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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.69870277404679,

Latest revision as of 11:24, 17 September 2013


Full id: C493_Adipocyte_basal_Mesenchymal_Smooth_mesenchymal_Aortic_Multipotent



Phase1 CAGE Peaks

Hg19::chr11:117070079..117070097,+p1@TAGLN
Hg19::chr11:117070904..117070918,+p4@TAGLN
Hg19::chr11:117073740..117073758,+p3@TAGLN
Hg19::chr11:117073759..117073770,+p6@TAGLN
Hg19::chr11:117073868..117073881,+p2@TAGLN
Hg19::chr11:117074035..117074046,+p@chr11:117074035..117074046
+
Hg19::chr11:117074061..117074089,+p@chr11:117074061..117074089
+
Hg19::chr11:117074100..117074165,+p@chr11:117074100..117074165
+
Hg19::chr11:117074945..117074955,+p@chr11:117074945..117074955
+
Hg19::chr11:117074952..117074998,-p@chr11:117074952..117074998
-
Hg19::chr11:117074969..117074997,+p@chr11:117074969..117074997
+
Hg19::chr11:117075014..117075028,+p@chr11:117075014..117075028
+
Hg19::chr11:117075034..117075109,+p@chr11:117075034..117075109
+
Hg19::chr11:117075077..117075102,-p@chr11:117075077..117075102
-
Hg19::chr11:117075111..117075122,+p@chr11:117075111..117075122
+
Hg19::chr11:117075129..117075140,+p@chr11:117075129..117075140
+
Hg19::chr11:117075245..117075293,-p@chr11:117075245..117075293
-
Hg19::chr9:35685106..35685122,-p@chr9:35685106..35685122
-
Hg19::chr9:35685133..35685147,-p@chr9:35685133..35685147
-


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
muscle tissue7.74e-2064
musculature7.74e-2064
musculature of body7.74e-2064
skeletal muscle tissue8.60e-1962
striated muscle tissue8.60e-1962
myotome8.60e-1962
dense mesenchyme tissue1.38e-1773
paraxial mesoderm5.44e-1772
presumptive paraxial mesoderm5.44e-1772
somite6.16e-1771
presomitic mesoderm6.16e-1771
presumptive segmental plate6.16e-1771
dermomyotome6.16e-1771
trunk paraxial mesoderm6.16e-1771
epithelial vesicle9.36e-1778
multilaminar epithelium8.13e-1683
mesenchyme1.10e-15160
entire embryonic mesenchyme1.10e-15160
trunk mesenchyme6.49e-15122
artery4.38e-1342
arterial blood vessel4.38e-1342
arterial system4.38e-1342
splanchnic layer of lateral plate mesoderm2.47e-1283
systemic artery8.02e-1233
systemic arterial system8.02e-1233
trunk7.39e-11199
epithelial tube open at both ends1.32e-0959
blood vessel1.32e-0959
blood vasculature1.32e-0959
vascular cord1.32e-0959
vasculature1.50e-0978
vascular system1.50e-0978
epithelial tube4.91e-09117
mesoderm9.26e-09315
mesoderm-derived structure9.26e-09315
presumptive mesoderm9.26e-09315
organism subdivision1.21e-08264
smooth muscle tissue1.31e-0815
circulatory system1.66e-08112
cardiovascular system3.96e-08109
vessel8.70e-0868
unilaminar epithelium3.68e-07148
primary circulatory organ5.29e-0727
multi-tissue structure6.17e-07342
multi-cellular organism6.90e-07656
blood vessel smooth muscle7.18e-0710
arterial system smooth muscle7.18e-0710
artery smooth muscle tissue7.18e-0710
aorta smooth muscle tissue7.18e-0710
Disease
Ontology termp-valuen
ovarian cancer2.22e-0714


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)
MA0003.10.0417237
MA0004.10.193314
MA0006.10.0925234
MA0007.10.532323
MA0009.10.580032
MA0014.10.25648
MA0017.10.367718
MA0019.10.305657
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.101383
MA0029.11.25496
MA0030.10.492344
MA0031.10.435419
MA0038.10.743126
MA0040.10.507819
MA0041.10.206566
MA0042.10.183918
MA0043.10.580321
MA0046.10.570066
MA0048.10.0472517
MA0050.10.542713
MA0051.11.35154
MA0052.10.511289
MA0055.13.77902
MA0056.10
MA0057.10.254333
MA0058.10.12994
MA0059.10.405044
MA0060.10.984515
MA0061.13.88826
MA0063.10
MA0066.10.270161
MA0067.10.879057
MA0068.11.37255
MA0069.10.566544
MA0070.10.556335
MA0071.10.240074
MA0072.10.552241
MA0073.10.0285812
MA0074.12.07723
MA0076.10.139892
MA0077.10.545231
MA0078.10.346453
MA0081.10.129245
MA0083.11.43365
MA0084.11.06048
MA0087.10.550016
MA0088.11.13073
MA0089.10
MA0090.10.149167
MA0091.10.195166
MA0092.12.21347
MA0093.10.0941737
MA0095.10
MA0098.10
MA0100.10.280715
MA0101.10.654976
MA0103.10.614572
MA0105.10.103598
MA0106.10.302526
MA0107.10.46886
MA0108.20.432749
MA0109.10
MA0111.10.15804
MA0113.10.315797
MA0114.10.793752
MA0115.10.805883
MA0116.10.0607301
MA0117.10.614633
MA0119.10.379868
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.10.27535
MA0139.10.0257123
MA0140.10.238066
MA0141.10.128074
MA0142.10.407878
MA0143.10.315941
MA0144.12.69955
MA0145.10.0209869
MA0146.10.431811
MA0147.10.0623218
MA0148.10.211171
MA0149.10.230803
MA0062.20.027823
MA0035.20.237534
MA0039.20.29451
MA0138.20.347473
MA0002.20.0346057
MA0137.22.97168
MA0104.20.0384802
MA0047.20.292798
MA0112.20.885708
MA0065.22.01276
MA0150.10.87566
MA0151.10
MA0152.11.26389
MA0153.10.67139
MA0154.10.00634321
MA0155.11.79698
MA0156.10.106343
MA0157.10.99963
MA0158.10
MA0159.10.487475
MA0160.10.222325
MA0161.10
MA0162.10.00153143
MA0163.10.933861
MA0164.12.378
MA0080.20.0942207
MA0018.20.30364
MA0099.20.243305
MA0079.20.129186
MA0102.21.09681
MA0258.11.53964
MA0259.10.0662172
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
POLR2A#5430151.69535777096690.004160730889787010.0198267360221958



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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