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{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0.698847673570409,0.828315275439956,0.548657071581092,0.955385570067558,1.03475451916457,1.0362096261404,1.24101098238354,0.212645603028643,0.251286965243594,0.23985027306034,0.736552190478504,0,0.18399087321112,0.0506760246065907,0.124307696593413,0.670778684877306,0.532853467332704,0.607897967303332,0.604045257526838,0,0.126582760749417,0.211363379907382,0,0.055712496781182,0.176719245822362,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.197027844193265,0.318963865966379,0.280824317219445,0.304043429527858,0,0.149311935585664,0.10843121454309,0.367426070652521,0.283699940769721,0.251850924713912,0,0,0,0.0137367552104715,0.117918942252007,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0948420448069823,0,0.257712632750166,0,0,0,0,0,0,0,0,0,0.651162024615577,0.3771002690887,0.184588301523704,0.210660635649395,0.243678907456134,0.689907734022287,0.529779388412506,0.790989776337165,0,0.181069831694359,0.122845985799448,0.0669400099387032,0,0,0.248842350231572,0,0.160872336741618,0,0,0,0,0.065626250812718,0.0427037663627782,0.528403173084411,0.838549032930245,0,0.466845714857489,0,0.0511982733942606,0.0684063651385804,0.504455652325158,0.94517830499524,0.728913839889083,0.195113592037213,0.297676740102059,0.336848314502118,0.356330217152619,0.215603713146953,0.284988249810417,0.307616288783483,0.441937812856837,0.0451187758426694,0.295428554772971,0.391151824492961,0.359588600349751,0.171533528270252,0.413546372748523,0.493568745421044,0.330160140426676,0,0,0,0.0948020209911413,0.102110964900826,0.0710051645249647,0.150647229477047,0.177433094296594,0,0.409001911408146,0.764581104674893,0.376823087293191,0.37896153349969,0.444259839618425,0.131913781701721,0.0841671633127106,0.0937756414473559,0.146851447677171,0.0856043003192711,0.0924647000597185,0.103688332502163,0.0778115911724362,0.141370482160471,0,0.380648525776858,0.26082193075914,0.733218244119286,0,0,0,0,0.0470083148829128,0.0687674306079092,0,0,0,0,0,0,0.305517992201869,0.0299966665114222,0.248187657274651,0.0585651160278124,0,0,0,0,0,0.0387924840234089,0.00414301171262645,0,0.0991427054231857,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0147357929118364,0.157142363216531,0.0366265837590911,0.321766994049631,0.660539583551993,0.403960991290709,0.562257776350536,0.887967343836891,0.061856228849409,0,0.102578507776567,0.269014845591616,0.188259409638053,0.260843920469556,0.0919042847182634,0.195921290949266,0,0.343557766208156,0.43823640236081,0.657893648130065,0,0,0,0.497967861819008,0.725739205877435,0,0.303944979097508,0.250487016088303,0.210652268229484,0,0,0,0,0,0,0,0,0,0,0,0,0.0953029273486504,0.385253535277902,0.188233632538465,0.892176233568756,0.963826328336574,0.672103185259325,0.514703755281144,0.300168781288661,1.00416225363406,0.487062179939574,0.221212197891035,0.379078716720459,0.386176356365178,0.225944254517563,0.226931452698605,0,0,0,0,0,0,0.466216659951238,0.283475779941398,0.791734247382836,0.386413589177157,0.609620390825032,0.702990852502706,0.736599019030167,0.363517147477893,0.519725985968423,0.15848192703393,0.336566155779684,0.409625946179613,0.0620817697626496,0.225967352622593,0,0.332063488140839