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Latest revision as of 03:29, 17 September 2013


Full id: C3592_Fibroblast_schwannoma_basal_salivary_mesenchymal_large_Multipotent



Phase1 CAGE Peaks

Hg19::chr16:82660560..82660585,+p1@CDH13
Hg19::chr16:82660594..82660607,+p3@CDH13
Hg19::chr16:82660635..82660650,+p2@CDH13


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
epithelium3.39e-19306
cell layer5.10e-19309
anatomical cluster1.70e-18373
vasculature2.08e-1878
vascular system2.08e-1878
vessel1.89e-1768
anatomical conduit2.31e-17240
splanchnic layer of lateral plate mesoderm5.53e-1783
multi-cellular organism9.74e-17656
circulatory system2.68e-15112
multi-tissue structure4.64e-15342
epithelial tube open at both ends6.31e-1559
blood vessel6.31e-1559
blood vasculature6.31e-1559
vascular cord6.31e-1559
anatomical system1.28e-14624
anatomical group2.37e-14625
cardiovascular system2.92e-14109
multilaminar epithelium1.21e-1383
surface structure1.53e-1299
paraxial mesoderm1.91e-1272
presumptive paraxial mesoderm1.91e-1272
epithelial tube2.00e-12117
somite2.89e-1271
presomitic mesoderm2.89e-1271
presumptive segmental plate2.89e-1271
dermomyotome2.89e-1271
trunk paraxial mesoderm2.89e-1271
dense mesenchyme tissue2.91e-1273
epithelial vesicle3.70e-1278
artery1.27e-1142
arterial blood vessel1.27e-1142
arterial system1.27e-1142
skeletal muscle tissue1.53e-1162
striated muscle tissue1.53e-1162
myotome1.53e-1162
tube2.94e-11192
muscle tissue3.63e-1164
musculature3.63e-1164
musculature of body3.63e-1164
structure with developmental contribution from neural crest7.83e-10132
developing anatomical structure1.06e-09581
unilaminar epithelium1.60e-09148
organism subdivision3.01e-09264
systemic artery3.13e-0933
systemic arterial system3.13e-0933
embryonic structure3.38e-09564
primary circulatory organ4.63e-0927
embryo8.85e-09592
germ layer3.40e-08560
germ layer / neural crest3.40e-08560
embryonic tissue3.40e-08560
presumptive structure3.40e-08560
germ layer / neural crest derived structure3.40e-08560
epiblast (generic)3.40e-08560
heart6.60e-0824
primitive heart tube6.60e-0824
primary heart field6.60e-0824
anterior lateral plate mesoderm6.60e-0824
heart tube6.60e-0824
heart primordium6.60e-0824
cardiac mesoderm6.60e-0824
cardiogenic plate6.60e-0824
heart rudiment6.60e-0824
mesenchyme8.50e-08160
entire embryonic mesenchyme8.50e-08160
compound organ1.11e-0768
trunk mesenchyme1.15e-07122
ectoderm-derived structure2.90e-07171
ectoderm2.90e-07171
presumptive ectoderm2.90e-07171
skin of body3.49e-0741
integument3.73e-0746
integumental system3.73e-0746
aorta8.91e-0721
aortic system8.91e-0721
Disease
Ontology termp-valuen
ovarian cancer3.62e-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)
MA0003.11.0927
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.12.26702
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.0185922
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.12.37462
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.22.13189
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.12.08673
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.455568
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.00160703
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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
SUZ12#23512350.11578091106297.93834897779404e-060.000221974090734091



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.