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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0.237220288771276,0.68608272108785,0.298128100889077,0.477333423353826,0.509848169110475,0.27238437317198,0,0,0.315106107923197,0.101828812088121,0.578777230871412,0.218883042328193,0.253168552512612,0,0.0936718252301529,0.169271094041415,0.204850754147253,0.238123940398271,0.100798226334018,0.0504265701716883,0.080626736260243,0.118415106013485,0,0.0332987141822611,0.0513619522818629,0,0,0,0,0,0,0,0.0569260182195504,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.175159034639729,0.0522561809686404,0.316628145078214,0.17647845120947,0.388893933933767,0,0.463910768566174,0.0085937096724666,0.0329253978915245,0.0128652660935037,0.027549189648299,0.0774883673979308,0,0,0,0,0,0,0,0.254076460438359,0.269567716763895,0.577161244085388,0.582806224546272,1.02728790636899,0.991393439238226,0.391458199030955,0.500338682412531,0.513238880074695,0.478324561771185,0.634519420116906,0.245579806949268,0.926206916372212,0.47532473176174,1.21465041178248,0.430831803726624,0.410221251976804,0.327586711626321,0.346243702688681,0.289871031843186,0.573802613339179,0,0,0,0.39635905700697,0.275636914561505,0.25393259243622,0.74736409751055,0.383577251490408,0.162677325779715,0.315443408671468,0.298125776038763,0,0.417725397336015,0.420717824619621,0,0,0,0.0605668081168584,0,0.060489586087507,0,0,0,0,0.0476628677986731,0.0427037663627782,0,0.29864956877975,0,0.38689763493088,0,0,0,0,0.207627795464294,0.243333341614666,0.0887965527720659,0.446210291375074,0.215021810472412,0.213729063154298,0.434031007520949,0.149899318418817,0.447698047811663,0.237949104502157,0.24972035627105,0.145876063440048,0.354525021943001,0.164427064187206,0.121655724261186,0.495552323371493,0.147060269021119,0.178597644615193,0.0701415821696134,0.0506921557752019,0.0554629769894442,0.019346807823699,0,0.0477396614475454,0.0818231540625959,0,0,0,0,0,0.140229865830499,0,0,0,0,0.014802110875933,0,0,0,0,0,0.790080158389657,0.820179839632715,0.149703653910611,0.392712270020621,0,0,0.129827736009895,0,0.050375285110278,0,0.13593209337019,0,0.0416014802313693,0.0384566032530418,0,0,0,0,0,0.412969461578611,0.378208248705171,0.490351229303755,0,0,0,0,0,0,0.0780551773380191,0.0575805665668305,0,0,0,0,0,0,0,0.0516318862226721,0,0,0,0,0.0449828205963032,0,0,0,0,0,0.0527984507438095,0.8572746832504,0,0.185223678206009,0,0.0419869078817296,0,0.0548388463290221,0.0580378687812504,0.271417054428637,0,0,0,0,0.204900672442429,0,0.31392187074911,0,0,0,0.177824173679326,0.33215948426107,0,0.156653296834752,0.291441080272466,0.0851990993808816,0,0,0,0,0,0,0,0,0,0,0,0,0.0502604313716981,0,0.0324510076348888,0.416724537164444,0.441054573211541,0.252491876641462,0.231176008559716,0.114259303421121,0,0,0,0.0734870933250891,0.0695819800362469,0.0776589694549609,0.128122390065496,0,0,0,0.060937307463216,0,0.205415661963911,0.251643679213752,0.34986318549779,0.645040419087949,0.278061388726493,0.306084857468188,0.359234140930206,0.395183177140817,0.116746970692643,0.13197886088098,0.00364242444471671,0.12421049928447,0.129893181862632,0.134361483765049,0.295282488882307,0.0734111122555477,0.0472025886002021,0.117501223368917,0.101144976784816,0.131091282509184,0.0622173525481225,0,0,0.0435790287959822,0.825209838733228,0.57071793982107,0.317975544424619,1.2901965022664,0.104127248139133,0.301763235794132,0,0,0.103273414584678,0,0,0,0.123202864573785,0,0,0.0730357444858842,0.0344317163371687,0,0.145714710429262,0.416114259418732,0.110593802369687,0.0622241049201175,0.116278029675102,0.10255913703202,0.0443124586324902,0.189070452162987,0.0988789363017444,0.155243902981181,0.117469411853009,0.0763454992192642,0.0446721012608136,0.0673624923578475,0,0.546357404115736,0,0.382785617153195,0,0,0.324682668660676,0,0,0,0.109639685814667,0.0989542966657617,0,0.0893465060020179,0,0,0.105352457754613,0,0.147479985915863,0.364738225785128,0.265411482942022,0,0.432326897899566,0.313129023768005,0.0555694062070307,0.105836289205503,0.274346526255431,0,0.843292016135087,0.439932954041292,0,0,0.0802332713627146,0.285438141673418,0.194067664482614,0.0104628382857921,0.0779120067805576,0.132474558164796,0.0841230450500863,0.414653651688419,0.422667707943698,0,0,0,0,0,0.0390744040629657,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0293360131927769,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.158219072164516,0,0,0,0.0929817338882301,0.065188488014835,0.116328982947523,0,0,0,0,0,0.341531053755066,0,0,0,0,0.351053498032414,0,0,0,0.174122933842314,0,0,0,0,0,0,0,0.18904933107111,0.0161687875291194,0.0266002828614029,0.0203695787204728,0,0,0,0,0,0,0,0,0,0.0549675313762191,0,0.141371779186911,0,0,0,0,0.214314512399756,0.0730563942977996,0.384187841069502,0,0,0.0667773874189013,0,0,0,0,0,0.265759093362812,0.187618914508428,0,0,0.245950290261662,0.0368115019473605,0,0,0,0,0,0.415833616916382,0,0,0,0,0.144444803709627,0,0,0.08555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|full_id=C547_Renal_Endothelial_Mesenchymal_Hepatic_Smooth_Fibroblast_Alveolar
|full_id=C547_Renal_Endothelial_Mesenchymal_Hepatic_Smooth_Fibroblast_Alveolar
|id=C547
|id=C547

