Personal tools

Coexpression cluster:C2011: 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=0,0,0,0,0,0,0,0.212645603028643,0,0.297308641786177,0.229886828011239,0.272715235743603,0.253168552512612,0.0960519401186186,0,0.370078076395268,0.204850754147253,0.238123940398271,0,0.0504265701716883,0.148603081231402,0,0,0.149411045406522,0.176719245822362,0,0,0,0,0,0,0.670030963153865,0.741788683653283,0.735363176854424,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.160060705412945,0,0,0,0.306367237405487,0.250506873342816,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.222898696087275,0.0522561809686404,0.236254602210782,0,0.156712528252229,0,0,0.139293107667917,0.159404390993283,0.208130439704827,0.027549189648299,0.450476428384029,0.324766563350378,0,0,0,0,0,0,0.254076460438359,0.269567716763895,0.309932685421046,0.194599788733868,0.264581462950963,0.190397841472823,0.310687967554266,0,0.315403250032236,0,0.344095034254912,0.745202298774693,0.0948420448069823,0.322837050827097,0,0.160318030086386,0.223648583799205,0.252435607706598,0,0,0.135578961919851,0,0,0.652125651996652,0,0.0517815087208527,0.184588301523704,0,0.314710775869444,0.193313197142976,0.315443408671468,0.240549908522397,0,0.257261843976877,0.392900360805954,0,0,0.654640582364595,0.117986819981215,0.330605235338509,0.113574834469897,0.200624128255923,0.216823255735109,0.354887406406094,0.0806820944291313,0.323357072410072,0.0427037663627782,0,0,0.5717651916362,0.235179391914214,0.177538907115697,0.211011713448001,0.323923440140686,0.158054039799331,0,0,0.351748782040451,0.187004028169722,0.084060318828564,0,0.204169432998994,0.11699192718931,0.180493200633673,0,0.0677314085379025,0.0403796003528171,0.0977547706744154,0.0382424828832804,0.0650738225586148,0.131942369721337,0.147060269021119,0.266655658836029,0.793653723492953,0.87771144231829,0.618555406750515,0,0,0,0,0,0,0,0,0.376823087293191,0,0,0.131913781701721,0.177754045794409,0,0.299430098248662,0.218440530929055,0.168656922891142,0.288655857957696,0.201032162386646,0.247849171410405,0,0.71660869671046,0,0,0,0,0,0,0.173755361595775,0.342615044900017,0.654369970062277,0.511620709152878,0,0.55539393160158,0.296100002047877,0.614876592441603,0.387979180422312,0,0.231584817481691,0.388041575741818,0.455140696674979,0.0756397051975275,0,0,0,0,0,1.17782713750697,0.686956862952637,0.785607659050113,0.916677110089228,0.833317911677673,0.566281749271713,0,0,0,0,0,0,0,0,0,0,0,0,0.390529593360222,0,0.322234657591074,0.181010447665502,0,0.548500988324796,0.102412476390192,0,0.248371094814393,0.383544533079954,0.457117843239535,0.0580378687812504,0,0,0.594572160705173,0,0.52838386410907,0.448495498731803,0.43823640236081,0.633378427002409,0,0,0,0.235244185543683,0.33215948426107,0,0.198416571487356,0.149512438051623,0.0715362608323278,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.188233632538465,0,0.0713034174053426,0.168234365485179,0.0914146875965646,0.114259303421121,0,0,0.476059816250789,0.191201518499852,0.129539879367107,0,0,0,0,0,0.344885298375197,0.425591991369837,0.205415661963911,0.0962521000248044,0.0620032815069762,0,0,0,0.0647775726819609,0,0.208666715931591,0.233058812211538,0.348676160484154,0.555852549301001,0.334876536979502,0,0.62408641548959,0.542350641855944,0.227600512804766,0.35691232378723,0.0535103765953433,0.161727153872444,0.187268914901325,0.251479989016808,0,0.152962663947244,0,0.431514462767495,0.317975544424619,0.405222104277016,0.258359310587411,0.176580223334895,0.580199292116721,0.712260686148696,0.479268992535553,0,0,0,0.219068014200448,0.122339886766207,0.0425916600387234,0,0,0.86432836115884,0.875096148018902,0,0.110593802369687,0.317716663005041,0.164504839448406,0.37627863752811,0.121317101469593,0.0588118185728318,0.305935667518657,0.0370406554214911,0.541488598029594,0.718350654516242,0.608815299277607,0.232514428188533,0.285487793508896,0.118