,0.149398,0.0530169,0.166112,0.0534404,0.392741,0.2321,0.179282,0.052046,0.0715212,0.00573076,0.118265,0.182591,0.234755,0.230552,0.0472274,0.205973,0.159869,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.108938,0.224443,0.140245,0.241581,0.160458,0.292792,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,0.177664,0.329956,0.346995,0.197158,0.265132,0.230439,0.0606832,0.136664,0.158184,0.147626,0.00174837,0.218801,0.21271,0.132273,0.000101987,0.134907,0.184613,0.128945,0.202467,0.208718,0.0972471,0.165147,0.180711,0.112956,0.0797807,0.0790532,2.07994e-11,5.9059e-05,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.435782,0.128998,0.109226,0.151958,0.178155,0.107176,0.146021,0.0253438,0.15291,0.206234,0.0311341,0.0313311,0.128521,0.1286,0.00174962,0.14037,0.259646,0.0916845,4.39927e-07,0.0816983,0.226367,0.0241753,0.167038,0.0457509,0.106603,0.106727,0.00761313,0.154253,0.0993998,0.00993324,0.00358623,5.57848e-05,0.00133086,0.113754,0.0504034,0.0152877,0.690367,2.60984e-08,5.40003e-05,1.94125e-07,0.000985425,5.90886e-06,3.45352e-13,0.420045,0.381628,0.332539,0.00863402,0.464128,0.389374,0.22808,0.414547,0.0308146,0.00220562,1.18123e-05,0.0406667,0.34505,0.369161,0.500422,0.00507494,0.00127744,0.00807111,0.241524,0.122191,0.234628,0.168228,0.143893,0.0172441,0.279946,0.524104,0.467825,0.00165106,2.92879e-11,1.03924e-05,0.076794,0.460819,0.00086985,0.0126595,0.322903,0.350886,0.380582,0.583749,0.0150105,0.0455719,0.0151426,8.10446e-08,0.359128,0.395864,0.0065023,0.0782875,0.547291,3.94178e-08,0.162437,0.0116693,0.00196408,0.0434864,0.464342,0.683088,0.000322852,0.235444,5.31026e-05,3.30196e-09,0.000639859,0.349116,0.005939,0.239545,0.000305093,0.640367,0.343881,0.0110284,0.0682924,0.00048534,0.626346,0.316925,0.356561,0.210197,0.211506,0.0883859,0.0962508,0.238465,0.00802494,1.76865e-08,0.0306084,8.53678e-07,0.00423142,0.0907578,0.28972,0.000175169,0.280307,0.0144019,0.000243703,0.0596868,0.0984075,0.00537023,2.80916e-12,0.694744,6.09636e-06,0.0799295,0.109146,0.0572193,0.0769243,0.000221302,1.1034e-10,0.35234,1.31751e-08,0.0071728,0.291917,0.421082,0.25441,0.202782,3.06212e-08,0.0378508,0.219758,0.165503,0.0746589,2.91706e-09,0.00025343,0.188259,0.189182,0.138387,0.131612,0.0460871,0.560187,0.321282,0.198207,0.0616078,0.178485,0.000776942,0.175552,0.129238,0.651295,0.370995,0.074448,0.429696,0.386216,0.0861729,0.00167285,0.0683036,0.627185,0.360203,0.333725,0.119902,0.289666,0.153861,0.0365674,0.452694,0.565545,0.00314045,0.265037,1.06896e-06,0.0032633,0.53531,0.341771,0.424526,1.11305e-11,0.356381,0.184395,0.00149131,0.00336238,0.206945,0.304719,0.00378814,0.296994,0.0326312,0.117049,0.0786167,0.000571771,1.24498e-06,0.433821,0.64428,0.113459,0.0563264,0.0330909,0.00283311,0.0115505,0.397546,0.0919254,0.0735469,0.248103,0.102621,0.0760107,0.187642,0.286156,0.000278118,1.13251e-08,0.183047,0.247151,0.146385,0.0769978,0.0576261,0.382413,0.164977,0.175633,0.139918,0.00937608,0.0828344,0.135364,0.0238089,0.383126,0.00107967,0.0294482,0.0614918,0.219485,0.149782,0.136923,0.118103,0.113892,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.270152,0.0340965,0.111145,0.0660736,0.108971,0.0879235,0.235214,0.145546,0.28124,0.417003,0.251882,0.172263,0.0323461,0.0637178,0.257309,0.153907,0.166608,7.65498e-06,0.030904,0.0259579,0.115115,0.124916,0.0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149794,0.28498,0.140114,0.348988,0.00641248,0.0273633,0.183585,0.271662,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.00571021,0.00852994,0.207615,0.161213,0.118999,0.0737069,0.0104244,0.0752771,0.178782,0.019419,0.0866228,0.0408454,0.044355,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.0593965,0.220368,0.258624,0.064656,0.0277507,0.000447146,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.515487,0.013521,0.142462,0.143935,4.28102e-06,0.0379537,0.00471564,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.0303627,0.302909,0.363016,0.100188,6.92761e-06,0.107653,9.38741e-06,2.26512e-05,0.191914,0.184022,0.216557,0.0178622,0.00710556,1.32358e-05,0.0757944,0.0625685,0.124464,0.00856472,0.173134,0.101893,0.142875,0.167635,0.171311,3.56798e-05,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,6.12362e-08,0.0560157,0.278645,0.011228,0.155708,0.248017,0.22995,0.000117736,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.00147405,0.00455803,0.286748,0.0114526,0.0471607,0.163865,0.226359,6.13141e-08,4.77058e-15,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.000433669,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.000138179,0.137423,0.284016,0.00292377,0.299492,0.100006,0.0756617,0.197817,0.251078,0.0434358,0.133127,0.410303,0.223717,0.107609,8.07734e-05,0.0826805,0.246601,0.193021,0.240896,0.202165,0.0946865,0.120618,0.079499,0.18762,0.0205193,0.127688,0.201169,0.0262879,1.27832e-05,0.178639,0.291976,0.320355,0.000109304,0.0127656,0.000243487,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.06079,0.135777,0.147842,0.0339286,0.217363,0.119015,0.0315791,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,6.38907e-09,0.0780061,0.315336,0.230477,0.043419,0.0487563,8.82193e-05,0.369553,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.514243,0.459091,0.54832,0.502211,0.296013,0.0895871,0.537932,0.459994,0.170061,0.0465928,0.25423,0.490559,0.45013,8.62945e-05,0.472542,0.685908,0.00294638,0.00109146,1.90238e-06,0.029441,0.224887,0.603763,1.77808e-05,0.627201,0.00233402,8.58382e-10,0.290703,9.13824e-07,1.1335e-10,0.0284983,0.360199,6.43357e-06,0.000126158,4.35335e-08,0.0111989,0.212703,0.201391,0.364079,2.58163e-05,0.215551,0.104625,0.206595,0.328518,0.00132729,0.310552,8.41878e-06,0.00472069,8.52123e-13,0.00493585,0.209437,0.00302432,2.94634e-09,0.0141441,8.0873e-05,0.12974,5.69321e-05,0.0572388,2.61836e-07,1.47997e-11,4.1262e-05,0.261575,0.257956,0.000289388,0.379063,0.326516,0.00100422,0.436016,0.475063,0.202522,0.183837,9.5659e-05,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.357409,0.000254095,0.721266,0.50338,0.620526,0.404625,0.0034658,0.424691,0.132999,0.0286876,0.003448,0.884725,1.42832e-07,0.284496,0.512545,0.512178,0.563206,2.64616e-06,2.83089e-05,0.263302,0.192292,0.180735,0.439629,0.216102,0.254659,0.109605,0.0149457,0.582542,0.226491,0.417131,0.463987,0.627953,0.000790209,0.000414202,0.0840572,0.483658,0.452129,0.301581,0.261657,0.346776,0.466529,0.187223,0.0208637,0.349112,0.000509621,0.385425,0.307816,0.461541,0.386339,0.382854,4.00803e-09,0.139139,0.0158475,0.319747,0.136743,0.557967,0.608127,0.282281,0.245336,0.2536,0.246827,0.564333,0.12664,0.387134,0.559969,0.358813,0.000153433,0.574252,0.493455,0.346636,0.457747,0.348802,0.476541,0.579645,0.119749,0.42505,0.254628,4.88736e-05,0.479347,0.102411,0.632833,0.378333,1.86504e-07,0.264038,0.22798,0.102495,0.0703938,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.0331645,0.211271,0.281295,0.267248,0.118257,0.000359908,0.215123,0.321224,0.469461,0.325254,0.266651,0.546295,0.231754,0.00317894,0.283107,0.285648,0.10809,0.391071,0.279553,0.0358792,0.240967,0.160955,0.036192,0.0432189,0.122439,0.000804479,0.23235,0.290415,0.353147,0.112422,0.0155121,0.267687,0.315656,0.284866,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.0238089,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.0369803,0.00289389,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.0311922,0.095257,0.0612213,0.332769,3.63812e-08,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.0554083,0.00224298,1.53509e-05,0.181895,0.253768,0.00626086,0.202977,0.170837,0.327002,0.0452813,0.222656,0.228479,0.127111,0.259989,0.390754,0.0102294,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.00193565,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.111581,0.0181468,0.334474,0.325785,0.257476,0.000444529,0.376537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}}
}}

