Personal tools

Coexpression cluster:C952: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=-0.0184859436035185,0.00169914096327087,0,0,0,0,0,0.308582306507645,0.1007790131153,0.23985027306034,0,-0.124037672048917,0,0.101015309386435,0.227565350518779,0.370078076395268,0.343485215114616,0.379879641959576,0.391605168214202,0.0220729952058294,0.148603081231402,0.160692681882058,0,0.055712496781182,0,-0.121111108522986,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,0,0.190283657260499,0,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.096764157013265,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,0,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,0,0,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.0530975854295559,0,0,-0.124037672048917,-0.0555133181123769,-0.124037672048917,0,-0.0634698324721987,-0.0991899838091464,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,0,-0.0894927413508433,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.0889537994790287,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.107888059465177,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.0301020637596469,0,-0.086895011524935,-0.124037672048917,-0.124037672048917,-0.0147907295041164,-0.124037672048917,-0.124037672048917,-0.124037672048917,0,0,0,0,0.236254602210782,0.575861014176969,0.209320383404263,0,0,0.0752072885286432,0,0.0050230765026823,0.0534545700183436,0.0846019347229403,0,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,0.378640756572746,0.43464381180907,0.188289394355754,0.430707616901028,0.303772534904847,0.108256925399537,0.365913732867528,0.125221917160996,0.195991095153702,0.12539036754857,0.147004833432507,0.092489600558918,0,0.198799378778179,0.294310675638806,0,0,0,0.196239410176247,0.309087790969388,0.380897946309198,-0.124037672048917,-0.124037672048917,0.0244783924968802,0.352211811922083,0.254893343887708,0.801012016296877,0.554068543182635,0.247397084551145,0.193313197142976,0.108019104294678,0.174088103989846,0,0.251179306823555,0.0110711862573195,0.0372948388517078,0,0.680551859187382,0.543730480608186,0.490963594348175,0.617290381229376,0.620212228271645,0.468551302649934,0.492307998545886,0.401588370973612,0.297251429416291,0.261644939175216,0.635782068260955,0.577369285912357,0.418707299988423,0.38689763493088,0.391376097705806,0.458010059484751,0.511925282031603,0.516796239583682,0.640617145589837,0.68975416004188,0.0576715103727621,0.866710060399188,0.663095174947495,0.742719575484047,0.913929629711276,0.602543353789637,0.717103824847717,0.43294420782395,0.836320334684382,0.30026055504265,0.79611589997642,0.736862642727717,0.491557605921483,0.971862574143604,0.625730812870025,0.580923533048377,0,0,0.145571877041516,0,0.0371702459606866,0.0477396614475454,0.176778134730578,0,0,0.945590515958902,0.68658672730129,0.820717504065653,0.45598193974009,0.602793566972744,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.107408992064713,0,0.580335882294449,0,0,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.102714921280072,0.0687674306079092,0.0258250269936373,0,0.0795639603670563,0.0411895033485145,0.296100002047877,0.281108020569808,0,0.365463403417677,0.131049308664644,0,0,0,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,0,0.0991800321771718,0.0298763195097143,0,0,-0.107837140492803,-0.0334624674625854,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.0712517082600084,0.0722714759357659,0.140504405746413,0.400273912697345,0,0.0425075842205678,0,0.196356628631157,0.251618169550103,0,0.135670470848458,0.306670681722944,0,0.59205417508155,0.638407262316059,0.366141259202036,0.157516981571498,0.459952162289596,0.371697745236413,0,0.195119043827265,-0.124037672048917,0.50510289137997,0,0,0.114423942847335,0,0,-0.124037672048917,-0.124037672048917,-0.124037672048917,0.596644692385467,0.518150390753963,0.732505674556348,0.626702218993502,0.340587578201916,0.726