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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0.301189131856195,0,0,0,0.212645603028643,0,0.173613902868862,0,0,0,0.0960519401186186,0.220838645003429,0.370078076395268,0.204850754147253,0.238123940398271,0.295757399657426,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.369475932942402,0.0522561809686404,0,0,0,0,0.172204315337917,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.194599788733868,0,0,0,0,0,0,0.147004833432507,0.245579806949268,0,0.239381113983383,0,0.0371473953017556,0,0,0,0,0.073058801099379,0,0,0,0,0.0517815087208527,0.0540033816753664,0.196914560204395,0.131832994540557,0,0,0.0957506546513297,0,0.499050395774134,0.613395268587082,0,0,0,0.35191999121208,0.196030148402437,0.370149907745283,0,0,0,0.0806820944291313,0,0,0,0.174505758397014,0,0,0,0,0,0,0,0.312106748713396,0.393508234473775,0,0,0,0.204169432998994,0.0425961947748989,0,0,0.0677314085379025,0.0403796003528171,0,0,0,0,0,0,0.141926672950355,0,0.109512603169101,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.240088615649191,0,0,0,0,0,0,0,0,0.0687674306079092,0,0,0.114473174685065,0,0,0,0,0,0.0916027365082372,0,0,0.0756397051975275,0,0,0,0,0,0,0,0.0575805665668305,0.160706356573277,0.110803081130275,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.279872640127852,0,0.266067629561646,0.102412476390192,0,0,0,0,0.196428222363883,0,0,0.122457109962761,0.233195153867752,0.52838386410907,0,0,0.0413820215904058,0,0,0,0,0,0,0.156653296834752,0.0811586845710415,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.208666715931591,0.275957966318471,0.0660478550963579,0.488129996818752,0.129893181862632,0,0,0,0.0897740605496476,0.237635380700642,0.101144976784816,0,0.0322218878591601,0,0,0.0831811723542952,0,0,0.0849035433286077,0,0,0,0,0,0,0,0,0,0,0,0.349567376168701,0,0,0,0,0.416114259418732,0,0.0622241049201175,0.0620189823948138,0.0560798888033103,0,0,0.154160071098162,0,0.066432124538699,0.0763454992192642,0.0521599633818348,0.0418495518922339,0,0.212087596895138,0.379137668186602,0.539611562605601,0.495436669296489,0.557483017432814,0.736219661287959,0.269220822754477,0,0.21292204628454,0.402268529144255,0,0,0.213891194797874,0.692383589290883,0.0718350632709503,0.321836143995524,0.382692075941723,0.345000035290412,0.620157552899625,1.1853377790702,0,1.32189875296349,0.865637408770163,0.0555694062070307,0.453053800977411,0.513239225317154,0.423916632477864,0.843292016135087,0.853595550039842,0,0,0.383882234777716,0.350111114970215,0.66857625932076,0.0582024997333375,0,0.385013263539357,0.383643813828359,0.0831827421014,0,0,0,0.0398985583070718,0,0,0.365115906775862,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0943736524828545,0,0,0,0,0,0,0,0.564832758801957,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0921546695012139,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0831434490344895,0.867236402834398,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.1241754307343,0,0,0,0,0.129406115216345,0,0,0,0,0,0,0,0,0,0,0,0.378579990597245,0,0,0.0645768949458293,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.387603278412367,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.417236804093294,0,0,0,0,0.629205413387583,0.726002029283562,0.837498317955001,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.16069789587836,0,0.191676169220254,0.075329031500352,0,0,0.331265360943095,0,0.645384774245006,1.04929577572107,0.885952555988638,0.370958690294713,0.715343034651124,1.12843759853023,0.622224447431987,0.182341901105911,0.243357583010778,0.140132417719247,0.628896080419471,0.450015973155444,0.657490731391673,0.521160164059801,0.145536958608929,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.297342782617725,0,0,0,0,0,0.359596773213664,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.123048870237934,0,0,0,0,0,0,0,0,0,0.214529171984106,0,0,0,0,0.728062759020253,0,0,0,0,0,0,0,0,0,0,0.648832252819498,0,0.132702316438765,0,0.129923174575149,0,0,0,0,0,0,0.092251718923439,0.0683442610773682,0,0.0895896456213401,0,0,0.251148425764861,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.225233909259803,0,0,0,0,0.231925498757082,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|full_id=C378_Smooth_mesenchymal_placenta_clear_leiomyoma_renal_Preadipocyte
|full_id=C378_Smooth_mesenchymal_placenta_clear_leiomyoma_renal_Preadipocyte
|gostat_on_coexpression_clusters=GO:0007596!blood coagulation!0.0115683504062169!7980$GO:0050817!coagulation!0.0115683504062169!7980$GO:0007599!hemostasis!0.0115683504062169!7980$GO:0005201!extracellular matrix structural constituent!0.0115683504062169!7980$GO:0050878!regulation of body fluid levels!0.0115683504062169!7980$GO:0042060!wound healing!0.0115683504062169!7980$GO:0004867!serine-type endopeptidase inhibitor activity!0.0127163546450018!7980$GO:0004866!endopeptidase inhibitor activity!0.0156599552572707!7980$GO:0030414!protease inhibitor activity!0.0156599552572707!7980$GO:0004857!enzyme inhibitor activity!0.0186771458848463!7980$GO:0005578!proteinaceous extracellular matrix!0.0186771458848463!7980$GO:0009611!response to wounding!0.0186771458848463!7980$GO:0009605!response to external stimulus!0.0257995272124555!7980$GO:0044421!extracellular region part!0.0336630166019074!7980$GO:0065008!regulation of biological quality!0.0336630166019074!7980$GO:0006950!response to stress!0.0404671494171671!7980
|gostat_on_coexpression_clusters=GO:0007596!blood coagulation!0.0115683504062169!7980$GO:0050817!coagulation!0.0115683504062169!7980$GO:0007599!hemostasis!0.0115683504062169!7980$GO:0005201!extracellular matrix structural constituent!0.0115683504062169!7980$GO:0050878!regulation of body fluid levels!0.0115683504062169!7980$GO:0042060!wound healing!0.0115683504062169!7980$GO:0004867!serine-type endopeptidase inhibitor activity!0.0127163546450018!7980$GO:0004866!endopeptidase inhibitor activity!0.0156599552572707!7980$GO:0030414!protease inhibitor activity!0.0156599552572707!7980$GO:0004857!enzyme inhibitor activity!0.0186771458848463!7980$GO:0005578!proteinaceous extracellular matrix!0.0186771458848463!7980$GO:0009611!response to wounding!0.0186771458848463!7980$GO:0009605!response to external stimulus!0.0257995272124555!7980$GO:0044421!extracellular region part!0.0336630166019074!7980$GO:0065008!regulation of biological quality!0.0336630166019074!7980$GO:0006950!response to stress!0.0404671494171671!7980