Revision as of 13:58, 5 September 2012


Full id: C2674_tubular_rectal_hepatoblastoma_anaplastic_glioblastoma_chorionic_tridermal



Phase1 CAGE Peaks

Hg19::chr2:182756701..182756720,+p7@SSFA2
Hg19::chr2:182756737..182756753,+p10@SSFA2
Hg19::chr2:182756779..182756790,+p18@SSFA2
Hg19::chr2:182756793..182756802,+p17@SSFA2


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
anatomical system4.41e-16625
anatomical group6.66e-16626
multi-cellular organism5.46e-14659
embryonic structure1.79e-12605
developing anatomical structure1.79e-12605
organ1.80e-12511
embryo2.06e-12612
germ layer3.03e-12604
embryonic tissue3.03e-12604
presumptive structure3.03e-12604
epiblast (generic)3.03e-12604
anatomical cluster2.05e-10286
anatomical conduit4.58e-08241
endothelium2.92e-0718
blood vessel endothelium2.92e-0718
cardiovascular system endothelium2.92e-0718
head6.09e-07123
ectoderm-derived structure9.44e-07169


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066445.360256373075030.001211145381643620.00818445891384525
E2F1#186944.907389214879320.001724022357361790.0106617225829292
E2F4#1874412.66806031528443.88145892637771e-050.000727914686320635
E2F6#187645.017155731697390.00157802193473060.00997923299069506
ELF1#199744.258097958807540.003041525565781240.0161098432175995
GABPB1#255347.067683836182170.0004006876864423170.0039054989532757
HMGN3#932448.178547723350590.0002234570284440470.00248351905860039
SPI1#668848.204323508522730.000220661881527680.00249628533848238
TAF1#687243.343046285745290.008005664898701650.0322732711759564
TCF7L2#6934410.77017656313737.42969445082454e-050.00115571918193277
ZNF263#1012748.221841637010680.0002187871180958320.00249317052120137



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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