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Coexpression cluster:C3293: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3293_Mesenchymal_Smooth_Synoviocyte_tenocyte_leiomyoma_Cardiac_Fibroblast
|id=C3293
}}

Latest revision as of 12:23, 17 September 2013


Full id: C3293_Mesenchymal_Smooth_Synoviocyte_tenocyte_leiomyoma_Cardiac_Fibroblast



Phase1 CAGE Peaks

Hg19::chr12:53491413..53491430,+p2@IGFBP6
Hg19::chr12:53491441..53491458,+p1@IGFBP6
Hg19::chr12:53491743..53491754,+p1@AK074416


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

GO IDGO nameFDR corrected p-value
GO:0005520insulin-like growth factor binding0.0246000908311046
GO:0019838growth factor binding0.0246000908311046
GO:0001558regulation of cell growth0.0246000908311046
GO:0016049cell growth0.0246000908311046
GO:0040008regulation of growth0.0246000908311046
GO:0008361regulation of cell size0.0246000908311046
GO:0008285negative regulation of cell proliferation0.0246000908311046
GO:0042127regulation of cell proliferation0.0365830684092782
GO:0000902cell morphogenesis0.0365830684092782
GO:0032989cellular structure morphogenesis0.0365830684092782
GO:0005615extracellular space0.0367361356411162
GO:0008283cell proliferation0.0475146198830409



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
organism subdivision6.41e-25264
dense mesenchyme tissue1.37e-2373
somite1.62e-2371
presomitic mesoderm1.62e-2371
presumptive segmental plate1.62e-2371
dermomyotome1.62e-2371
trunk paraxial mesoderm1.62e-2371
epithelial vesicle2.74e-2378
paraxial mesoderm3.61e-2372
presumptive paraxial mesoderm3.61e-2372
skeletal muscle tissue2.63e-2262
striated muscle tissue2.63e-2262
myotome2.63e-2262
muscle tissue4.02e-2264
musculature4.02e-2264
musculature of body4.02e-2264
mesenchyme6.10e-22160
entire embryonic mesenchyme6.10e-22160
multilaminar epithelium6.99e-2283
trunk mesenchyme1.19e-20122
trunk6.24e-20199
multi-tissue structure1.20e-19342
unilaminar epithelium1.63e-16148
cell layer3.43e-15309
epithelium1.46e-14306
splanchnic layer of lateral plate mesoderm2.41e-1483
multi-cellular organism6.24e-13656
surface structure1.74e-1299
epithelial tube1.80e-12117
artery1.88e-1242
arterial blood vessel1.88e-1242
arterial system1.88e-1242
anatomical system1.15e-11624
systemic artery1.53e-1133
systemic arterial system1.53e-1133
anatomical group1.68e-11625
anatomical cluster1.86e-11373
vasculature1.73e-1078
vascular system1.73e-1078
epithelial tube open at both ends1.83e-1059
blood vessel1.83e-1059
blood vasculature1.83e-1059
vascular cord1.83e-1059
anatomical conduit4.17e-09240
vessel9.63e-0968
compound organ6.04e-0868
heart9.45e-0824
primitive heart tube9.45e-0824
primary heart field9.45e-0824
anterior lateral plate mesoderm9.45e-0824
heart tube9.45e-0824
heart primordium9.45e-0824
cardiac mesoderm9.45e-0824
cardiogenic plate9.45e-0824
heart rudiment9.45e-0824
circulatory system1.31e-07112
primary circulatory organ1.33e-0727
cardiovascular system1.78e-07109
organ component layer4.70e-0766


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
MA0019.10.990656
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
MA0048.13.37768
MA0050.10.81185
MA0051.12.15619
MA0052.11.24796
MA0055.17.8496
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.99448
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.04561
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.11.31954
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.11.55947
MA0103.10.628063
MA0105.14.18141
MA0106.10.986396
MA0107.12.34614
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.11.35563
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.11.66081
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
MA0145.10.752137
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.12.04956
MA0062.20.449458
MA0035.20.894194
MA0039.21.62945
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.13.48527
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.24.62164
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-060.000221618077757774
TCF7L2#6934310.77017656313730.0008003181298398380.00612250404060525



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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