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Coexpression cluster:C2827: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!2.97e-25!365;UBERON:0002100!1.98e-16!216;UBERON:0000914!7.39e-16!83;UBERON:0002329!7.39e-16!83;UBERON:0003077!7.39e-16!83;UBERON:0003059!7.39e-16!83;UBERON:0007282!7.39e-16!83;UBERON:0009618!7.39e-16!83;UBERON:0007285!7.39e-16!83;UBERON:0005256!1.47e-14!143;UBERON:0003102!4.85e-14!95;UBERON:0000486!3.37e-13!82;UBERON:0002199!4.61e-13!45;UBERON:0002416!4.61e-13!45;UBERON:0002097!1.06e-12!40;UBERON:0004290!2.63e-12!70;UBERON:0000481!1.01e-10!347;UBERON:0003104!1.94e-10!238;UBERON:0009142!1.94e-10!238;UBERON:0000468!4.34e-10!659;UBERON:0001134!1.18e-09!61;UBERON:0002036!1.18e-09!61;UBERON:0003082!1.18e-09!61;UBERON:0002385!4.75e-09!63;UBERON:0001015!4.75e-09!63;UBERON:0000383!4.75e-09!63;UBERON:0000480!3.31e-08!626;UBERON:0000467!4.95e-08!625;UBERON:0000119!6.64e-08!312;UBERON:0001637!2.86e-07!42;UBERON:0003509!2.86e-07!42;UBERON:0004572!2.86e-07!42;UBERON:0000483!3.72e-07!309
|ontology_enrichment_uberon=UBERON:0000475!2.97e-25!365;UBERON:0002100!1.98e-16!216;UBERON:0000914!7.39e-16!83;UBERON:0002329!7.39e-16!83;UBERON:0003077!7.39e-16!83;UBERON:0003059!7.39e-16!83;UBERON:0007282!7.39e-16!83;UBERON:0009618!7.39e-16!83;UBERON:0007285!7.39e-16!83;UBERON:0005256!1.47e-14!143;UBERON:0003102!4.85e-14!95;UBERON:0000486!3.37e-13!82;UBERON:0002199!4.61e-13!45;UBERON:0002416!4.61e-13!45;UBERON:0002097!1.06e-12!40;UBERON:0004290!2.63e-12!70;UBERON:0000481!1.01e-10!347;UBERON:0003104!1.94e-10!238;UBERON:0009142!1.94e-10!238;UBERON:0000468!4.34e-10!659;UBERON:0001134!1.18e-09!61;UBERON:0002036!1.18e-09!61;UBERON:0003082!1.18e-09!61;UBERON:0002385!4.75e-09!63;UBERON:0001015!4.75e-09!63;UBERON:0000383!4.75e-09!63;UBERON:0000480!3.31e-08!626;UBERON:0000467!4.95e-08!625;UBERON:0000119!6.64e-08!312;UBERON:0001637!2.86e-07!42;UBERON:0003509!2.86e-07!42;UBERON:0004572!2.86e-07!42;UBERON:0000483!3.72e-07!309
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106756297272921!MAX#4149;3:4.83941663175534:0.0131573713783684:0.0466427721185775!TCF7L2#6934;3:8.07763242235301:0.00297838168583462:0.0158695579249468!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483318993692271!USF2#7392;3:9.7441480388022:0.00171834184841007:0.010725669633403!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00249780365400203
|tfbs_overrepresentation=0.191353,0.0774498,0.0285313,0.0631091,0.257053,0.363996,0.0569281,0.510252,0.043387,0.0341265,0.181435,0.288577,0.243414,0.164339,0.193153,0.0816702,0.183412,0.128744,0.00249768,0.141416,0.243245,0.172742,0.107781,0.124486,0.0550418,0.276459,0.268949,0.119094,0.186914,0.000337432,0.26347,0.149094,0.0239693,0.267529,0.0877018,0.111013,0.0725724,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.182216,0.2375,0.000743793,0.0480278,0.0503649,0.234372,0.145553,0.158244,0.19996,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.0412226,0.103044,0.138225,0.0390464,0.194086,0.142115,0.0999599,0.00266319,0.0667453,0.439574,0.0792005,0.00664966,0.216289,4.75393e-06,0.0892037,0.116917,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.150119,0.0114792,0.00723919,0.0848546,0.268505,0.713984,0.0827752,0.112676,0.0655645,0.00817476,0.0626609,0.112199,0.150351,0.0314145,0.199405,0.121709,0.347653,0.0759036,0.0010213,0.184542,0.0491142,0.280878,0.0541957,0.0883058,0.105785,0.00127811,0.34189,0.23573,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.025182,0.275495,0.182323,0.00660477,0.134107,0.228632,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.262198,9.09875e-05,0.0346699,0.0913381,0.129544,0.110696,0.0515825,0.157774,0.258146,0.186826,0.00256648,0.0352845,0.0565357,0.153577,0.00501002,0.29227,0.0683304,0.0447121,0.291455,0.124982,0.152417,0.192028,0.346873,0.149398,0.0530169,0.166112,0.00145408,0.392741,0.0293007,0.179282,0.564569,0.0715212,0.105131,0.118265,0.182591,0.234755,0.230552,0.0472274,0.205973,0.000773546,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.108938,0.224443,0.140245,0.00286806,0.160458,0.292792,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,0.177664,0.329956,0.346995,0.197158,0.265132,0.00246422,0.0606832,0.136664,0.158184,0.147626,0.393313,0.218801,0.21271,0.132273,0.0830988,0.134907,0.0181987,0.462724,0.202467,0.208718,0.0972471,0.165147,0.180711,0.112956,0.0797807,0.0790532,0.309911,0.000556141,0.0553945,0.10068,0.00826774,0.122288,0.0624687,0.334388,0.000110669,0.275612,0.235571,0.112872,0.128998,0.109226,0.151958,0.178155,0.107176,0.146021,0.463127,0.15291,0.206234,0.238926,0.239646,0.128521,0.1286,0.207017,0.14037,0.259646,0.0916845,0.00685525,0.0816983,0.226367,0.211672,0.167038,0.0457509,0.106603,0.106727,0.12083,0.154253,0.0993998,0.352707,0.0834863,0.324356,0.0458938,0.113754,0.0504034,0.169684,0.690367,0.233666,0.869559,0.0122628,0.100371,0.0307547,0.0719958,0.420045,0.381628,0.332539,0.0457383,0.00385231,0.389374,0.0135348,0.101113,0.146105,0.017023,0.084046,0.137229,0.0092283,0.369161,0.500422,0.49089,0.323639,0.123196,0.241524,0.122191,0.234628,0.520726,0.143893,0.101233,0.279946,0.524104,0.467825,0.563725,0.164225,0.632838,0.624969,0.460819,0.511459,0.221488,0.322903,0.350886,0.380582,0.00209301,0.398372,0.286293,0.239547,0.127626,0.359128,0.395864,0.109703,0.368633,0.0463511,0.317802,0.00630994,0.0116693,0.0569945,0.181193,0.464342,0.683088,0.131933,0.235444,0.0835105,0.199727,0.279301,0.349116,0.302142,0.239545,0.432689,0.640367,0.343881,0.377117,0.0682924,0.0733855,0.626346,0.316925,0.356561,0.573659,0.211506,0.0883859,0.0962508,0.238465,0.70198,0.0456265,0.323783,0.508325,0.0636247,0.0907578,0.093482,0.188468,0.280307,0.393583,0.469888,0.0596868,0.00500916,0.293026,0.0537754,0.694744,0.0678767,0.372182,0.429205,0.578951,0.365653,0.41035,0.0201516,0.35234,0.072148,0.525923,0.291917,0.421082,0.25441,0.202782,0.103116,0.517933,0.584705,0.517001,0.252778,0.000386543,0.419676,0.188259,0.189182,0.477589,0.131612,0.0460871,0.198922,0.321282,0.198207,0.0616078,0.178485,0.329745,0.175552,0.129238,0.0904061,0.370995,0.360161,0.429696,0.386216,0.385297,0.706685,0.0151224,0.259338,0.360203,0.333725,0.0225184,0.289666,0.500627,0.16264,0.452694,0.565545,0.0122456,0.0387162,0.261923,0.410093,0.53531,0.341771,0.424526,0.657528,0.356381,0.184395,0.0489035,0.256884,0.206945,0.304719,0.462531,0.296994,0.244339,0.117049,0.0786167,0.629381,0.0109535,0.433821,0.276604,0.436806,0.0563264,0.499072,0.158149,0.734628,0.397546,0.0919254,0.0735469,0.00312528,0.102621,0.0760107,0.187642,0.286156,0.261868,0.541583,0.00823386,0.247151,0.146385,0.365815,0.0576261,0.382413,0.164977,0.175633,0.139918,0.34669,0.0828344,0.00422161,0.0238089,0.0131382,0.354433,0.48311,0.0614918,0.219485,0.149782,0.136923,0.118103,0.113892,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.270152,0.249506,0.432751,0.0660736,0.108971,0.0879235,0.235214,0.145546,0.28124,0.417003,0.251882,0.172263,0.243319,0.0637178,0.257309,0.500692,0.166608,0.227224,0.238082,0.219023,0.115115,0.124916,0.0149794,0.28498,0.140114,0.348988,0.00641248,0.0273633,0.183585,0.271662,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,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}}
}}

