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{{Coexpression_clusters
{
|full_id=C846_pancreas_leiomyoma_Smooth_tenocyte_Fibroblast_Adipocyte_Hepatocyte
|

Latest revision as of 11:32, 17 September 2013


Full id: C846_pancreas_leiomyoma_Smooth_tenocyte_Fibroblast_Adipocyte_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr17:79803082..79803112,-p6@P4HB
Hg19::chr17:79803474..79803506,-p2@P4HB
Hg19::chr17:79803795..79803822,-p11@P4HB
Hg19::chr17:79803824..79803843,-p18@P4HB
Hg19::chr17:79804916..79804933,-p4@P4HB
Hg19::chr17:79804935..79804958,-p9@P4HB
Hg19::chr17:79805146..79805197,-p3@P4HB
Hg19::chr17:79813398..79813436,-p5@P4HB
Hg19::chr17:79817107..79817135,-p7@P4HB
Hg19::chr3:127783792..127783816,+p2@SEC61A1


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

p.valueFDRnGenesnPathwayName
3.40211704163772e-050.02153540087356682167Protein processing in endoplasmic reticulum (KEGG):04141



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:0019511peptidyl-proline hydroxylation0.00145708230307312
GO:0018401peptidyl-proline hydroxylation to 4-hydroxy-L-proline0.00145708230307312
GO:00194714-hydroxyproline metabolic process0.00145708230307312
GO:0018208peptidyl-proline modification0.00145708230307312
GO:0031545peptidyl-proline 4-dioxygenase activity0.00291407882225392
GO:0004656procollagen-proline 4-dioxygenase activity0.00291407882225392
GO:0044432endoplasmic reticulum part0.00330733669435169
GO:0019798procollagen-proline dioxygenase activity0.00437092521962316
GO:0031543peptidyl-proline dioxygenase activity0.00453274461806331
GO:0016864intramolecular oxidoreductase activity, transposing S-S bonds0.00476807149730774
GO:0003756protein disulfide isomerase activity0.00476807149730774
GO:0016862intramolecular oxidoreductase activity, interconverting keto- and enol-groups0.00485629763105131
GO:0005783endoplasmic reticulum0.00541052206410783
GO:0015450P-P-bond-hydrolysis-driven protein transmembrane transporter activity0.0100987199993063
GO:0022884macromolecule transmembrane transporter activity0.0100987199993063
GO:0008320protein transmembrane transporter activity0.0101955228325995
GO:0005793ER-Golgi intermediate compartment0.014238010123144
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0.014238010123144
GO:0009306protein secretion0.017470575942967
GO:0005788endoplasmic reticulum lumen0.018261464437518
GO:0016860intramolecular oxidoreductase activity0.018261464437518
GO:0065002intracellular protein transport across a membrane0.018261464437518
GO:0048770pigment granule0.0201319783103799
GO:0042470melanosome0.0201319783103799
GO:0006575amino acid derivative metabolic process0.0209545000051523
GO:0045454cell redox homeostasis0.0241718552410727
GO:0018193peptidyl-amino acid modification0.0260734167618831
GO:0046483heterocycle metabolic process0.0270087214901337
GO:0009986cell surface0.0296802210019959
GO:0008565protein transporter activity0.02985138195407
GO:0005792microsome0.0303855457068317
GO:0042598vesicular fraction0.0307047518939551
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.031180058507942
GO:0044446intracellular organelle part0.0417957995859935
GO:0044422organelle part0.0417957995859935
GO:0032940secretion by cell0.0455416090038608
GO:0015399primary active transmembrane transporter activity0.0455416090038608
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.0455416090038608
GO:0044444cytoplasmic part0.0455416090038608
GO:0016853isomerase activity0.0455416090038608
GO:0016023cytoplasmic membrane-bound vesicle0.0485945978872026
GO:0031988membrane-bound vesicle0.0485945978872026



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
epithelial tube5.34e-16117
trunk mesenchyme4.15e-15122
unilaminar epithelium1.62e-13148
trunk2.35e-13199
mesenchyme7.60e-13160
entire embryonic mesenchyme7.60e-13160
epithelial vesicle9.16e-1278
artery1.62e-1142
arterial blood vessel1.62e-1142
arterial system1.62e-1142
organism subdivision2.34e-11264
splanchnic layer of lateral plate mesoderm2.51e-1183
multilaminar epithelium2.56e-1083
skeletal muscle tissue3.05e-1062
striated muscle tissue3.05e-1062
myotome3.05e-1062
muscle tissue5.51e-1064
musculature5.51e-1064
musculature of body5.51e-1064
somite5.86e-1071
presomitic mesoderm5.86e-1071
presumptive segmental plate5.86e-1071
dermomyotome5.86e-1071
trunk paraxial mesoderm5.86e-1071
dense mesenchyme tissue6.85e-1073
vasculature9.71e-1078
vascular system9.71e-1078
vessel1.03e-0968
paraxial mesoderm1.67e-0972
presumptive paraxial mesoderm1.67e-0972
systemic artery3.17e-0933
systemic arterial system3.17e-0933
epithelial tube open at both ends4.60e-0959
blood vessel4.60e-0959
blood vasculature4.60e-0959
vascular cord4.60e-0959
subdivision of trunk1.72e-07112
surface structure2.51e-0799
mesoderm2.54e-07315
mesoderm-derived structure2.54e-07315
presumptive mesoderm2.54e-07315
circulatory system3.95e-07112
cardiovascular system4.30e-07109
Disease
Ontology termp-valuen
ovarian cancer1.24e-0714


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)
MA0003.10.312279
MA0004.10.380329
MA0006.10.665232
MA0007.10.363007
MA0009.10.828613
MA0014.10.15363
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
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.11.75547
MA0050.10.368721
MA0051.10.473017
MA0052.10.753928
MA0055.10.867653
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.291897
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.12.08608
MA0067.11.1435
MA0068.10.304755
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.10.742548
MA0074.12.06891
MA0076.10.307383
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.126492
MA0089.10
MA0090.10.320494
MA0091.10.995927
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.10.49029
MA0101.10.241637
MA0103.11.20737
MA0105.10.0508589
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.11.59097
MA0113.10.532314
MA0114.10.174997
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
MA0139.10.353333
MA0140.11.11568
MA0141.10.789887
MA0142.10.638837
MA0143.10.532484
MA0144.10.163394
MA0145.10.602634
MA0146.10.128432
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.00259594
MA0138.20.569505
MA0002.20.80943
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.24.04027
MA0065.20.340764
MA0150.10.315136
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.10.414714
MA0155.10.866026
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.11.07255
MA0161.10
MA0162.10.00711618
MA0163.10.00405048
MA0164.10.544294
MA0080.20.238846
MA0018.20.517858
MA0099.20.444294
MA0079.20.00464855
MA0102.21.36707
MA0258.11.47203
MA0259.10.560522
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

No analysis results for this cluster

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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