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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.946913473388255

Latest revision as of 12:08, 17 September 2013


Full id: C2574_Mesenchymal_Pericytes_Fibroblast_Adipocyte_Nucleus_Meningeal_stomach



Phase1 CAGE Peaks

Hg19::chr1:236228379..236228402,-p1@NID1
Hg19::chr1:236228403..236228414,-p3@NID1
Hg19::chr1:236228417..236228446,-p2@NID1
Hg19::chr1:236228490..236228507,-p4@NID1


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
mesenchyme1.16e-19160
entire embryonic mesenchyme1.16e-19160
multi-cellular organism2.94e-18656
trunk mesenchyme8.41e-17122
unilaminar epithelium7.64e-16148
epithelial vesicle1.62e-1478
anatomical system2.09e-14624
vasculature2.19e-1478
vascular system2.19e-1478
anatomical group4.37e-14625
dense mesenchyme tissue6.36e-1373
somite6.79e-1371
presomitic mesoderm6.79e-1371
presumptive segmental plate6.79e-1371
dermomyotome6.79e-1371
trunk paraxial mesoderm6.79e-1371
epithelial tube7.21e-13117
paraxial mesoderm1.53e-1272
presumptive paraxial mesoderm1.53e-1272
splanchnic layer of lateral plate mesoderm3.20e-1283
circulatory system3.34e-12112
mesoderm3.86e-12315
mesoderm-derived structure3.86e-12315
presumptive mesoderm3.86e-12315
muscle tissue8.22e-1264
musculature8.22e-1264
musculature of body8.22e-1264
multilaminar epithelium8.45e-1283
cardiovascular system1.67e-11109
skeletal muscle tissue1.72e-1162
striated muscle tissue1.72e-1162
myotome1.72e-1162
cell layer1.80e-11309
trunk2.18e-11199
vessel6.73e-1168
organism subdivision8.97e-11264
anatomical cluster1.33e-10373
epithelium1.34e-10306
multi-tissue structure5.28e-09342
epithelial tube open at both ends1.90e-0859
blood vessel1.90e-0859
blood vasculature1.90e-0859
vascular cord1.90e-0859
anatomical conduit2.88e-07240
embryo4.16e-07592
developing anatomical structure5.47e-07581
abdominal segment of trunk8.50e-0760
abdomen8.50e-0760
germ layer8.65e-07560
germ layer / neural crest8.65e-07560
embryonic tissue8.65e-07560
presumptive structure8.65e-07560
germ layer / neural crest derived structure8.65e-07560
epiblast (generic)8.65e-07560


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)
MA0003.16.84463
MA0004.10.71247
MA0006.10.532262
MA0007.11.65296
MA0009.11.20602
MA0014.15.26462
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
MA0048.12.02223
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.16.61141
MA0056.10
MA0057.18.81203
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.11.51122
MA0077.11.16637
MA0078.10.926725
MA0081.11.4709
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.11.54523
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
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
MA0139.17.78226
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.569905
MA0146.11.25938
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.777367
MA0138.20.928035
MA0002.20.98779
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.533581
MA0156.11.37856
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.13.14178
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.29.97441
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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#1066445.360256373075030.001211145381643620.00817810903946973
HEY1#2346244.040111043105710.00375304636917980.0186206370427919
HNF4A#3172423.13229036295373.48990320893214e-060.000115671850599068
TAF1#687243.343046285745290.008005664898701650.0322471319174445
TBP#690843.706770687096390.005296377814784350.0244474676300832
YY1#752844.911170749853860.00171871838055440.0106922342713081
ZNF263#1012748.221841637010680.0002187871180958320.00249126775259601



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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