,0.52663103582749,0.709833454020177,0,0.00101837903104803,0.192403044562783,0,0,0,0,0.0849035433286077,0.405222104277016,0.104127248139133,0.545115151677475,0,0,0.101980484891939,0,0,0,0.123202864573785,0.117640598475846,0.10754377229123,0.0591329979090258,0,0,0,0.62466140623093,0.110593802369687,0.0622241049201175,0.0620189823948138,0.105739413005624,0.0443124586324902,0.156867057756393,0.068354073672271,0.159915985962935,0,0.0763454992192642,0,0,0.728433727983529,0.266181252865072,0.177320489376396,0.0547520817695533,0.314838459985835,0,0.378058805615224,0.17586830385699,0.137404238899705,0.289842649570622,0.596994840375969,0.325784289864154,0.154709651609437,0.00578476025778855,0.525672578939941,0.257003711187985,0.348538127945276,0.24669495131698,0.317291047975868,0.412477887232674,0.354833330216448,0.179854537981964,0.269645949690972,0.493179530162882,0.398200338030807,0.481417526264775,0,0.0458108553217296,0.421245411637428,0.606968526554863,0.266140735891978,0.319315334455121,0.504187019532636,0.539673553233929,0.332712552364066,0.109518714890925,0.319393153334841,0.496933286849266,0.219615573160451,0.294625412002711,0.42224445252525,0,0.130312767515111,0,0,0,0.0908905864998999,0,0,0.107024882575293,0,0,0,0.097901023057347,0,0,0,0,0.253610608288505,0.200476652835998,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.238683494858807,0.275989732428356,0,0,0,0,0,0,0,0.10621117545989,0,0,0.992363998637193,0.378058590738136,0,0,0,0.856967139945993,0,0,0,0.970125370685875,0,0.324564326194432,0,0,0,0,0,0.501743555404659,0,0,0,0,0,0,0,0,0,0,0,0.246607501269895,0,0,0.493582754667301,0.149365571553368,0,0,0.0294164143815226,0,0.437806712299684,0,0,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|full_id=C384_Adipocyte_smooth_bladder_left_aorta_Osteoblast_colon
|full_id=C384_Adipocyte_smooth_bladder_left_aorta_Osteoblast_colon
|gostat_on_coexpression_clusters=GO:0005859!muscle myosin complex!0.0105086541858001!10398$GO:0016460!myosin II complex!0.0105086541858001!10398$GO:0006937!regulation of muscle contraction!0.0105086541858001!10398$GO:0008307!structural constituent of muscle!0.0105086541858001!10398$GO:0044449!contractile fiber part!0.0106754582204953!10398$GO:0043292!contractile fiber!0.0106754582204953!10398$GO:0016459!myosin complex!0.0152983128963348!10398$GO:0003012!muscle system process!0.0183484438164763!10398$GO:0006936!muscle contraction!0.0183484438164763!10398$GO:0051239!regulation of multicellular organismal process!0.0269312696017041!10398$GO:0015629!actin cytoskeleton!0.0269312696017041!10398
|gostat_on_coexpression_clusters=GO:0005859!muscle myosin complex!0.0105086541858001!10398$GO:0016460!myosin II complex!0.0105086541858001!10398$GO:0006937!regulation of muscle contraction!0.0105086541858001!10398$GO:0008307!structural constituent of muscle!0.0105086541858001!10398$GO:0044449!contractile fiber part!0.0106754582204953!10398$GO:0043292!contractile fiber!0.0106754582204953!10398$GO:0016459!myosin complex!0.0152983128963348!10398$GO:0003012!muscle system process!0.0183484438164763!10398$GO:0006936!muscle contraction!0.0183484438164763!10398$GO:0051239!regulation of multicellular organismal process!0.0269312696017041!10398$GO:0015629!actin cytoskeleton!0.0269312696017041!10398

