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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.292888198009602,

Latest revision as of 11:57, 17 September 2013


Full id: C2058_Smooth_basal_mesenchymal_tubular_Renal_lung_Urothelial



Phase1 CAGE Peaks

Hg19::chr10:33246815..33246830,-p4@ITGB1
Hg19::chr10:33246846..33246855,-p11@ITGB1
Hg19::chr10:33246856..33246867,-p8@ITGB1
Hg19::chr10:33246874..33246907,-p2@ITGB1


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
epithelial tube3.19e-21117
unilaminar epithelium3.52e-19148
trunk1.04e-18199
artery3.23e-1842
arterial blood vessel3.23e-1842
arterial system3.23e-1842
organism subdivision1.54e-17264
vasculature2.11e-1778
vascular system2.11e-1778
multilaminar epithelium3.10e-1783
splanchnic layer of lateral plate mesoderm3.64e-1783
epithelial tube open at both ends1.58e-1659
blood vessel1.58e-1659
blood vasculature1.58e-1659
vascular cord1.58e-1659
mesenchyme4.65e-16160
entire embryonic mesenchyme4.65e-16160
trunk mesenchyme7.14e-16122
systemic artery1.26e-1533
systemic arterial system1.26e-1533
epithelial vesicle1.37e-1578
somite1.98e-1571
presomitic mesoderm1.98e-1571
presumptive segmental plate1.98e-1571
dermomyotome1.98e-1571
trunk paraxial mesoderm1.98e-1571
vessel6.49e-1568
dense mesenchyme tissue1.15e-1473
paraxial mesoderm1.21e-1472
presumptive paraxial mesoderm1.21e-1472
skeletal muscle tissue1.22e-1362
striated muscle tissue1.22e-1362
myotome1.22e-1362
cardiovascular system2.63e-13109
muscle tissue4.97e-1364
musculature4.97e-1364
musculature of body4.97e-1364
circulatory system1.23e-12112
anatomical system6.23e-11624
anatomical group1.20e-10625
multi-cellular organism2.82e-10656
surface structure4.36e-0999
aorta6.26e-0921
aortic system6.26e-0921
mesoderm1.51e-07315
mesoderm-derived structure1.51e-07315
presumptive mesoderm1.51e-07315
cell layer1.79e-07309
epithelium3.82e-07306
integument4.33e-0746
integumental system4.33e-0746
Disease
Ontology termp-valuen
ovarian cancer2.97e-0814


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)
MA0003.19.1772
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.896009
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.11.35734
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.12.82503
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
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
MA0068.11.52107
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.153.2078
MA0074.10.819248
MA0076.11.51122
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
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.13665
MA0115.11.45393
MA0116.10.457606
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
MA0145.12.41215
MA0146.19.23949
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.27.89088
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
MA0154.10.229241
MA0155.12.30186
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.113.6423
MA0163.13.14178
MA0164.10.90014
MA0080.22.27911
MA0018.20.870662
MA0099.20.7872
MA0079.211.9208
MA0102.21.75932
MA0258.10.418966
MA0259.12.06681
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
CCNT2#90534.752151182721970.01386206996689490.0486995669157876
EGR1#195844.988179094810140.001615011500076050.0101218306562916
GABPB1#255347.067683836182170.0004006876864423170.00389604518055573
HEY1#2346244.040111043105710.00375304636917980.0185448717709486
HMGN3#932436.133910792512940.006640696683324720.0282849804612459
IRF1#365935.727872815172930.008097114790333330.0319814904919303
SIN3A#2594245.408884726815140.001168172384885160.00793978626220362
TAF1#687243.343046285745290.008005664898701650.0321084345758641
TAF7#6879411.43306940492395.85061525419808e-050.000966976430658638
ZBTB7A#5134147.35190930787590.000342223540015990.00345796094192434
ZEB1#6935312.66632401315790.000793336075912850.00612879846381109



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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