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Coexpression cluster:C2270: Difference between revisions

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|full_id=C2270_bone_basal_Fibroblast_Olfactory_Preadipocyte_Chondrocyte_osteoclastoma
|full_id=C2270_bone_basal_Fibroblast_Olfactory_Preadipocyte_Chondrocyte_osteoclastoma
|id=C2270
|id=C2270
|ontology_enrichment_celltype=CL:0000055!7.36e-25!180;CL:0000057!1.38e-16!75;CL:0002620!1.39e-08!23;CL:0000680!4.09e-07!57;CL:0000056!4.09e-07!57;CL:0000355!4.09e-07!57;CL:0000183!8.63e-07!59
|ontology_enrichment_celltype=CL:0000057!1.63e-16!76;CL:0002620!4.50e-09!23;CL:0000055!1.77e-08!106
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!2.05e-11!365;UBERON:0002100!5.62e-09!216;UBERON:0005256!6.21e-09!143;UBERON:0000914!6.92e-09!83;UBERON:0002329!6.92e-09!83;UBERON:0003077!6.92e-09!83;UBERON:0003059!6.92e-09!83;UBERON:0007282!6.92e-09!83;UBERON:0009618!6.92e-09!83;UBERON:0007285!6.92e-09!83;UBERON:0003102!2.76e-08!95;UBERON:0004290!2.91e-08!70;UBERON:0000486!6.64e-08!82;UBERON:0004923!1.60e-07!57;UBERON:0000481!4.81e-07!347
|ontology_enrichment_uberon=UBERON:0003102!1.07e-09!99;UBERON:0002199!5.05e-09!46;UBERON:0002416!5.05e-09!46;UBERON:0004923!7.08e-08!66;UBERON:0003104!7.19e-08!160;UBERON:0009142!7.19e-08!160;UBERON:0002329!3.89e-07!71;UBERON:0003059!3.89e-07!71;UBERON:0007282!3.89e-07!71;UBERON:0004290!3.89e-07!71;UBERON:0009618!3.89e-07!71;UBERON:0002097!5.03e-07!41;UBERON:0007503!5.51e-07!78;UBERON:0007524!6.47e-07!73;UBERON:0003077!7.43e-07!72;UBERON:0007285!7.43e-07!72
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106327607759837!NR3C1#2908;3:11.2297674983798:0.00113167206806385:0.00775326024117822!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321553586783902!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162740792114947!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115211560319178!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613015880676696
|tf_chipseq_enrich=E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106327607759837!NR3C1#2908;3:11.2297674983798:0.00113167206806385:0.00775326024117822!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321553586783902!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162740792114947!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115211560319178!ZEB1#6935;3:12.6663240131579:0.00079333607591285:0.00613015880676696
|tfbs_overrepresentation=0.191353,0.0774498,0.814139,0.0631091,0.257053,0.363996,0.0569281,0.510252,0.043387,0.0341265,0.181435,0.288577,0.243414,0.164339,0.193153,0.0816702,0.183412,0.128744,0.0698403,0.141416,0.243245,0.172742,0.107781,0.124486,0.0550418,0.276459,0.039931,0.119094,0.186914,0.122514,0.26347,0.149094,0.0239693,0.267529,0.0877018,0.111013,0.0725724,0.0568767,0.157159,0.0879352,0.126525,0.0326801,0.182216,0.0307461,0.157881,0.0480278,0.0503649,0.234372,0.145553,0.158244,0.19996,0.0715789,0.0924421,0.12203,0.255843,0.0508907,0.140644,0.273035,0.103044,0.138225,0.0390464,0.194086,0.142115,0.0999599,0.0720888,0.0667453,0.439574,0.0792005,7.85195e-06,0.216289,0.470097,0.0892037,0.116917,0.155921,0.00995563,0.0227583,0.126543,0.0578308,0.0493551,0.00965832,0.125428,0.290468,0.0562614,0.150119,0.368178,0.320801,0.0848546,0.268505,0.713984,0.0827752,0.112676,0.0655645,0.12511,0.0626609,0.112199,0.150351,0.690341,0.199405,0.121709,0.347653,0.0759036,0.350158,0.184542,0.0491142,0.280878,0.0541957,0.0883058,0.423154,0.187509,0.34189,0.23573,0.0450707,0.194256,0.0235108,0.132631,0.0447483,0.0270258,0.0748174,0.180926,0.110194,0.215858,0.275495,0.182323,0.112709,0.134107,0.228632,0.119051,0.0196757,0.110868,0.175735,0.078637,0.0985137,0.0755515,0.0302655,0.164103,0.141472,0.085537,0.0730922,0.0438087,0