863773699242,0,0.116618893451534,0.563662614770321,0.557483017432814,0,0.0580936797916625,0,0,0.140275557177927,0.179493072024499,0,0.213891194797874,0.251625724314337,0.18741280294663,0,0.131438111403229,0.508396016128199,0,0.428949761133964,0.172496019467973,0.172435654547321,0.313129023768005,0.149064998316823,0,0.328396152435088,0.190714085371158,0,0,0,0,0.147929950453612,0,0.381742685932373,0.457025716963957,0.2012589601207,0.132474558164796,0.314769276471791,0,0,0.2452525925408,0.311712370336256,0.630585680628715,0.70086059310767,0.728811327437894,0,0.434891549687679,0.428898149930474,0.275739748541768,0.332159007785004,0,0,0,0,0,0,0,0,0,0,0.173209711509263,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.106668859343321,0,0,0,0,0.42882536662243,0,0,0,0,0.992710150837532,0.340019274855688,1.22181042075241,0,0,0.192161269222053,1.09816837861029,0,0,0,0,0.116211135592663,0,0,0.922684195155844,0,0,0,0,0.508225242921722,0,0,0,0,0,0,0.04680465889238,0.356268430234937,0,0,0,0,0,0,0,0,0,0,0,0.353110664594184,0,0,0,0.0373299241805104,0,0.982860356952409,0.238743613897599,0.869021406446451,0,0,0,0,0,0.0673764988462845,0,0,0.46224560579794,0.929863679878213,0,0,0,0.0368115019473605,0,0,0,0,0,0,0,0,0.337257085318794,0,0,0,0,0,0.114159389744683,0,0,0,0,0,0.195683583376492,0,0,0.485414806520799,0.871711915964537,0,0.434546601915608,0,0,0,0,0,0,1.01363133624388,0.203072024846461,0,0,0.342892708826334,0,0,0,0,0,1.10763365587248,0.83504779490633,0.288422760749283,1.12604313460363,1.17657685893537,0,0.110236269607548,0,0,0,0,0,0,0,0,0,0,0,0,0.235679859774857,0,0.0635458990071735,0.0343941464470872,0.103671762731433,0,0,0,0,0,0,0,0,0,0,0,0,0.0222033657448865,0.833020727769502,0,0.918700013069911,0,0,0,0,0.555416659434928,0.12273585496983,0.341889734335766,0,0.550939808243393,0,0,0,0,0,0.592007476631764,0,0,0,0,0,0,0,0.785808723155398,0,0,0,0,0,0,0,0,0,0,0,0,0.61537238186081,0,0,0.88009543872309,0,0,0.113445166687003,0,0.324202530144468,0.075329031500352,0,0,0.089495363820231,0.114765010550142,0.0627463460232421,0.27580202584006,0.487259730831511,0,0.350655686652484,0.351045809883433,0.456501463585907,0.182341901105911,0.371496120621099,0.463000509421289,0.346472721415205,0.0725618668317725,0.482987939975821,0.521160164059801,0.145536958608929,0.146136648478548,0,0,0,0.930040461258082,1.28874042185451,0.251147172149137,0.412786604281026,0.816674674270033,0.99169208777997,0.23460721171067,1.17307156227914,0.79676973493599,0.811398271328548,1.09278828334254,1.37361600212601,0,0.53377363293676,0.74491067714397,0,0,0,0,0.297285381790176,0.173636598619994,1.47944678812252,0,0,0,0.859899026911097,0.13615336353379,0.528653426632249,0.958420737406049,0,0,0,0,0,0,0,0,0.11991684384043,0,0,0,0,0,0,0,0,0,0,0,0,0.14382354480865,0,0.358696135635415,0.377726496072456,0.516970451538659,0.81443934959171,0,0,0.665645824249398,0,0,0.630980648494429,0.36748726610132,0,0,0,0,0,0,0,0,0.483473016450836,0.18630690345421,0,0,0,0.254867295858233,0,0.405413315424919,0,0,0.757984329637568,0.301265019360327,0,0,0.107302302820485,0,0.0849077133655763,0,0,0,0.0907808850426298,0,0,0.424510746462007,0.226051577088081,0.37703643170745,0,0.495541009304777,0.341036189210412,0,0.163821185185472,0.117339711759041,0.464053823959474,0.552993502644175,0.0406617582988581,0.23842438954415,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.225233909259803,0,0,0,0,1.25379711241259,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.23399100484241,0,0.190715220165844,0,0,0,0,0,0,0,0,0.0261550693490902,0.661644196043995,0,0,0,0,0.0283076897745917,0.0582150559773052,0,0.122416778853372,0.292377061551937,0,0.0373568467037749,0,0.0500863030838633,0,0,0,0
|full_id=C2011_mucinous_mesothelioma_squamous_glioblastoma_anaplastic_Mallassezderived_amniotic
|full_id=C2011_mucinous_mesothelioma_squamous_glioblastoma_anaplastic_Mallassezderived_amniotic
|id=C2011
|id=C2011

