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Coexpression cluster:C4165: Difference between revisions

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{{Coexpression_clusters
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|full_id=C4165_schwannoma_CD14_Smooth_Fibroblast_mesenchymal_Mesenchymal_Preadipocyte
|id=C4165
}}

Latest revision as of 12:40, 17 September 2013


Full id: C4165_schwannoma_CD14_Smooth_Fibroblast_mesenchymal_Mesenchymal_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr2:197143317..197143335,-p14@HECW2
Hg19::chr2:197143341..197143358,-p8@HECW2
Hg19::chr2:197143373..197143393,-p6@HECW2


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>

Cell Type
Ontology termp-valuen
multi fate stem cell6.55e-18427
somatic cell8.54e-18588
vascular associated smooth muscle cell2.39e-1732
somatic stem cell4.72e-17433
stem cell1.87e-16441
endothelial cell of vascular tree3.46e-1624
fibroblast1.01e-1476
mesodermal cell1.60e-14121
classical monocyte1.38e-1242
CD14-positive, CD16-negative classical monocyte1.38e-1242
animal cell2.52e-12679
eukaryotic cell2.52e-12679
blood vessel endothelial cell3.33e-1218
embryonic blood vessel endothelial progenitor cell3.33e-1218
endothelial cell2.00e-1136
smooth muscle cell1.36e-1043
smooth muscle myoblast1.36e-1043
aortic smooth muscle cell1.55e-1010
native cell2.47e-10722
meso-epithelial cell4.66e-1045
defensive cell6.89e-1048
phagocyte6.89e-1048
endothelial cell of artery1.12e-099
muscle precursor cell1.33e-0858
myoblast1.33e-0858
multi-potent skeletal muscle stem cell1.33e-0858
mesenchymal cell1.33e-08354
connective tissue cell6.67e-08361
lining cell1.85e-0758
barrier cell1.85e-0758
muscle cell3.19e-0755
skin fibroblast3.63e-0723
monopoietic cell4.67e-0759
monocyte4.67e-0759
monoblast4.67e-0759
promonocyte4.67e-0759
motile cell5.83e-07386
aortic endothelial cell7.12e-076
Uber Anatomy
Ontology termp-valuen
artery1.37e-2942
arterial blood vessel1.37e-2942
arterial system1.37e-2942
vessel7.88e-2968
epithelial tube open at both ends5.85e-2759
blood vessel5.85e-2759
blood vasculature5.85e-2759
vascular cord5.85e-2759
systemic artery9.82e-2633
systemic arterial system9.82e-2633
splanchnic layer of lateral plate mesoderm2.84e-2483
vasculature1.14e-2378
vascular system1.14e-2378
lateral plate mesoderm2.50e-19203
cardiovascular system7.37e-19109
aorta1.17e-1821
aortic system1.17e-1821
circulatory system8.10e-18112
mesoderm1.72e-17315
mesoderm-derived structure1.72e-17315
presumptive mesoderm1.72e-17315
epithelial tube5.47e-15117
musculoskeletal system6.59e-14167
blood vessel endothelium3.33e-1218
endothelium3.33e-1218
cardiovascular system endothelium3.33e-1218
squamous epithelium8.54e-1125
blood vessel smooth muscle1.55e-1010
arterial system smooth muscle1.55e-1010
artery smooth muscle tissue1.55e-1010
aorta smooth muscle tissue1.55e-1010
simple squamous epithelium2.14e-1022
endothelial tube1.12e-099
arterial system endothelium1.12e-099
endothelium of artery1.12e-099
dense mesenchyme tissue1.59e-0973
epithelial vesicle1.64e-0978
somite2.47e-0971
presomitic mesoderm2.47e-0971
presumptive segmental plate2.47e-0971
dermomyotome2.47e-0971
trunk paraxial mesoderm2.47e-0971
paraxial mesoderm4.66e-0972
presumptive paraxial mesoderm4.66e-0972
multilaminar epithelium7.41e-0983
unilaminar epithelium6.82e-08148
connective tissue1.24e-07371
skeletal muscle tissue1.74e-0762
striated muscle tissue1.74e-0762
myotome1.74e-0762
muscle tissue5.47e-0764
musculature5.47e-0764
musculature of body5.47e-0764
Disease
Ontology termp-valuen
ovarian cancer2.13e-1214


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)
MA0003.10.0471418
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
MA0019.10.990656
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
MA0073.10.211629
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
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.0526989
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.11.76247
MA0151.10
MA0152.10.902317
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
MA0162.10.149099
MA0163.10.122425
MA0164.13.79952
MA0080.20.643061
MA0018.20.987913
MA0099.24.92261
MA0079.20.0107199
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
EP300#203336.77394172622320.003216880500103790.0167782552212515
FOS#235338.99795530889440.001372499272417130.0089920614460807
GATA2#2624312.7449317335540.0004829527704283790.00437611525167183
JUN#3725312.51282919233630.0005103313992726250.004449699533197



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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