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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0.611138253391405,0

Latest revision as of 11:23, 17 September 2013


Full id: C453_hepatic_Ewing_neurofibroma_spindle_tridermal_Olfactory_bone



Phase1 CAGE Peaks

Hg19::chr15:33025921..33025938,+p@chr15:33025921..33025938
+
Hg19::chr15:39882081..39882094,+p@chr15:39882081..39882094
+
Hg19::chr15:39882095..39882106,+p@chr15:39882095..39882106
+
Hg19::chr15:39883408..39883415,+p37@THBS1
Hg19::chr15:39888563..39888574,+p@chr15:39888563..39888574
+
Hg19::chr15:39888595..39888609,+p@chr15:39888595..39888609
+
Hg19::chr15:39888702..39888705,+p@chr15:39888702..39888705
+
Hg19::chr15:39888716..39888727,+p@chr15:39888716..39888727
+
Hg19::chr15:39888784..39888798,+p@chr15:39888784..39888798
+
Hg19::chr15:39888826..39888850,+p@chr15:39888826..39888850
+
Hg19::chr15:39888934..39888945,+p@chr15:39888934..39888945
+
Hg19::chr15:39889064..39889095,+p@chr15:39889064..39889095
+
Hg19::chr15:39889119..39889166,+p@chr15:39889119..39889166
+
Hg19::chr15:39889167..39889181,+p@chr15:39889167..39889181
+
Hg19::chr15:39889186..39889187,+p@chr15:39889186..39889187
+
Hg19::chr15:39889193..39889209,+p@chr15:39889193..39889209
+
Hg19::chr15:39889224..39889239,+p@chr15:39889224..39889239
+
Hg19::chr15:39889243..39889260,+p@chr15:39889243..39889260
+
Hg19::chr15:39889273..39889278,+p@chr15:39889273..39889278
+
Hg19::chr15:39889279..39889395,+p2@BC015134
Hg19::chr15:39889397..39889411,+p4@BC015134
Hg19::chr15:39889413..39889446,+p3@BC015134


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:0008201heparin binding0.0154244672082892
GO:0007596blood coagulation0.0154244672082892
GO:0050817coagulation0.0154244672082892
GO:0007599hemostasis0.0154244672082892
GO:0005539glycosaminoglycan binding0.0154244672082892
GO:0030247polysaccharide binding0.0154244672082892
GO:0050878regulation of body fluid levels0.0154244672082892
GO:0001871pattern binding0.0154244672082892
GO:0042060wound healing0.0154244672082892
GO:0004866endopeptidase inhibitor activity0.0256253813300793
GO:0030414protease inhibitor activity0.0256253813300793
GO:0051674localization of cell0.0298834334157541
GO:0006928cell motility0.0298834334157541
GO:0004857enzyme inhibitor activity0.0298834334157541
GO:0009611response to wounding0.0298834334157541
GO:0030246carbohydrate binding0.0316584245849523
GO:0009605response to external stimulus0.039458100442579
GO:0007399nervous system development0.042152360767691
GO:0065008regulation of biological quality0.0484432557904829
GO:0022610biological adhesion0.0484432557904829
GO:0007155cell adhesion0.0484432557904829



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
vessel1.40e-1668
splanchnic layer of lateral plate mesoderm9.17e-1683
epithelial tube open at both ends3.82e-1559
blood vessel3.82e-1559
blood vasculature3.82e-1559
vascular cord3.82e-1559
vasculature8.32e-1578
vascular system8.32e-1578
artery2.12e-1242
arterial blood vessel2.12e-1242
arterial system2.12e-1242
epithelial tube2.91e-11117
simple squamous epithelium3.72e-1122
blood vessel endothelium6.47e-1118
endothelium6.47e-1118
cardiovascular system endothelium6.47e-1118
circulatory system2.88e-10112
cardiovascular system3.62e-10109
squamous epithelium1.12e-0925
systemic artery4.60e-0933
systemic arterial system4.60e-0933
aorta1.24e-0821
aortic system1.24e-0821
organ component layer1.52e-0866
mesoderm5.03e-08315
mesoderm-derived structure5.03e-08315
presumptive mesoderm5.03e-08315
anatomical system5.05e-08624
unilaminar epithelium6.02e-08148
anatomical group6.62e-08625
multi-cellular organism1.42e-07656
endothelial tube2.17e-079
arterial system endothelium2.17e-079
endothelium of artery2.17e-079
lateral plate mesoderm3.34e-07203