Revision as of 16:45, 12 September 2012


Full id: C378_Smooth_mesenchymal_placenta_clear_leiomyoma_renal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr3:119012895..119012908,+p6@ARHGAP31
Hg19::chr7:93515840..93515856,-p@chr7:93515840..93515856
-
Hg19::chr7:93515914..93515935,-p@chr7:93515914..93515935
-
Hg19::chr7:93515962..93515978,-p@chr7:93515962..93515978
-
Hg19::chr7:93516018..93516037,-p@chr7:93516018..93516037
-
Hg19::chr7:93516035..93516056,+p1@CU675118
Hg19::chr7:93516064..93516108,-p@chr7:93516064..93516108
-
Hg19::chr7:93516178..93516195,-p@chr7:93516178..93516195
-
Hg19::chr7:93516564..93516575,+p@chr7:93516564..93516575
+
Hg19::chr7:93516582..93516600,+p@chr7:93516582..93516600
+
Hg19::chr7:93516601..93516634,+p@chr7:93516601..93516634
+
Hg19::chr7:93516618..93516631,-p@chr7:93516618..93516631
-
Hg19::chr7:93516635..93516656,-p@chr7:93516635..93516656
-
Hg19::chr7:93516672..93516693,+p@chr7:93516672..93516693
+
Hg19::chr7:93516698..93516745,-p@chr7:93516698..93516745
-
Hg19::chr7:93518340..93518370,+p@chr7:93518340..93518370
+
Hg19::chr7:93518374..93518429,-p@chr7:93518374..93518429
-
Hg19::chr7:93518433..93518444,-p@chr7:93518433..93518444
-
Hg19::chr7:93518473..93518503,+p@chr7:93518473..93518503
+
Hg19::chr7:93518492..93518540,-p@chr7:93518492..93518540
-
Hg19::chr7:93519471..93519485,-p5@TFPI2
Hg19::chr7:93519497..93519525,-p2@TFPI2
Hg19::chr7:93519528..93519538,-p7@TFPI2
Hg19::chr7:93519532..93519563,+p@chr7:93519532..93519563
+
Hg19::chr7:93519562..93519586,-p4@TFPI2
Hg19::chr7:93519576..93519598,+p@chr7:93519576..93519598
+
Hg19::chr7:93519591..93519595,-p9@TFPI2
Hg19::chr7:93519597..93519625,-p3@TFPI2
Hg19::chr7:93520056..93520072,-p1@TFPI2