.0052702,0.0302521,0.166414,0.262198,0.202388,0.341095,0.0913381,0.129544,0.110696,0.0515825,0.157774,0.258146,0.186826,0.233377,0.0352845,0.0565357,0.153577,0.0984158,0.29227,0.0683304,0.0447121,0.291455,0.124982,0.152417,0.00137816,0.346873,0.149398,0.0530169,0.166112,0.0534404,0.392741,0.2321,0.179282,0.202544,0.0715212,0.105131,0.118265,0.182591,0.234755,0.230552,0.0472274,0.205973,0.159869,0.0363736,0.15105,0.0970713,0.155237,0.236268,0.0532055,0.108938,0.224443,0.140245,0.241581,0.0136231,0.292792,0.147332,0.0622664,0.102951,0.0795624,0.0891668,0.14349,0.117261,0.0797088,0.0408965,0.0799774,0.177664,0.329956,0.346995,0.197158,0.265132,0.230439,0.0606832,0.136664,0.158184,0.147626,0.393313,0.218801,0.21271,0.132273,0.0830988,0.134907,0.184613,0.462724,0.202467,0.208718,0.0972471,0.165147,0.180711,0.112956,0.0797807,0.0790532,0.00594786,0.000556141,0.0553945,0.10068,0.125804,0.122288,0.0624687,0.334388,0.21183,0.275612,0.235571,0.435782,0.128998,0.109226,0.151958,0.178155,0.107176,0.146021,0.129196,0.15291,0.206234,0.238926,0.239646,0.128521,0.1286,0.207017,0.14037,0.259646,0.0916845,0.687863,0.0816983,0.226367,0.211672,0.167038,0.0457509,0.106603,0.106727,0.12083,0.154253,0.0993998,0.352707,0.0834863,0.0594434,0.00867491,0.113754,0.0504034,0.169684,0.690367,0.810881,0.869559,0.73998,0.668426,0.672445,0.0246898,0.420045,0.73391,0.332539,0.545329,0.464128,0.389374,0.22808,0.414547,0.489273,0.413223,0.639461,0.720642,0.34505,0.369161,0.500422,0.49089,0.687176,0.341822,0.241524,0.45167,0.234628,0.520726,0.143893,0.41477,0.279946,0.524104,0.0262654,0.051755,0.751064,0.264959,0.624969,0.460819,0.511459,0.221488,0.322903,0.350886,0.380582,0.583749,0.398372,0.286293,0.606558,0.708425,0.359128,0.395864,0.683133,0.368633,0.547291,0.682118,0.162437,0.369971,0.214221,0.537928,0.464342,0.683088,0.714007,0.235444,0.48585,5.44744e-06,0.0391412,0.349116,0.302142,0.239545,0.432689,0.640367,0.343881,0.730486,0.239383,0.617741,0.626346,0.316925,0.356561,0.573659,0.211506,0.0883859,0.0962508,0.238465,0.70198,0.853221,0.323783,0.159267,0.436735,0.284591,0.28972,0.54723,0.280307,0.393583,0.794849,0.0596868,0.0984075,0.293026,0.16661,0.117621,0.0149898,0.372182,0.429205,0.578951,0.0769243,0.41035,0.784024,0.35234,0.888839,0.525923,0.291917,0.421082,0.25441,0.202782,0.672876,0.517933,0.0594062,0.517001,0.620475,8.9551e-05,0.419676,0.188259,0.189182,0.477589,0.131612,0.187849,0.198922,0.321282,0.198207,0.0616078,0.178485,0.329745,0.175552,0.129238,0.651295,0.370995,0.0106572,0.429696,0.386216,0.385297,0.706685,0.606408,0.627185,0.360203,0.333725,0.447838,0.289666,0.500627,0.513045,0.452694,0.565545,0.00314045,0.265037,0.629795,0.754776,0.53531,0.341771,0.424526,0.657528,0.356381,0.184395,0.55524,0.256884,0.206945,0.304719,4.68738e-05,0.296994,0.244339,0.117049,0.0786167,0.629381,0.729876,0.433821,0.64428,0.436806,0.576549,0.499072,0.744662,0.734628,0.397546,0.0919254,0.0735469,0.248103,0.102621,0.0760107,0.187642,0.286156,0.261868,0.541583,0.00124449,0.247151,0.146385,0.365815,0.0576261,0.0847761,0.164977,0.175633,0.139918,0.34669,0.0828344,0.0272905,0.0238089,0.383126,0.354433,0.0294482,0.0614918,0.219485,0.149782,0.00983379,0.118103,0.113892,0.207214,0.140201,0.0580534,0.00518407,0.161297,0.168389,0.270152,0.249506,0.432751,0.0660736,0.108971,0.0879235,0.235214,0.145546,0.28124,0.417003,0.251882,0.172263,0.243319,0.0637178,0.257309,0.0334797,0.166608,0.227224,0.030904,0.219023,0.115115,0.124916,0.0149794,0.28498,0.140114,0.348988,0.00641248,0.224626,0.183585,0.00419343,0.03989,0.171436,0.05892,0.0691994,0.268299,0.198844,0.104946,0.127738,0.207615,0.161213,0.118999,0.0737069,0.0734014,0.0173365,0.0170294,0.019419,0.0866228,0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}}
}}

