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{{Coexpression_clusters
{
|full_id=C2854_mesothelioma_Smooth_liposarcoma_papillary_mesodermal_mesenchymal_Olfactory

Latest revision as of 12:14, 17 September 2013


Full id: C2854_mesothelioma_Smooth_liposarcoma_papillary_mesodermal_mesenchymal_Olfactory



Phase1 CAGE Peaks

Hg19::chr6:169562893..169562942,-p1@ENST00000439703
Hg19::chr6:169562947..169562969,-p6@ENST00000439703
Hg19::chr6:169562989..169563008,-p2@ENST00000439703
Hg19::chr6:169563013..169563043,-p4@ENST00000439703


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><br>

Uber Anatomy
Ontology termp-valuen
skeletal muscle tissue2.48e-1162
striated muscle tissue2.48e-1162
myotome2.48e-1162
dense mesenchyme tissue3.73e-1173
somite5.00e-1171
presomitic mesoderm5.00e-1171
presumptive segmental plate5.00e-1171
dermomyotome5.00e-1171
trunk paraxial mesoderm5.00e-1171
multilaminar epithelium6.63e-1183
paraxial mesoderm1.16e-1072
presumptive paraxial mesoderm1.16e-1072
muscle tissue1.55e-1064
musculature1.55e-1064
musculature of body1.55e-1064
heart8.55e-1024
primitive heart tube8.55e-1024
primary heart field8.55e-1024
anterior lateral plate mesoderm8.55e-1024
heart tube8.55e-1024
heart primordium8.55e-1024
cardiac mesoderm8.55e-1024
cardiogenic plate8.55e-1024
heart rudiment8.55e-1024
splanchnic layer of lateral plate mesoderm7.31e-0983
primary circulatory organ8.59e-0927
surface structure9.35e-0999
epithelial vesicle1.01e-0878
artery1.22e-0842
arterial blood vessel1.22e-0842
arterial system1.22e-0842
systemic artery5.91e-0833
systemic arterial system5.91e-0833
connective tissue1.66e-07371
integument6.13e-0746
integumental system6.13e-0746


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)
MA0003.11.05935
MA0004.12.8475
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
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
MA0038.10.824639
MA0040.11.12314
MA0041.11.73823
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.13.66086
MA0059.17.61786
MA0060.10.393285
MA0061.11.68681
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.13.06856
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.536981
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.15.76405
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.13.51257
MA0106.10.869173
MA0107.11.1497
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.13.3942
MA0114.10.447443
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
MA0141.13.64588
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.10.8309
MA0147.13.01834
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.24.29465
MA0138.25.02795
MA0002.21.75253
MA0137.20.558189
MA0104.22.6968
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.11.78721
MA0161.10
MA0162.11.06783
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.21.85039
MA0079.20.20937
MA0102.21.75932
MA0258.10.418966
MA0259.13.06353
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
JUN#3725412.51282919233634.07770316866756e-050.000744790558293934
STAT3#6774410.51946499715428.16377768286615e-050.00123460292125812
TFAP2A#7020416.5186343730451.34240829060362e-050.00032734013416379
TFAP2C#7022410.80922860986027.32289634782688e-050.00114834229980584



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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