Revision as of 18:08, 12 September 2012


Full id: C547_Renal_Endothelial_Mesenchymal_Hepatic_Smooth_Fibroblast_Alveolar



Phase1 CAGE Peaks

Hg19::chr1:22163333..22163340,-p6@HSPG2
Hg19::chr1:22181125..22181132,-p15@HSPG2
Hg19::chr1:22186101..22186129,-p@chr1:22186101..22186129
-
Hg19::chr1:22203039..22203053,-p@chr1:22203039..22203053
-
Hg19::chr1:22203092..22203119,-p@chr1:22203092..22203119
-
Hg19::chr1:22204962..22204969,-p4@HSPG2
Hg19::chr1:22206973..22206987,-p@chr1:22206973..22206987
-
Hg19::chr1:22207217..22207234,-p@chr1:22207217..22207234
-
Hg19::chr1:22211127..22211133,+p@chr1:22211127..22211133
+
Hg19::chr1:22211913..22211920,+p@chr1:22211913..22211920
+
Hg19::chr1:22213979..22214020,-p@chr1:22213979..22214020
-
Hg19::chr1:22214092..22214113,+p@chr1:22214092..22214113
+
Hg19::chr1:22214103..22214127,-p@chr1:22214103..22214127
-
Hg19::chr1:22214518..22214534,-p@chr1:22214518..22214534
-
Hg19::chr1:22216505..22216565,-p@chr1:22216505..22216565
-
Hg19::chr1:22222766..22222805,-p2@HSPG2
Hg19::chr1:22263793..22263811,-p1@HSPG2


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
mesodermal cell9.34e-26119
non-terminally differentiated cell3.74e-19180
embryonic cell7.60e-19248
meso-epithelial cell5.23e-1644
endothelial cell of vascular tree8.32e-1624
lining cell8.25e-1557
barrier cell8.25e-1557
endothelial cell1.37e-1435
blood vessel endothelial cell3.16e-1218
embryonic blood vessel endothelial progenitor cell3.16e-1218
fibroblast7.53e-1275
contractile cell3.02e-1159
muscle precursor cell1.39e-1057
myoblast1.39e-1057
multi-potent skeletal muscle stem cell1.39e-1057
muscle cell7.57e-1054
vascular associated smooth muscle cell3.73e-0932
smooth muscle cell8.78e-0942
smooth muscle myoblast8.78e-0942
epithelial cell4.89e-08254
electrically responsive cell5.86e-0860
electrically active cell5.86e-0860
endothelial cell of artery3.69e-079
squamous epithelial cell8.95e-0762
Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm8.73e-3084
epithelial tube5.80e-29118
vessel8.40e-2969
vasculature5.68e-2779
vascular system5.68e-2779
blood vessel1.35e-2560
epithelial tube open at both ends1.35e-2560
blood vasculature1.35e-2560
vascular cord1.35e-2560
circulatory system9.64e-20113
cardiovascular system4.68e-19110
artery1.02e-1742
arterial blood vessel1.02e-1742
arterial system1.02e-1742
unilaminar epithelium1.66e-16138
trunk1.71e-16216
trunk mesenchyme4.00e-16143
anatomical conduit5.40e-15241
systemic artery6.69e-1433
systemic arterial system6.69e-1433
mesenchyme1.01e-13238
entire embryonic mesenchyme1.01e-13238
anatomical cluster2.00e-13286
multi-cellular organism3.29e-13659
epithelium9.32e-13309
cell layer1.54e-12312
endothelium3.16e-1218
blood vessel endothelium3.16e-1218
cardiovascular system endothelium3.16e-1218
squamous epithelium8.54e-1225
muscle tissue1.27e-1163
musculature1.27e-1163
musculature of body1.27e-1163
compound organ2.24e-1169
simple squamous epithelium2.51e-1122
skeletal muscle tissue2.62e-1161
striated muscle tissue2.62e-1161
myotome2.62e-1161
multilaminar epithelium3.31e-1182
organism subdivision4.22e-11365
dermomyotome2.29e-1070
somite3.54e-1083
paraxial mesoderm3.54e-1083
presomitic mesoderm3.54e-1083
presumptive segmental plate3.54e-1083
trunk paraxial mesoderm3.54e-1083
presumptive paraxial mesoderm3.54e-1083
anatomical system9.56e-10625
tube9.64e-10194
multi-tissue structure1.11e-09347
aorta1.14e-0921
aortic system1.14e-0921
mesoderm1.38e-09448
mesoderm-derived structure1.38e-09448
presumptive mesoderm1.38e-09448
anatomical group1.53e-09626
subdivision of trunk1.07e-08113
primary circulatory organ1.24e-0827
heart4.79e-0824
primitive heart tube4.79e-0824
primary heart field4.79e-0824
anterior lateral plate mesoderm4.79e-0824
heart tube4.79e-0824
heart primordium4.79e-0824
cardiac mesoderm4.79e-0824
cardiogenic plate4.79e-0824
heart rudiment4.79e-0824
surface structure2.19e-0795
endothelial tube3.69e-079
arterial system endothelium3.69e-079
endothelium of artery3.69e-079
organ component layer5.15e-0757
intermediate mesoderm5.54e-0737


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

No analysis results for this cluster

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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