Revision as of 14:40, 12 September 2012


Full id: C2011_mucinous_mesothelioma_squamous_glioblastoma_anaplastic_Mallassezderived_amniotic



Phase1 CAGE Peaks

Hg19::chr8:38261817..38261833,+p4@LETM2
Hg19::chr8:38261837..38261848,+p6@LETM2
Hg19::chr8:38261849..38261864,+p2@LETM2
Hg19::chr8:38261866..38261877,+p5@LETM2
Hg19::chr8:38261880..38261914,+p3@LETM2


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
epithelial cell1.23e-31254
embryonic cell1.48e-26248
animal cell8.20e-25679
eukaryotic cell8.20e-25679
mesodermal cell2.42e-20119
native cell1.99e-17722
squamous epithelial cell1.15e-1662
lining cell5.52e-1357
barrier cell5.52e-1357
non-terminally differentiated cell9.37e-13180
somatic cell4.28e-11591
mesothelial cell4.10e-1019
endo-epithelial cell3.22e-0943
meso-epithelial cell1.18e-0744
muscle precursor cell1.28e-0757
myoblast1.28e-0757
multi-potent skeletal muscle stem cell1.28e-0757
contractile cell1.38e-0759
fibroblast1.81e-0775
muscle cell2.63e-0754
endodermal cell4.09e-0759
Uber Anatomy
Ontology termp-valuen
vasculature1.33e-1179
vascular system1.33e-1179
epithelial tube2.28e-11118
unilaminar epithelium4.35e-11138
trunk mesenchyme8.10e-11143
vessel3.00e-1069
splanchnic layer of lateral plate mesoderm7.83e-1084
blood vessel2.94e-0960
epithelial tube open at both ends2.94e-0960
blood vasculature2.94e-0960
vascular cord2.94e-0960
multilaminar epithelium5.79e-0982
mesenchyme1.57e-08238
entire embryonic mesenchyme1.57e-08238
cell layer2.89e-08312
somite2.95e-0883
paraxial mesoderm2.95e-0883
presomitic mesoderm2.95e-0883
presumptive segmental plate2.95e-0883
trunk paraxial mesoderm2.95e-0883
presumptive paraxial mesoderm2.95e-0883
artery4.52e-0842
arterial blood vessel4.52e-0842
arterial system4.52e-0842
epithelium7.37e-08309
female organism3.55e-0741
cardiovascular system4.05e-07110
surface structure4.61e-0795
dermomyotome6.17e-0770


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
BCL3#602534.54710280373832.02839878970325e-081.44801053450319e-06
EGR1#195854.988179094810140.0003237398000590710.00331188764603481
FOS#235358.99795530889441.69470025615156e-050.000390023799145467
FOSL1#8061539.7135797163731.01017090471068e-087.65611314347454e-07
FOSL2#2355516.93020060456177.18315284751475e-073.21147816884244e-05
JUN#3725512.51282919233633.25800591331781e-060.000109303848243174
JUND#372756.994663941871035.97069468343598e-050.00098573092324276



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.