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{{Coexpression_clusters
{
|full_id=C2086_smooth_bladder_heart_gall_esophagus_seminal_uterus
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Latest revision as of 11:58, 17 September 2013


Full id: C2086_smooth_bladder_heart_gall_esophagus_seminal_uterus



Phase1 CAGE Peaks

Hg19::chr10:97197552..97197590,-p9@SORBS1
Hg19::chr2:220284774..220284780,+p10@DES
Hg19::chr2:220284788..220284812,+p2@DES
Hg19::chr2:220284844..220284855,+p8@DES


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

p.valueFDRnGenesnPathwayName
2.88643650599953e-060.0018271143082977249Muscle contraction (Reactome):REACT_17044



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:0045098type III intermediate filament0.00535727426246884
GO:0005915zonula adherens0.00535727426246884
GO:0007010cytoskeleton organization and biogenesis0.00749885925619792
GO:0043149stress fiber formation0.00749885925619792
GO:0001725stress fiber0.00749885925619792
GO:0032432actin filament bundle0.00749885925619792
GO:0044430cytoskeletal part0.00749885925619792
GO:0048041focal adhesion formation0.00749885925619792
GO:0005913cell-cell adherens junction0.00749885925619792
GO:0030018Z disc0.00749885925619792
GO:0042383sarcolemma0.00758779626979266
GO:0031674I band0.00758779626979266
GO:0051017actin filament bundle formation0.00765122132711095
GO:0005626insoluble fraction0.00765122132711095
GO:0005158insulin receptor binding0.00821194817254023
GO:0005856cytoskeleton0.00856785393064033
GO:0015758glucose transport0.00856785393064033
GO:0008645hexose transport0.00856785393064033
GO:0008286insulin receptor signaling pathway0.00856785393064033
GO:0015749monosaccharide transport0.00856785393064033
GO:0006996organelle organization and biogenesis0.00873810035451232
GO:0005924cell-substrate adherens junction0.00886120895483628
GO:0030055cell-matrix junction0.00886120895483628
GO:0007015actin filament organization0.00886120895483628
GO:0008016regulation of heart contraction0.00886120895483628
GO:0045121lipid raft0.00886120895483628
GO:0060047heart contraction0.00886120895483628
GO:0003015heart process0.00886120895483628
GO:0030017sarcomere0.00886120895483628
GO:0030016myofibril0.00932488368221589
GO:0005912adherens junction0.00932488368221589
GO:0044449contractile fiber part0.0100363141022865
GO:0043292contractile fiber0.0103803838974261
GO:0005200structural constituent of cytoskeleton0.0129946289266619
GO:0016323basolateral plasma membrane0.0129946289266619
GO:0007160cell-matrix adhesion0.0140415253671652
GO:0032403protein complex binding0.0140415253671652
GO:0031589cell-substrate adhesion0.0140415253671652
GO:0043296apical junction complex0.0140415253671652
GO:0016327apicolateral plasma membrane0.0140415253671652
GO:0008643carbohydrate transport0.0144805710846923
GO:0043232intracellular non-membrane-bound organelle0.0156300524876296
GO:0043228non-membrane-bound organelle0.0156300524876296
GO:0016043cellular component organization and biogenesis0.0183714485940823
GO:0008015blood circulation0.0183714485940823
GO:0003013circulatory system process0.0183714485940823
GO:0003012muscle system process0.0183714485940823
GO:0006936muscle contraction0.0183714485940823
GO:0005911intercellular junction0.0188668525064153
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0224316669169304
GO:0005886plasma membrane0.0225084027646801
GO:0005882intermediate filament0.0237728719017302
GO:0045111intermediate filament cytoskeleton0.0237728719017302
GO:0030036actin cytoskeleton organization and biogenesis0.0240114757722564
GO:0044446intracellular organelle part0.0240114757722564
GO:0044422organelle part0.0240114757722564
GO:0030029actin filament-based process0.0243438934286215
GO:0051239regulation of multicellular organismal process0.0254820419003628
GO:0015629actin cytoskeleton0.0266688820400185
GO:0007167enzyme linked receptor protein signaling pathway0.0266688820400185
GO:0030054cell junction0.0374397760363107
GO:0003779actin binding0.0376036765297134



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.08e-36114
male reproductive organ1.48e-1111
reproductive organ9.33e-1048
reproductive structure3.66e-0859
reproductive system3.66e-0859
male genital duct7.60e-083
internal male genitalia7.60e-083
valve1.08e-073
cardiac mesenchyme1.08e-073
cardial valve1.08e-073
tunica intima1.08e-073
heart layer1.08e-073
endocardium1.08e-073
endocardial cushion1.08e-073
presumptive endocardium1.08e-073
compound organ1.52e-0768
cardiac chamber1.97e-073
internal genitalia9.77e-0725


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)
MA0003.10.443649
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.11.92746
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.396851
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.0343867
MA0074.11.91637
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.11.9583
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.12.01976
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.8309
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.21.66396
MA0035.20.778873
MA0039.23.66694
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.88496
MA0155.10.533581
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.11.78721
MA0161.10
MA0162.10.640035
MA0163.10.0725493
MA0164.10.90014
MA0080.21.32578
MA0018.20.870662
MA0099.20.7872
MA0079.20.0626799
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
MA0442.10



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
TAL1#6886322.40146250808020.0001462756395930170.00188883302713342
ZBTB7A#5134135.513931980906920.009038352821081090.0342224025769818



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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