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{{Coexpression_clusters
{
|full_id=C934_basal_Preadipocyte_Adipocyte_Fibroblast_Mesenchymal_spindle_Myoblast

Latest revision as of 11:34, 17 September 2013


Full id: C934_basal_Preadipocyte_Adipocyte_Fibroblast_Mesenchymal_spindle_Myoblast



Phase1 CAGE Peaks

Hg19::chr1:86043705..86043730,-p11@DDAH1
Hg19::chr1:86043743..86043752,-p25@DDAH1
Hg19::chr1:86043758..86043791,-p5@DDAH1
Hg19::chr1:86043792..86043803,-p18@DDAH1
Hg19::chr1:86043808..86043860,-p2@DDAH1
Hg19::chr1:86043864..86043895,-p3@DDAH1
Hg19::chr1:86043921..86043937,-p6@DDAH1
Hg19::chr1:86043992..86044008,-p7@DDAH1
Hg19::chr1:86044028..86044041,-p10@DDAH1


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
dense mesenchyme tissue4.90e-2173
paraxial mesoderm1.93e-2072
presumptive paraxial mesoderm1.93e-2072
somite2.35e-2071
presomitic mesoderm2.35e-2071
presumptive segmental plate2.35e-2071
dermomyotome2.35e-2071
trunk paraxial mesoderm2.35e-2071
epithelial vesicle7.25e-1978
muscle tissue1.89e-1764
musculature1.89e-1764
musculature of body1.89e-1764
skeletal muscle tissue2.82e-1762
striated muscle tissue2.82e-1762
myotome2.82e-1762
multilaminar epithelium3.91e-1783
trunk mesenchyme1.43e-13122
mesenchyme7.33e-13160
entire embryonic mesenchyme7.33e-13160
splanchnic layer of lateral plate mesoderm3.76e-1283
vasculature9.00e-1278
vascular system9.00e-1278
unilaminar epithelium1.42e-11148
artery1.88e-1142
arterial blood vessel1.88e-1142
arterial system1.88e-1142
epithelial tube open at both ends3.73e-1059
blood vessel3.73e-1059
blood vasculature3.73e-1059
vascular cord3.73e-1059
integument1.13e-0946
integumental system1.13e-0946
cardiovascular system3.56e-09109
vessel3.93e-0968
systemic artery4.04e-0933
systemic arterial system4.04e-0933
trunk4.60e-09199
organism subdivision1.09e-08264
epithelial tube1.65e-08117
circulatory system2.33e-08112
skin of body4.66e-0841
surface structure6.14e-0899
mesoderm1.71e-07315
mesoderm-derived structure1.71e-07315
presumptive mesoderm1.71e-07315
cell layer3.51e-07309
smooth muscle tissue4.87e-0715
aorta5.44e-0721
aortic system5.44e-0721
multi-tissue structure9.00e-07342
organ component layer9.99e-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)
MA0003.10.000472949
MA0004.10.415381
MA0006.10.265592
MA0007.11.02827
MA0009.10.870971
MA0014.10.0324647
MA0017.10.301634
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.10.402577
MA0043.10.871285
MA0046.10.860127
MA0048.10.0764047
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.10.0199484
MA0056.10
MA0057.10.539841
MA0058.10.325084
MA0059.11.55919
MA0060.10.162248
MA0061.10.139804
MA0063.10
MA0066.10.514973
MA0067.11.18766
MA0068.13.774
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.124.1102
MA0074.10.509711
MA0076.10.339975
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.363555
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.271368
MA0103.10.257174
MA0105.10.0643619
MA0106.10.554855
MA0107.10.205358
MA0108.22.83198
MA0109.10
MA0111.10.959847
MA0113.10.57094
MA0114.10.200901
MA0115.11.11137
MA0116.10.208403
MA0117.14.94642
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.129876
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.046841
MA0146.10.0045741
MA0147.11.14329
MA0148.10.439278
MA0149.10.464973
MA0062.20.135498
MA0035.20.473658
MA0039.20.00489248
MA0138.20.608783
MA0002.22.0863
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.0433683
MA0065.20.0483532
MA0150.10.34802
MA0151.10
MA0152.10.480711
MA0153.10.969315
MA0154.10.062786
MA0155.11.00468
MA0156.10.785298
MA0157.10.652111
MA0158.10
MA0159.10.60858
MA0160.10.453945
MA0161.10
MA0162.10.767014
MA0163.10.00648562
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.60575
MA0102.21.41188
MA0258.10.180288
MA0259.10.218904
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#1066474.169088290169470.0001982812163300480.00238163219692856
MAX#414996.452555509007125.15172852378632e-083.28876146268777e-06
POLR2A#543092.147453176558070.001029412892608020.00728837726873361



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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