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Coexpression cluster:C2788: Difference between revisions

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{{Coexpression_clusters
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|full_id=C2788_Urothelial_Fibroblast_Small_Smooth_Mallassezderived_Myoblast_Gingival
|id=C2788
}}

Latest revision as of 12:13, 17 September 2013


Full id: C2788_Urothelial_Fibroblast_Small_Smooth_Mallassezderived_Myoblast_Gingival



Phase1 CAGE Peaks

Hg19::chr4:177713756..177713777,-p4@VEGFC
Hg19::chr4:177713788..177713805,-p6@VEGFC
Hg19::chr4:177714068..177714085,-p1@VEGFC
Hg19::chr4:177714098..177714111,-p3@VEGFC


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
multilaminar epithelium2.27e-2183
organism subdivision2.15e-20264
epithelial vesicle2.60e-1978
somite5.55e-1871
presomitic mesoderm5.55e-1871
presumptive segmental plate5.55e-1871
dermomyotome5.55e-1871
trunk paraxial mesoderm5.55e-1871
paraxial mesoderm1.32e-1772
presumptive paraxial mesoderm1.32e-1772
dense mesenchyme tissue1.63e-1773
surface structure3.41e-1799
trunk6.69e-16199
trunk mesenchyme9.21e-16122
skeletal muscle tissue6.18e-1562
striated muscle tissue6.18e-1562
myotome6.18e-1562
unilaminar epithelium1.18e-14148
muscle tissue1.62e-1464
musculature1.62e-1464
musculature of body1.62e-1464
artery5.11e-1442
arterial blood vessel5.11e-1442
arterial system5.11e-1442
mesenchyme1.25e-13160
entire embryonic mesenchyme1.25e-13160
multi-tissue structure2.17e-13342
epithelium3.62e-13306
cell layer4.19e-13309
splanchnic layer of lateral plate mesoderm5.33e-1383
epithelial tube open at both ends7.31e-1359
blood vessel7.31e-1359
blood vasculature7.31e-1359
vascular cord7.31e-1359
vessel8.59e-1368
multi-cellular organism2.81e-12656
vasculature5.69e-1278
vascular system5.69e-1278
systemic artery2.00e-1133
systemic arterial system2.00e-1133
anatomical system2.79e-11624
epithelial tube4.48e-11117
anatomical group4.67e-11625
integument1.16e-0946
integumental system1.16e-0946
anatomical cluster1.23e-09373
skin of body6.90e-0941
anatomical conduit1.55e-08240
cardiovascular system1.46e-07109
circulatory system1.56e-07112
Disease
Ontology termp-valuen
ovarian cancer2.00e-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)
MA0003.13.49532
MA0004.11.69588
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.18.67501
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
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.28333
MA0058.11.47358
MA0059.12.50216
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
MA0073.10.380957
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.11.32557
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
MA0114.10.447443
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
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.11.70272
MA0146.10.481
MA0147.12.03364
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.22.1393
MA0002.20.379056
MA0137.21.37305
MA0104.21.01696
MA0047.20.856092
MA0112.20.187982
MA0065.21.09513
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.16.73484
MA0163.12.49771
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.220.7411
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
CTCF#1066445.360256373075030.001211145381643620.00819187957473469
E2F1#186944.907389214879320.001724022357361790.0106724658277819
TAF1#687243.343046285745290.008005664898701650.0323031965520033



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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