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

GO IDGO nameFDR corrected p-value
GO:0007596blood coagulation0.0115683504062169
GO:0050817coagulation0.0115683504062169
GO:0007599hemostasis0.0115683504062169
GO:0005201extracellular matrix structural constituent0.0115683504062169
GO:0050878regulation of body fluid levels0.0115683504062169
GO:0042060wound healing0.0115683504062169
GO:0004867serine-type endopeptidase inhibitor activity0.0127163546450018
GO:0004866endopeptidase inhibitor activity0.0156599552572707
GO:0030414protease inhibitor activity0.0156599552572707
GO:0004857enzyme inhibitor activity0.0186771458848463
GO:0005578proteinaceous extracellular matrix0.0186771458848463
GO:0009611response to wounding0.0186771458848463
GO:0009605response to external stimulus0.0257995272124555
GO:0044421extracellular region part0.0336630166019074
GO:0065008regulation of biological quality0.0336630166019074
GO:0006950response to stress0.0404671494171671



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm6.16e-2884
vasculature1.22e-2679
vascular system1.22e-2679
epithelial tube8.23e-26118
vessel3.23e-2469
trunk mesenchyme4.07e-24143
blood vessel1.84e-2360
epithelial tube open at both ends1.84e-2360
blood vasculature1.84e-2360
vascular cord1.84e-2360
somite5.64e-2383
paraxial mesoderm5.64e-2383
presomitic mesoderm5.64e-2383
presumptive segmental plate5.64e-2383
trunk paraxial mesoderm5.64e-2383
presumptive paraxial mesoderm5.64e-2383
dermomyotome7.63e-2370
multilaminar epithelium1.32e-2282
trunk9.92e-22216
skeletal muscle tissue1.32e-2161
striated muscle tissue1.32e-2161
myotome1.32e-2161
unilaminar epithelium2.25e-21138
cardiovascular system4.41e-21110
circulatory system5.09e-21113
muscle tissue1.04e-2063
musculature1.04e-2063
musculature of body1.04e-2063
artery5.36e-2042
arterial blood vessel5.36e-2042
arterial system5.36e-2042
cell layer8.62e-20312
epithelium2.33e-19309
systemic artery1.80e-1633
systemic arterial system1.80e-1633
multi-cellular organism6.66e-15659
organism subdivision7.25e-15365
mesenchyme1.66e-14238
entire embryonic mesenchyme1.66e-14238
multi-tissue structure1.52e-13347
anatomical system2.10e-13625
anatomical group4.28e-13626
anatomical cluster2.78e-12286
anatomical conduit9.81e-12241
mesoderm2.60e-11448
mesoderm-derived structure2.60e-11448
presumptive mesoderm2.60e-11448
embryo5.10e-10612
germ layer8.37e-10604
embryonic tissue8.37e-10604
presumptive structure8.37e-10604
epiblast (generic)8.37e-10604
embryonic structure9.65e-10605
developing anatomical structure9.65e-10605
tube1.06e-09194
heart1.53e-0924
primitive heart tube1.53e-0924
primary heart field1.53e-0924
anterior lateral plate mesoderm1.53e-0924
heart tube1.53e-0924
heart primordium1.53e-0924
cardiac mesoderm1.53e-0924
cardiogenic plate1.53e-0924
heart rudiment1.53e-0924
aorta2.94e-0921
aortic system2.94e-0921
primary circulatory organ3.79e-0927
compound organ1.23e-0869
smooth muscle tissue6.55e-0715
Disease
Ontology termp-valuen
ovarian cancer1.91e-0914


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
RAD21#588593.213631208934720.001208593323296330.00819106282230664



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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