490494339863,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.0688337380735115,0.233058138693924,0.154567528597376,0.000908385274604462,0.0672629396841865,0,-0.124037672048917,-0.124037672048917,-0.124037672048917,0.136109740124972,0.35318231325443,0.432254549085643,0.522338693963035,0.811971856070692,0.70752456402904,0.80909900686074,0.244417422081721,0,0.279637875562783,0.352022144201872,0.486517449428444,0.637784870688304,0.25120118306085,0.283863726705891,-0.0984725845749347,-0.12259281463408,-0.124037672048917,0,0,0,0,0.0404299650507625,0.180905041833071,0.0523626705930769,0,0,-0.124037672048917,0.775751992248474,0.528098198504384,0.70106956811193,0.614425410394021,0.544502303937859,-0.103539048829906,0.0793645050922885,0,0.128542505561081,0.42140985127625,0.183126762043246,0.0718773561608523,0.0322218878591601,0.127442316967891,0,0.0435790287959822,0,0.0682206429897042,0,0,0,0,-0.0285185336891246,0,0,-0.124037672048917,-0.124037672048917,0,0,0.010258787763554,-0.124037672048917,0,-0.0279871961920554,0.399150247986895,0.237712915130319,0.416114259418732,0.631230494680456,0.375192974628546,0.283532349465927,0.656826348451113,0.13135533817354,0.236810113610532,0.281860185692414,0.35149646662684,0,0.0763454992192642,0.0521599633818348,0,0.285487793508896,0.93301587281462,0.590478477483775,0.647529452571426,0.62261146220814,0.651252030031524,0.791237848764644,0.399022269039885,0,0.147743154984885,0.122096572886376,0.485639266172132,0.344955981036526,0.80682111730562,0.692383589290883,0,0,0.0483689238882358,0.601270241123935,0.372286463949045,0.534250336745807,0.172496019467973,0.750551305576967,0.85148658035796,0.149064998316823,0.0706491678139905,0.328396152435088,0.510257384065745,0.592433767418161,0.884880380169162,0.437167932714935,0.116077198681759,0.6736224127444,0.649695212614205,0.682476281183884,0.234784651940436,0.2012589601207,0.659603482418428,0.53374560194577,0.213072052700123,0.422667707943698,0.214132250844346,0.536802266769934,0.110140484268162,0,0,-0.0803413847614247,0.00239928687087976,0,0.00630556716237235,0.124734703408214,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,0,-0.124037672048917,0,-0.124037672048917,-0.124037672048917,0.382239346160252,-0.0579068266079397,-0.124037672048917,-0.0655094588197137,0,0,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.044205578184085,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,0,0,-0.124037672048917,-0.124037672048917,-0.0533580043035756,0,-0.124037672048917,-0.04078946913427,0,0.157311461214549,0.444191506487439,-0.124037672048917,0,0,0.0670129113649365,-0.124037672048917,-0.00782653645625384,0,1.0395436665615,0.257394189329734,0,-0.124037672048917,0,-0.124037672048917,0.429475595543357,0.384530054891289,0.192179422446085,0.450427495056139,0,0,0,-0.121227535857724,0,-0.115269634875577,0.0203304848374648,0,0.229041567979078,0,0.0290067968613514,0,0.0455495587624001,0.0776585038639226,0.312349450520138,0,0,0.0408210357471045,0,-0.0840912677238242,0,-0.124037672048917,0,0.419970103691489,0,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.124037672048917,-0.0408942230144276,-0.124037672048917,-0.095251425998882,0.085072355470482,0.351734480622083,0.191171618186803,0.461537264446048,0,0,0,0.0878114418647872,0,0.0914082188667263,0,-0.124037672048917,0.345158372529908,0,0.458130560787303,0.2828980264685,0.0266094859650764,0,-0.0260263948881297,0.476246228490381,0.562047168363184,0.297390381696189,0.34137997173303,0,0.60014926979992,0.0234589779083607,-0.0219356125317525,0.00385127809181632,-0.0831533783215497,0.26949663740505,-0.124037672048917,-0.124037672048917,-0.124037672048917,0.230235463061477,-0.11635908555212,0,0.0735637240700286,0,0.231263613890623,-0.124037672048917,0.150523565532673,0.00751459721008724,0,0.0282182777384133,0,-0.0792868559237439,0.00290266583695251,0.271787664499001,0,0.149190107790669,0.125010917599838,0,-0.124037672