Revision as of 16:50, 12 September 2012


Full id: C384_Adipocyte_smooth_bladder_left_aorta_Osteoblast_colon



Phase1 CAGE Peaks

Hg19::chr11:117075220..117075249,+p1@uc001pqq.1
Hg19::chr1:201869414..201869432,+p@chr1:201869414..201869432
+
Hg19::chr20:35173246..35173275,+p3@MYL9
Hg19::chr20:35173334..35173350,+p6@MYL9
Hg19::chr20:35173392..35173405,+p8@MYL9
Hg19::chr20:35173425..35173448,+p4@MYL9
Hg19::chr20:35176429..35176448,+p@chr20:35176429..35176448
+
Hg19::chr20:35176459..35176471,+p@chr20:35176459..35176471
+
Hg19::chr20:35176468..35176476,-p@chr20:35176468..35176476
-
Hg19::chr20:35176474..35176493,+p@chr20:35176474..35176493
+
Hg19::chr20:35176518..35176542,+p@chr20:35176518..35176542
+
Hg19::chr20:35176544..35176572,+p@chr20:35176544..35176572
+
Hg19::chr20:35177479..35177514,+p@chr20:35177479..35177514
+
Hg19::chr20:35177539..35177547,+p@chr20:35177539..35177547
+
Hg19::chr20:35177588..35177615,-p@chr20:35177588..35177615
-
Hg19::chr20:35177596..35177615,+p@chr20:35177596..35177615
+
Hg19::chr20:35177635..35177755,-p@chr20:35177635..35177755
-
Hg19::chr20:35177642..35177704,+p@chr20:35177642..35177704
+
Hg19::chr20:35177709..35177724,+p@chr20:35177709..35177724
+
Hg19::chr20:35177756..35177772,+p@chr20:35177756..35177772
+
Hg19::chr20:35177820..35177829,+p@chr20:35177820..35177829
+
Hg19::chr20:35177847..35177864,+p@chr20:35177847..35177864
+
Hg19::chr20:35177969..35177986,+p@chr20:35177969..35177986
+
Hg19::chr20:35178012..35178028,+p@chr20:35178012..35178028
+
Hg19::chr20:35178034..35178046,+p@chr20:35178034..35178046
+
Hg19::chr20:35178050..35178086,-p@chr20:35178050..35178086
-
Hg19::chr20:35178057..35178112,+p@chr20:35178057..35178112
+
Hg19::chr20:35178101..35178139,-p@chr20:35178101..35178139
-


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:0005859muscle myosin complex0.0105086541858001
GO:0016460myosin II complex0.0105086541858001
GO:0006937regulation of muscle contraction0.0105086541858001
GO:0008307structural constituent of muscle0.0105086541858001
GO:0044449contractile fiber part0.0106754582204953
GO:0043292contractile fiber0.0106754582204953
GO:0016459myosin complex0.0152983128963348
GO:0003012muscle system process0.0183484438164763
GO:0006936muscle contraction0.0183484438164763
GO:0051239regulation of multicellular organismal process0.0269312696017041
GO:0015629actin cytoskeleton0.0269312696017041



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
trunk mesenchyme2.60e-18143
somite5.69e-1683
paraxial mesoderm5.69e-1683
presomitic mesoderm5.69e-1683
presumptive segmental plate5.69e-1683
trunk paraxial mesoderm5.69e-1683
presumptive paraxial mesoderm5.69e-1683
multi-tissue structure1.66e-15347
multi-cellular organism3.11e-15659
muscle tissue5.51e-1563
musculature5.51e-1563
musculature of body5.51e-1563
dermomyotome6.65e-1570
trunk3.41e-14216
skeletal muscle tissue5.03e-1461
striated muscle tissue5.03e-1461
myotome5.03e-1461
multilaminar epithelium5.63e-1482
mesenchyme3.14e-13238
entire embryonic mesenchyme3.14e-13238
circulatory system4.33e-12113
splanchnic layer of lateral plate mesoderm2.08e-1184
organism subdivision2.42e-11365
cardiovascular system3.73e-11110
anatomical system4.64e-11625
anatomical group6.84e-11626
epithelial tube1.99e-10118
vasculature8.73e-1079
vascular system8.73e-1079
mesoderm2.67e-09448
mesoderm-derived structure2.67e-09448
presumptive mesoderm2.67e-09448
unilaminar epithelium2.70e-09138
blood vessel1.24e-0860
epithelial tube open at both ends1.24e-0860
blood vasculature1.24e-0860
vascular cord1.24e-0860
artery2.07e-0842
arterial blood vessel2.07e-0842
arterial system2.07e-0842
embryo2.56e-08612
anatomical cluster2.65e-08286
vessel4.22e-0869
primary circulatory organ6.60e-0827
cell layer7.06e-08312
epithelium8.57e-08309
embryonic structure1.68e-07605
developing anatomical structure1.68e-07605
germ layer3.05e-07604
embryonic tissue3.05e-07604
presumptive structure3.05e-07604
epiblast (generic)3.05e-07604
systemic artery3.32e-0733
systemic arterial system3.32e-0733
compound organ5.62e-0769
heart8.62e-0724
primitive heart tube8.62e-0724
primary heart field8.62e-0724
anterior lateral plate mesoderm8.62e-0724
heart tube8.62e-0724
heart primordium8.62e-0724
cardiac mesoderm8.62e-0724
cardiogenic plate8.62e-0724
heart rudiment8.62e-0724


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
CTCFL#14069064.231387362637360.002416712809055170.0136196346354907
SPI1#6688113.223127092633930.000256585273209660.00276149107056303



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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