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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:51, 17 September 2013


Full id: C1770_normal_sacrococcigeal_tridermal_Prostate_Smooth_rectum_smooth



Phase1 CAGE Peaks

Hg19::chr16:86256667..86256687,-p@chr16:86256667..86256687
-
Hg19::chr16:86542381..86542392,-p1@ENST00000499071
Hg19::chr16:86542455..86542500,-p1@LOC400550
Hg19::chr16:86544113..86544145,+p1@FOXF1
Hg19::chr16:86547162..86547166,+p@chr16:86547162..86547166
+


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:0030859polarized epithelial cell differentiation0.00135405628164371
GO:0045198establishment of epithelial cell polarity0.00135405628164371
GO:0035089establishment of apical/basal cell polarity0.00270811256328741
GO:0030010establishment of cell polarity0.00270811256328741
GO:0001738morphogenesis of a polarized epithelium0.00270811256328741
GO:0045197establishment and/or maintenance of epithelial cell polarity0.00270811256328741
GO:0048566embryonic gut development0.00270811256328741
GO:0035088establishment and/or maintenance of apical/basal cell polarity0.00304662663369834
GO:0048565gut development0.00330991535512906
GO:0001570vasculogenesis0.00487460261391734
GO:0048568embryonic organ development0.00492384102415893
GO:0007163establishment and/or maintenance of cell polarity0.00654460536127792
GO:0030855epithelial cell differentiation0.00749938863679591
GO:0030324lung development0.00776325601475725
GO:0030323respiratory tube development0.00776325601475725
GO:0030198extracellular matrix organization and biogenesis0.00778582361945131
GO:0002009morphogenesis of an epithelium0.0100359465580651
GO:0043062extracellular structure organization and biogenesis0.0126378586286746
GO:0035295tube development0.0166762721002435
GO:0048514blood vessel morphogenesis0.0199046273401625
GO:0001568blood vessel development0.0204339402502596
GO:0001944vasculature development0.0204339402502596
GO:0003713transcription coactivator activity0.0220181325797716
GO:0005667transcription factor complex0.0236959849287649
GO:0045893positive regulation of transcription, DNA-dependent0.0241563640645237
GO:0009790embryonic development0.0244771712450978
GO:0045941positive regulation of transcription0.0278935594018604
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0278935594018604
GO:0003712transcription cofactor activity0.0278935594018604
GO:0016563transcription activator activity0.0278935594018604
GO:0009887organ morphogenesis0.030889408924997
GO:0031325positive regulation of cellular metabolic process0.030889408924997
GO:0009893positive regulation of metabolic process0.0320870306741024
GO:0006357regulation of transcription from RNA polymerase II promoter0.0334258464954332
GO:0008134transcription factor binding0.0334258464954332
GO:0044451nucleoplasm part0.0340018577390531
GO:0000902cell morphogenesis0.0340652054013522
GO:0032989cellular structure morphogenesis0.0340652054013522
GO:0005654nucleoplasm0.0360387287268248
GO:0006366transcription from RNA polymerase II promoter0.0433298010125986
GO:0031981nuclear lumen0.0455755528943491



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
multi-tissue structure3.48e-18342
anatomical cluster1.07e-15373
smooth muscle tissue2.06e-1115
digestive system3.95e-11145
digestive tract3.95e-11145
primitive gut3.95e-11145
organ system subdivision1.01e-10223
endoderm-derived structure6.68e-10160
endoderm6.68e-10160
presumptive endoderm6.68e-10160
muscle tissue1.18e-0964
musculature1.18e-0964
musculature of body1.18e-0964
skeletal muscle tissue1.21e-0862
striated muscle tissue1.21e-0862
myotome1.21e-0862
organ segment3.76e-0898
dense mesenchyme tissue1.26e-0773
subdivision of digestive tract1.87e-07118
trunk mesenchyme2.30e-07122
somite2.49e-0771
presomitic mesoderm2.49e-0771
presumptive segmental plate2.49e-0771
dermomyotome2.49e-0771
trunk paraxial mesoderm2.49e-0771
systemic artery2.99e-0733
systemic arterial system2.99e-0733
anatomical conduit3.29e-07240
paraxial mesoderm4.31e-0772
presumptive paraxial mesoderm4.31e-0772
blood vessel smooth muscle4.53e-0710
arterial system smooth muscle4.53e-0710
artery smooth muscle tissue4.53e-0710
aorta smooth muscle tissue4.53e-0710
organism subdivision4.55e-07264
mesenchyme4.55e-07160
entire embryonic mesenchyme4.55e-07160
intestine4.78e-0717
epithelial vesicle7.83e-0778
organ part8.79e-07218


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)
MA0003.11.80249
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.161847
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.15.37773
MA0031.12.1751
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.11.05691
MA0058.10.523638
MA0059.10.522232
MA0060.10.860776
MA0061.10.791444
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.692739
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.11.05325
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.973423
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.11.25946
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.143698
MA0146.11.35428
MA0147.11.77656
MA0148.11.57313
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.0575907
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.20.858845
MA0047.20.767096
MA0112.20.136971
MA0065.20.880827
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.10.130813
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.11.72541
MA0163.10.680296
MA0164.10.810347
MA0080.21.15604
MA0018.20.781393
MA0099.20.699641
MA0079.24.80311
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
CTBP2#1488225.08680013573130.002461438599678380.0138485258800738
SUZ12#23512330.06946854663777.70283100694034e-050.00118847092263827



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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