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Coexpression cluster:C608: Difference between revisions

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{{Coexpression_clusters
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|coexpression_dpi_cluster_scores_median=0.

Latest revision as of 11:26, 17 September 2013


Full id: C608_Smooth_mesenchymal_hepatic_Olfactory_Ewing_basal_Fibroblast



Phase1 CAGE Peaks

Hg19::chr8:23155120..23155153,-p@chr8:23155120..23155153
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Hg19::chr8:23155270..23155284,-p@chr8:23155270..23155284
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Hg19::chr8:23155299..23155339,-p@chr8:23155299..23155339
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Hg19::chr8:23156379..23156401,-p@chr8:23156379..23156401
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Hg19::chr8:23156447..23156464,-p@chr8:23156447..23156464
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Hg19::chr8:23159569..23159589,-p@chr8:23159569..23159589
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Hg19::chr8:23159605..23159623,-p@chr8:23159605..23159623
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Hg19::chr8:23159627..23159644,-p@chr8:23159627..23159644
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Hg19::chr8:23160831..23160851,-p@chr8:23160831..23160851
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Hg19::chr8:23160879..23160895,-p@chr8:23160879..23160895
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Hg19::chr8:23160901..23160919,-p@chr8:23160901..23160919
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Hg19::chr8:23167261..23167303,-p@chr8:23167261..23167303
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Hg19::chr8:23198609..23198642,-p4@LOXL2
Hg19::chr8:23217696..23217708,-p@chr8:23217696..23217708
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Hg19::chr8:23261625..23261641,-p1@LOXL2


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
vasculature1.13e-1978
vascular system1.13e-1978
cardiovascular system6.83e-16109
vessel7.87e-1668
artery3.76e-1542
arterial blood vessel3.76e-1542
arterial system3.76e-1542
splanchnic layer of lateral plate mesoderm5.91e-1583
circulatory system8.02e-15112
epithelial vesicle1.18e-1478
epithelial tube open at both ends2.39e-1459
blood vessel2.39e-1459
blood vasculature2.39e-1459
vascular cord2.39e-1459
unilaminar epithelium5.80e-14148
epithelial tube1.50e-13117
somite1.75e-1371
presomitic mesoderm1.75e-1371
presumptive segmental plate1.75e-1371
dermomyotome1.75e-1371
trunk paraxial mesoderm1.75e-1371
dense mesenchyme tissue1.93e-1373
skeletal muscle tissue3.67e-1362
striated muscle tissue3.67e-1362
myotome3.67e-1362
paraxial mesoderm4.70e-1372
presumptive paraxial mesoderm4.70e-1372
muscle tissue2.94e-1264
musculature2.94e-1264
musculature of body2.94e-1264
systemic artery1.22e-1133
systemic arterial system1.22e-1133
multilaminar epithelium1.31e-1183
trunk mesenchyme5.55e-11122
mesenchyme7.61e-11160
entire embryonic mesenchyme7.61e-11160
trunk2.41e-07199
aorta3.13e-0721
aortic system3.13e-0721
mesoderm6.42e-07315
mesoderm-derived structure6.42e-07315
presumptive mesoderm6.42e-07315
Disease
Ontology termp-valuen
ovarian cancer1.80e-0914


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)
MA0003.10.0972587
MA0004.11.31328
MA0006.10.426713
MA0007.10.241375
MA0009.10.669377
MA0014.10.729427
MA0017.10.95676
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.454219
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.34128
MA0040.10.594421
MA0041.10.27117
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.818185
MA0056.10
MA0057.10.0873069
MA0058.11.63025
MA0059.11.62489
MA0060.10.0671843
MA0061.11.17249
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.964815
MA0069.10.655419
MA0070.11.55511
MA0071.10.308534
MA0072.10.640598
MA0073.10.484411
MA0074.10.337035
MA0076.10.567195
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.10.63829
MA0088.11.28272
MA0089.10
MA0090.10.205547
MA0091.11.32108
MA0092.10.228476
MA0093.11.98429
MA0095.10
MA0098.10
MA0100.10.930697
MA0101.11.38853
MA0103.10.411001
MA0105.10.623178
MA0106.10.983008
MA0107.10.650533
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.11.09759
MA0117.10.705104
MA0119.11.55801
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.11.10476
MA0140.10.30631
MA0141.10.533493
MA0142.10.489543
MA0143.10.391385
MA0144.11.00343
MA0145.11.04117
MA0146.13.04028
MA0147.11.11205
MA0148.10.276339
MA0149.10.298252
MA0062.20.425026
MA0035.20.305721
MA0039.20.282666
MA0138.20.425279
MA0002.20.480166
MA0137.20.908044
MA0104.21.31795
MA0047.20.366327
MA0112.20.124752
MA0065.20.491386
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.11.26909
MA0155.10.6552
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.671959
MA0160.10.288813
MA0161.10
MA0162.10.234575
MA0163.11.00044
MA0164.10.402162
MA0080.20.139746
MA0018.20.378086
MA0099.20.839067
MA0079.20.171864
MA0102.21.1957
MA0258.10.964206
MA0259.10.340204
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

No analysis results for this cluster

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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