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{{Coexpression_clusters
{
|full_id=C1948_mesenchymal_Smooth_Skeletal_Lens_Keratocytes_cervical_salivary
 

Latest revision as of 11:55, 17 September 2013


Full id: C1948_mesenchymal_Smooth_Skeletal_Lens_Keratocytes_cervical_salivary



Phase1 CAGE Peaks

Hg19::chr5:110409038..110409052,+p4@TSLP
Hg19::chr5:110409053..110409100,+p1@TSLP
Hg19::chr5:110409111..110409126,+p2@TSLP
Hg19::chr5:110409130..110409145,+p5@TSLP
Hg19::chr5:110409170..110409189,+p6@TSLP


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
muscle tissue2.57e-1464
musculature2.57e-1464
musculature of body2.57e-1464
skeletal muscle tissue1.37e-1362
striated muscle tissue1.37e-1362
myotome1.37e-1362
paraxial mesoderm7.08e-1372
presumptive paraxial mesoderm7.08e-1372
somite8.52e-1371
presomitic mesoderm8.52e-1371
presumptive segmental plate8.52e-1371
dermomyotome8.52e-1371
trunk paraxial mesoderm8.52e-1371
dense mesenchyme tissue1.94e-1273
multilaminar epithelium8.29e-1183
epithelial vesicle1.56e-1078
trunk mesenchyme1.54e-08122
artery1.99e-0842
arterial blood vessel1.99e-0842
arterial system1.99e-0842
organism subdivision6.52e-08264
mesenchyme2.20e-07160
entire embryonic mesenchyme2.20e-07160
unilaminar epithelium2.22e-07148
germ layer3.51e-07560
germ layer / neural crest3.51e-07560
embryonic tissue3.51e-07560
presumptive structure3.51e-07560
germ layer / neural crest derived structure3.51e-07560
epiblast (generic)3.51e-07560
embryonic structure3.61e-07564
multi-tissue structure8.90e-07342


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)
MA0003.10.0497246
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.11.9468
MA0017.11.24112
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.12.06887
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.15.56275
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.0469445
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.412364
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.11.77562
MA0101.10.459973
MA0103.11.12656
MA0105.11.58771
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.16.96845
MA0140.10.692258
MA0141.12.22808
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.21.12758
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.24.30878
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.813062
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.11.60707
MA0161.10
MA0162.14.22787
MA0163.10.0439995
MA0164.10.810347
MA0080.21.15604
MA0018.20.781393
MA0099.20.699641
MA0079.22.44686
MA0102.21.66336
MA0258.10.345771
MA0259.11.02361
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#1066455.360256373075030.0002259278299937090.00250166206920196
EGR1#195854.988179094810140.0003237398000590710.00331026639694237
HMGN3#932458.178547723350592.73180911341838e-050.00058273572711663
IRF1#365957.63716375356393.84754333311872e-050.000724938802395069
PAX5#507956.669565531177837.57493746384605e-050.00117133386702194
RAD21#5885510.35503389545638.39503550283973e-060.000229821523690977
SPI1#668858.204323508522732.68916109982495e-050.000575401139325175
ZNF263#1012758.221841637010682.6606316672286e-050.000572227575563608



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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