Revision as of 13:49, 19 October 2012


Full id: C2270_bone_basal_Fibroblast_Olfactory_Preadipocyte_Chondrocyte_osteoclastoma



Phase1 CAGE Peaks

Hg19::chr13:76210057..76210116,-p@chr13:76210057..76210116
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Hg19::chr13:76210118..76210129,-p@chr13:76210118..76210129
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Hg19::chr13:76210135..76210148,-p@chr13:76210135..76210148
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Hg19::chr13:76210283..76210375,-p@chr13:76210283..76210375
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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>


Cell Type
Ontology termp-valuen
fibroblast1.63e-1676
skin fibroblast4.50e-0923
non-terminally differentiated cell1.77e-08106
Uber Anatomy
Ontology termp-valuen
surface structure1.07e-0999
integument5.05e-0946
integumental system5.05e-0946
organ component layer7.08e-0866
mesenchyme7.19e-08160
entire embryonic mesenchyme7.19e-08160
somite3.89e-0771
presomitic mesoderm3.89e-0771
presumptive segmental plate3.89e-0771
dermomyotome3.89e-0771
trunk paraxial mesoderm3.89e-0771
skin of body5.03e-0741
epithelial vesicle5.51e-0778
dense mesenchyme tissue6.47e-0773
paraxial mesoderm7.43e-0772
presumptive paraxial mesoderm7.43e-0772


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#186944.907389214879320.001724022357361790.0106327607759837
NR3C1#2908311.22976749837980.001131672068063850.00775326024117822
TAF1#687243.343046285745290.008005664898701650.0321553586783902
TCF12#693837.975848676639820.003090920396013070.0162740792114947
TCF7L2#6934410.77017656313737.42969445082454e-050.00115211560319178
ZEB1#6935312.66632401315790.000793336075912850.00613015880676696



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.