048917,0,0.0125419384767343,-0.124037672048917,0.26940339545949,0,-0.0170712465880389,0,0,-0.0614954691071839,-0.0927701661816603,0,0.0547535628453514,0.38167586971264,-0.124037672048917,-0.036521147271105,-0.0288475290850475,-0.0250148266609757,0,-0.124037672048917,0,0.124506681731383,0.121069236870266,0.055966461856338,0,-0.119297471901503,0,0.323363440833414,-0.123156821485051,-0.124037672048917,0,0.0832161034844002,0.0716196360387782,0.0399746240158088,0,0,-0.124037672048917,0.681331453793888,0.601964357234645,0.471927035839364,0.188799527945415,0,0.625725282393718,-0.106473280487312,-0.0100407674824507,0,0.0998759650431728,0.133038335144119,0.0685890998680107,0,0,0,-0.124037672048917,-0.032444516759949,-0.0747742009152754,-0.124037672048917,0,0,0,0,0.12315641958565,-0.0606840078648822,0.235390284806248,0.11443010919234,0.138483577189796,0,0.0870207733122038,0.156753476242836,0.106087929675156,-0.0048622139776649,0.0613201791501264,0.109060369074458,0,0.166825123124581,0.383464385802453,0.468393480985451,0.372880101004638,0.512333377254697,0.514924251997028,0.577105863675168,0.658892919675077,0.604150583785539,0.600271020082031,0.225514409552951,0.201784975435766,0.38626184996867,0.444025369389827,0.406987795644538,0.621175219329369,0.622224447431987,0.465952019409687,0.149607816702465,0.338962837372372,0.419539903689146,0.68294087028916,0.277951558439734,0.700960999437792,0.766250864375626,0.477141350988027,0.325831802323916,0.452295160517901,0.393908469189369,0.141524917346346,0,0.182411394908525,0,0.0368054643406245,0.433474914488853,0.56968527710899,-0.00716390551562014,0,0.586596781523651,0.25931588190875,0.265928620748145,-0.0277337917314361,0,0.115230947587976,0.198877220339098,-0.124037672048917,-0.124037672048917,-0.124037672048917,0,0,0.065270425843215,-0.124037672048917,0,0.155109092280233,0.329404369753802,0.52645820423135,-0.0144339040169054,0,0.272220096979119,0.0341834199986081,0,0.254219876843618,-0.124037672048917,0,-0.124037672048917,0,0.413303411681324,-0.124037672048917,0,0.620561131907297,0,0.141567456144141,0,0.0438979349413473,0.260182442680742,0.106306232507065,0.228290622506315,0.171558826597626,0,-0.124037672048917,0,0,0,0,0.367929800107392,0,0.0608566712043477,0.0550062270675239,0,-0.124037672048917,0.247539322004134,-0.0641502307462904,0.168132892145335,0.126645291239927,0.0815945607332269,0.215626677576094,0.113541923647986,0,0,0,0,0,0,0,-0.0444644987413076,-0.0390188066563064,0,0.18025896238923,0.126120793376874,0.268354696568878,0,-0.065854552792694,0.167600437054528,0,0,0.419827883432705,0.0849077133655763,0,0.124682719870726,0,0,0.182293311785431,0.166765217958634,0,-0.120300822745242,0,0,0.16829944338126,0.154139937423722,0,-0.021581864055783,-0.0391538167960221,0,-0.124037672048917,0,-0.0292746021108872,-0.0310644251893019,0,0.273218442975889,0.0460001214530356,0.0912938539198686,-0.103302887691869,-0.124037672048917,0.194439523064409,0,0.0911409380920225,0.259347546108682,0.218976056853198,-0.0400132382074221,0.0489242137765972,0.130709882023763,0.0892486501440648,0.112955512742184,0.26606967772796,0.506376820972055,-0.0283160512695541,0.0996224845265148,-0.124037672048917,0,0.0245011943802916,-0.0771846182771526,0.238130540907848,0,0,0,0.321723724449989,0.310609974309358,0.313456698449451,0.820816241066437,0.330609426876206,0.865033830096931,0,0,0.0518077165209662,0,0.0328582360496969,-0.124037672048917,-0.110268536586314,-0.0229513438387595,0,0,0.117370405459493,0,0.092743246865863,-0.124037672048917,-0.111283485129006,0.370250685180371,0.0139656348485367,-0.00565060533401696,0,0.0993651423879183,0,0.0313995571041937,0.22149788379633,0,0.290542891013189,0.466974746384346,0,0,0.0500863030838633,0,0,0,-0.124037672048917
|full_id=C952_basal_Fibroblast_tenocyte_Hair_Smooth_Preadipocyte_Myoblast
|full_id=C952_basal_Fibroblast_tenocyte_Hair_Smooth_Preadipocyte_Myoblast
|id=C952
|id=C952