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)
MA0003.12.47965e-08
MA0004.10.158412
MA0006.10.0694838
MA0007.10.146569
MA0009.10.526253
MA0014.11.18834e-05
MA0017.10.0884918
MA0019.10.262545
MA0024.10.434294
MA0025.10.647545
MA0027.12.09389
MA0028.10.0770177
MA0029.12.96904
MA0030.10.441064
MA0031.10.386141
MA0038.10.22896
MA0040.10.456051
MA0041.16.49074
MA0042.10.457543
MA0043.10.526535
MA0046.13.26595
MA0048.10.0283321
MA0050.12.07019
MA0051.16.31201
MA0052.10.459414
MA0055.10.0584391
MA0056.10
MA0057.10.1739
MA0058.10.101748
MA0059.10.101051
MA0060.10.0258987
MA0061.10.0189504
MA0063.10
MA0066.10.22927
MA0067.10.820123
MA0068.10.0112936
MA0069.10.51311
MA0070.10.503171
MA0071.10.201311
MA0072.10.499187
MA0073.13.42403e-11
MA0074.10.225345
MA0076.10.110503
MA0077.10.49237
MA0078.10.30111
MA0081.11.12539
MA0083.10.532971
MA0084.10.999884
MA0087.10.497023
MA0088.10.00120138
MA0089.10
MA0090.10.118716
MA0091.10.160096
MA0092.12.63369
MA0093.10.0708814
MA0095.10
MA0098.10
MA0100.10.672223
MA0101.10.0724124
MA0103.10.0653004
MA0105.10.00342752
MA0106.10.259598
MA0107.10.041912
MA0108.20.383574
MA0109.10
MA0111.10.126618
MA0113.10.272101
MA0114.10.0401034
MA0115.10.747865
MA0116.10.0431675
MA0117.10.560027
MA0119.10.0925355
MA0122.10.583485
MA0124.10.70896
MA0125.10.631059
MA0130.10
MA0131.10.315517
MA0132.10
MA0133.10
MA0135.10.553498
MA0136.11.91093
MA0139.10.0162019
MA0140.10.199454
MA0141.10.100114
MA0142.12.54162
MA0143.10.272236
MA0144.14.81369
MA0145.10.00165086
MA0146.16.28585e-06
MA0147.10.0444528
MA0148.10.518828
MA0149.10.192747
MA0062.20.0177333
MA0035.20.198962
MA0039.25.36166e-08
MA0138.20.302079
MA0002.20.0984982
MA0137.20.0801516
MA0104.20.0256869
MA0047.20.250458
MA0112.20.00138028
MA0065.20.0116842
MA0150.10.369323
MA0151.10
MA0152.11.74834
MA0153.10.615584
MA0154.10.0194777
MA0155.10.00116092
MA0156.10.58361
MA0157.10.337287
MA0158.10
MA0159.10.0446884
MA0160.10.18494
MA0161.10
MA0162.15.0328e-05
MA0163.11.468e-05
MA0164.10.28168
MA0080.20.0709213
MA0018.20.260646
MA0099.20.204301
MA0079.20
MA0102.21.03595
MA0258.10.032189
MA0259.10.0476147
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
ESR1#2099811.18858301678342.63298906687883e-071.35728896917946e-05
GATA3#26251214.85628164938512.7254465311872e-123.64926808039308e-10
POLR2A#5430212.04984166853271.30673372631837e-065.18715179182685e-05



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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