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Coexpression cluster:C3498: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3498_Myoblast_Mesothelial_Endothelial_myxofibrosarcoma_mesenchymal_Lymphatic_immature
|id=C3498
}}

Latest revision as of 12:27, 17 September 2013


Full id: C3498_Myoblast_Mesothelial_Endothelial_myxofibrosarcoma_mesenchymal_Lymphatic_immature



Phase1 CAGE Peaks

Hg19::chr15:51386859..51386938,-p3@TNFAIP8L3
Hg19::chr15:51386999..51387039,-p1@TNFAIP8L3
Hg19::chr15:51387094..51387110,-p2@TNFAIP8L3


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
vessel6.46e-2868
splanchnic layer of lateral plate mesoderm4.28e-2783
vasculature1.50e-2678
vascular system1.50e-2678
epithelial tube open at both ends1.40e-2459
blood vessel1.40e-2459
blood vasculature1.40e-2459
vascular cord1.40e-2459
circulatory system3.71e-22112
cardiovascular system1.40e-21109
anatomical conduit3.23e-20240
cell layer5.53e-19309
multi-cellular organism9.65e-19656
paraxial mesoderm1.02e-1872
presumptive paraxial mesoderm1.02e-1872
epithelial vesicle1.04e-1878
epithelial tube1.23e-18117
epithelium1.69e-18306
dense mesenchyme tissue1.87e-1873
somite2.11e-1871
presomitic mesoderm2.11e-1871
presumptive segmental plate2.11e-1871
dermomyotome2.11e-1871
trunk paraxial mesoderm2.11e-1871
tube3.39e-18192
mesoderm1.20e-17315
mesoderm-derived structure1.20e-17315
presumptive mesoderm1.20e-17315
muscle tissue1.29e-1764
musculature1.29e-1764
musculature of body1.29e-1764
artery1.30e-1742
arterial blood vessel1.30e-1742
arterial system1.30e-1742
anatomical system1.96e-17624
unilaminar epithelium2.78e-17148
anatomical group3.81e-17625
skeletal muscle tissue3.98e-1762
striated muscle tissue3.98e-1762
myotome3.98e-1762
trunk mesenchyme6.61e-16122
germ layer1.61e-14560
germ layer / neural crest1.61e-14560
embryonic tissue1.61e-14560
presumptive structure1.61e-14560
germ layer / neural crest derived structure1.61e-14560
epiblast (generic)1.61e-14560
embryonic structure1.99e-14564
multilaminar epithelium4.30e-1483
systemic artery1.91e-1333
systemic arterial system1.91e-1333
anatomical cluster2.25e-13373
blood vessel endothelium1.05e-1218
endothelium1.05e-1218
cardiovascular system endothelium1.05e-1218
developing anatomical structure5.40e-12581
mesenchyme1.58e-11160
entire embryonic mesenchyme1.58e-11160
embryo4.15e-11592
adult organism6.11e-11114
multi-tissue structure1.87e-10342
aorta3.31e-1021
aortic system3.31e-1021
simple squamous epithelium3.53e-1022
squamous epithelium1.12e-0925
primary circulatory organ2.40e-0827
tissue2.52e-08773
trunk3.37e-08199
heart6.72e-0824
primitive heart tube6.72e-0824
primary heart field6.72e-0824
anterior lateral plate mesoderm6.72e-0824
heart tube6.72e-0824
heart primordium6.72e-0824
cardiac mesoderm6.72e-0824
cardiogenic plate6.72e-0824
heart rudiment6.72e-0824
structure with developmental contribution from neural crest1.22e-07132
endothelial tube6.35e-079


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)
MA0003.18.53684
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.90467
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.11.58389
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
MA0055.10.190716
MA0056.10
MA0057.10.886807
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
MA0088.10.715722
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
MA0145.12.11725
MA0146.11.16674
MA0147.10.565108
MA0148.10.854239
MA0149.12.04956
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.11.51687
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.23.61229
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
E2F1#186934.907389214879320.008460985347239390.0324551676159817
ZNF263#1012738.221841637010680.001799043925565870.0109175100837986



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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