Revision as of 13:22, 5 September 2012


Full id: C2827_Pericytes_Osteoblast_Smooth_astrocytoma_Fibroblast_transitionalcell_alveolar



Phase1 CAGE Peaks

Hg19::chr5:72743793..72743855,-p4@FOXD1
Hg19::chr5:72744445..72744466,-p2@FOXD1
Hg19::chr5:72744562..72744573,-p3@FOXD1
Hg19::chr5:72744594..72744609,-p1@FOXD1


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
organism subdivision2.97e-25365
trunk1.98e-16216
somite7.39e-1683
paraxial mesoderm7.39e-1683
presomitic mesoderm7.39e-1683
presumptive segmental plate7.39e-1683
trunk paraxial mesoderm7.39e-1683
presumptive paraxial mesoderm7.39e-1683
trunk mesenchyme1.47e-14143
surface structure4.85e-1495
multilaminar epithelium3.37e-1382
integument4.61e-1345
integumental system4.61e-1345
skin of body1.06e-1240
dermomyotome2.63e-1270
multi-tissue structure1.01e-10347
mesenchyme1.94e-10238
entire embryonic mesenchyme1.94e-10238
multi-cellular organism4.34e-10659
skeletal muscle tissue1.18e-0961
striated muscle tissue1.18e-0961
myotome1.18e-0961
muscle tissue4.75e-0963
musculature4.75e-0963
musculature of body4.75e-0963
anatomical group3.31e-08626
anatomical system4.95e-08625
cell layer6.64e-08312
artery2.86e-0742
arterial blood vessel2.86e-0742
arterial system2.86e-0742
epithelium3.72e-07309


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
E2F1#186944.907389214879320.001724022357361790.0106756297272921
MAX#414934.839416631755340.01315737137836840.0466427721185775
TCF7L2#693438.077632422353010.002978381685834620.0158695579249468
USF1#739134.771124457905970.01370465887188020.0483318993692271
USF2#739239.74414803880220.001718341848410070.010725669633403
ZNF263#1012748.221841637010680.0002187871180958320.00249780365400203



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.