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Coexpression cluster:C855: Difference between revisions

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{{Coexpression_clusters
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|full_id=C855_Mesothelial_Fibroblast_mesenchymal_Smooth_Sertoli_Myoblast_CD4
|id=C855
}}

Latest revision as of 11:32, 17 September 2013


Full id: C855_Mesothelial_Fibroblast_mesenchymal_Smooth_Sertoli_Myoblast_CD4



Phase1 CAGE Peaks

Hg19::chr2:162930622..162930641,-p4@DPP4
Hg19::chr2:162930654..162930665,-p7@DPP4
Hg19::chr2:162930688..162930752,-p2@DPP4
Hg19::chr2:162930797..162930810,-p6@DPP4
Hg19::chr2:162930861..162930874,-p10@DPP4
Hg19::chr2:162931058..162931063,-p16@DPP4
Hg19::chr2:162931082..162931100,-p9@DPP4
Hg19::chr2:162931120..162931131,-p15@DPP4
Hg19::chr2:162931138..162931149,-p14@DPP4
Hg19::chr4:120060444..120060452,-p@chr4:120060444..120060452
-


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
skeletal muscle tissue1.80e-1862
striated muscle tissue1.80e-1862
myotome1.80e-1862
muscle tissue3.47e-1864
musculature3.47e-1864
musculature of body3.47e-1864
somite5.42e-1871
presomitic mesoderm5.42e-1871
presumptive segmental plate5.42e-1871
dermomyotome5.42e-1871
trunk paraxial mesoderm5.42e-1871
unilaminar epithelium1.16e-17148
paraxial mesoderm1.65e-1772
presumptive paraxial mesoderm1.65e-1772
dense mesenchyme tissue4.85e-1773
multilaminar epithelium2.41e-1683
trunk mesenchyme4.27e-16122
splanchnic layer of lateral plate mesoderm5.17e-1683
epithelial vesicle6.69e-1578
mesenchyme3.31e-13160
entire embryonic mesenchyme3.31e-13160
trunk1.59e-12199
mesoderm3.15e-12315
mesoderm-derived structure3.15e-12315
presumptive mesoderm3.15e-12315
artery6.49e-1042
arterial blood vessel6.49e-1042
arterial system6.49e-1042
systemic artery1.28e-0933
systemic arterial system1.28e-0933
epithelial tube1.42e-09117
organism subdivision2.10e-09264
epithelial tube open at both ends9.65e-0959
blood vessel9.65e-0959
blood vasculature9.65e-0959
vascular cord9.65e-0959
smooth muscle tissue1.65e-0815
cardiovascular system4.72e-08109
heart1.64e-0724
primitive heart tube1.64e-0724
primary heart field1.64e-0724
anterior lateral plate mesoderm1.64e-0724
heart tube1.64e-0724
heart primordium1.64e-0724
cardiac mesoderm1.64e-0724
cardiogenic plate1.64e-0724
heart rudiment1.64e-0724
vasculature1.73e-0778
vascular system1.73e-0778
circulatory system1.78e-07112
vessel1.80e-0768
blood vessel smooth muscle2.11e-0710
arterial system smooth muscle2.11e-0710
artery smooth muscle tissue2.11e-0710
aorta smooth muscle tissue2.11e-0710
female gonad2.55e-0713
Disease
Ontology termp-valuen
ovarian cancer1.23e-1214
female reproductive organ cancer5.92e-0727
reproductive organ cancer9.18e-0729


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)
MA0003.13.05066
MA0004.11.75693
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.686562
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.25013
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.963243
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.12.58476
MA0051.10.473017
MA0052.10.753928
MA0055.10.0662377
MA0056.10
MA0057.11.70795
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.13.90306
MA0063.10
MA0066.13.08978
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.11.11021e-05
MA0074.10.4723
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.0309101
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.918839
MA0093.12.7134
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.13.59036
MA0103.10.646502
MA0105.13.32465
MA0106.10.516528
MA0107.14.73954
MA0108.22.70251
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.998594
MA0115.11.06753
MA0116.11.62509
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.10.585907
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.11.72746
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.11.3186
MA0144.10.951129
MA0145.10.0359093
MA0146.10.243477
MA0147.12.33266
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.00259594
MA0138.20.569505
MA0002.20.129981
MA0137.21.31174
MA0104.23.3966
MA0047.20.504873
MA0112.20.904106
MA0065.21.37627
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.13.51652
MA0154.12.67016
MA0155.10.296882
MA0156.10.715501
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.108522
MA0163.11.66479
MA0164.10.544294
MA0080.21.24809
MA0018.22.21993
MA0099.20.444294
MA0079.20.117453
MA0102.21.36707
MA0258.10.919347
MA0259.10.191914
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
CHD2#110655.172011417058430.001400750610919290.00910971997346032
E2F1#186994.416650293391394.94361321523441e-060.000152708080622853
EBF1#187998.01582016191212.54528393136776e-081.77336163114154e-06
EP300#203353.38697086311160.009216261698114180.0348404515687315
FOXA1#316955.540709874692730.001021651775689810.00724669178221058
HDAC2#306656.707810118313130.0004211114379446040.00393948920346619
IRF4#3662919.72306141806978.19313855480698e-121.034683431107e-09
POLR2A#543091.932707858902260.005980089183606110.0268152734638546
SPI1#668897.383891157670455.27911959243962e-083.35981700862158e-06
TAF1#687293.008741657170760.0001400644243887550.00182738143894281
USF1#739185.089199421766371.24116492349793e-050.000306516962509342
USF2#7392911.69297764656268.80406743651317e-108.23913977600358e-08



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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