Revision as of 18:45, 12 September 2012


Full id: C952_basal_Fibroblast_tenocyte_Hair_Smooth_Preadipocyte_Myoblast



Phase1 CAGE Peaks

Hg19::chr5:98104978..98105010,+p5@RGMB
Hg19::chr5:98105021..98105033,+p11@RGMB
Hg19::chr5:98105080..98105096,+p9@RGMB
Hg19::chr5:98105123..98105126,+p26@RGMB
Hg19::chr5:98105127..98105145,+p8@RGMB
Hg19::chr5:98105219..98105258,+p6@RGMB
Hg19::chr5:98105268..98105295,+p2@RGMB
Hg19::chr5:98105586..98105654,+p@chr5:98105586..98105654
+
Hg19::chr5:98109470..98109495,+p3@RGMB


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 subdivision7.30e-25365
somite2.89e-2483
paraxial mesoderm2.89e-2483
presomitic mesoderm2.89e-2483
presumptive segmental plate2.89e-2483
trunk paraxial mesoderm2.89e-2483
presumptive paraxial mesoderm2.89e-2483
dermomyotome4.61e-2170
multilaminar epithelium9.59e-2182
cell layer2.43e-19312
epithelium6.69e-19309
artery2.67e-1742
arterial blood vessel2.67e-1742
arterial system2.67e-1742
multi-tissue structure8.68e-17347
muscle tissue1.23e-1663
musculature1.23e-1663
musculature of body1.23e-1663
skeletal muscle tissue1.43e-1661
striated muscle tissue1.43e-1661
myotome1.43e-1661
blood vessel4.14e-1660
epithelial tube open at both ends4.14e-1660
blood vasculature4.14e-1660
vascular cord4.14e-1660
vasculature6.52e-1679
vascular system6.52e-1679
integument7.97e-1645
integumental system7.97e-1645
vessel1.29e-1569
surface structure6.89e-1595
skin of body1.75e-1440
systemic artery2.06e-1433
systemic arterial system2.06e-1433
splanchnic layer of lateral plate mesoderm4.28e-1484
trunk mesenchyme8.81e-14143
multi-cellular organism3.53e-13659
anatomical system2.11e-12625
anatomical group3.03e-12626
unilaminar epithelium6.96e-11138
trunk1.32e-10216
anatomical conduit1.40e-10241
anatomical cluster5.48e-10286
cardiovascular system8.16e-10110
tube1.04e-09194
circulatory system4.05e-09113
aorta1.92e-0821
aortic system1.92e-0821
epithelial tube2.88e-08118
ectoderm-derived structure7.49e-08169
embryo1.02e-07612
mesenchyme1.88e-07238
entire embryonic mesenchyme1.88e-07238
embryonic structure2.81e-07605
developing anatomical structure2.81e-07605
germ layer3.19e-07604
embryonic tissue3.19e-07604
presumptive structure3.19e-07604
epiblast (generic)3.19e-07604
ectoderm4.68e-07173
presumptive ectoderm4.68e-07173


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#1066484.764672331622251.10088565904027e-050.000285157235477447
EGR1#195873.8796948515190.0003186557858542290.00326307398949209
RAD21#588578.053915252021592.36147727378579e-068.3802353040066e-05
ZBTB7A#5134175.718151683903472.40589727322203e-050.000524352056172862



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.