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Coexpression cluster:C453: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!1.25e-20!659;UBERON:0000055!2.52e-20!69;UBERON:0004872!4.08e-20!84;UBERON:0002049!2.84e-19!79;UBERON:0007798!2.84e-19!79;UBERON:0001981!4.83e-19!60;UBERON:0007500!4.83e-19!60;UBERON:0004537!4.83e-19!60;UBERON:0006965!4.83e-19!60;UBERON:0000480!1.88e-18!626;UBERON:0000467!2.14e-18!625;UBERON:0003914!2.48e-17!118;UBERON:0001009!7.53e-15!113;UBERON:0004535!1.88e-14!110;UBERON:0000490!3.07e-14!138;UBERON:0001637!1.11e-13!42;UBERON:0003509!1.11e-13!42;UBERON:0004572!1.11e-13!42;UBERON:0000926!1.47e-13!448;UBERON:0004120!1.47e-13!448;UBERON:0006603!1.47e-13!448;UBERON:0002100!8.29e-13!216;UBERON:0005256!1.13e-10!143;UBERON:0004573!1.60e-10!33;UBERON:0004571!1.60e-10!33;UBERON:0000914!4.88e-10!83;UBERON:0002329!4.88e-10!83;UBERON:0003077!4.88e-10!83;UBERON:0003059!4.88e-10!83;UBERON:0007282!4.88e-10!83;UBERON:0009618!4.88e-10!83;UBERON:0007285!4.88e-10!83;UBERON:0000486!5.86e-10!82;UBERON:0000487!7.29e-10!22;UBERON:0001986!7.83e-10!18;UBERON:0004638!7.83e-10!18;UBERON:0004852!7.83e-10!18;UBERON:0002050!1.90e-09!605;UBERON:0005423!1.90e-09!605;UBERON:0000923!2.25e-09!604;UBERON:0005291!2.25e-09!604;UBERON:0006598!2.25e-09!604;UBERON:0002532!2.25e-09!604;UBERON:0000922!3.96e-09!612;UBERON:0000475!8.03e-09!365;UBERON:0006914!1.19e-08!25;UBERON:0003102!1.95e-08!95;UBERON:0004290!3.29e-08!70;UBERON:0003081!3.62e-08!216;UBERON:0002385!3.70e-08!63;UBERON:0001015!3.70e-08!63;UBERON:0000383!3.70e-08!63;UBERON:0001134!4.17e-08!61;UBERON:0002036!4.17e-08!61;UBERON:0003082!4.17e-08!61;UBERON:0000947!4.30e-08!21;UBERON:0010191!4.30e-08!21;UBERON:0000477!7.03e-08!286;UBERON:0003104!8.07e-08!238;UBERON:0009142!8.07e-08!238;UBERON:0004111!2.88e-07!241;UBERON:0000483!5.43e-07!309
|ontology_enrichment_uberon=UBERON:0000468!1.25e-20!659;UBERON:0000055!2.52e-20!69;UBERON:0004872!4.08e-20!84;UBERON:0002049!2.84e-19!79;UBERON:0007798!2.84e-19!79;UBERON:0001981!4.83e-19!60;UBERON:0007500!4.83e-19!60;UBERON:0004537!4.83e-19!60;UBERON:0006965!4.83e-19!60;UBERON:0000480!1.88e-18!626;UBERON:0000467!2.14e-18!625;UBERON:0003914!2.48e-17!118;UBERON:0001009!7.53e-15!113;UBERON:0004535!1.88e-14!110;UBERON:0000490!3.07e-14!138;UBERON:0001637!1.11e-13!42;UBERON:0003509!1.11e-13!42;UBERON:0004572!1.11e-13!42;UBERON:0000926!1.47e-13!448;UBERON:0004120!1.47e-13!448;UBERON:0006603!1.47e-13!448;UBERON:0002100!8.29e-13!216;UBERON:0005256!1.13e-10!143;UBERON:0004573!1.60e-10!33;UBERON:0004571!1.60e-10!33;UBERON:0000914!4.88e-10!83;UBERON:0002329!4.88e-10!83;UBERON:0003077!4.88e-10!83;UBERON:0003059!4.88e-10!83;UBERON:0007282!4.88e-10!83;UBERON:0009618!4.88e-10!83;UBERON:0007285!4.88e-10!83;UBERON:0000486!5.86e-10!82;UBERON:0000487!7.29e-10!22;UBERON:0001986!7.83e-10!18;UBERON:0004638!7.83e-10!18;UBERON:0004852!7.83e-10!18;UBERON:0002050!1.90e-09!605;UBERON:0005423!1.90e-09!605;UBERON:0000923!2.25e-09!604;UBERON:0005291!2.25e-09!604;UBERON:0006598!2.25e-09!604;UBERON:0002532!2.25e-09!604;UBERON:0000922!3.96e-09!612;UBERON:0000475!8.03e-09!365;UBERON:0006914!1.19e-08!25;UBERON:0003102!1.95e-08!95;UBERON:0004290!3.29e-08!70;UBERON:0003081!3.62e-08!216;UBERON:0002385!3.70e-08!63;UBERON:0001015!3.70e-08!63;UBERON:0000383!3.70e-08!63;UBERON:0001134!4.17e-08!61;UBERON:0002036!4.17e-08!61;UBERON:0003082!4.17e-08!61;UBERON:0000947!4.30e-08!21;UBERON:0010191!4.30e-08!21;UBERON:0000477!7.03e-08!286;UBERON:0003104!8.07e-08!238;UBERON:0009142!8.07e-08!238;UBERON:0004111!2.88e-07!241;UBERON:0000483!5.43e-07!309
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}}
}}

Revision as of 20:06, 8 August 2012


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
multi-cellular organism1.25e-20659
vessel2.52e-2069
splanchnic layer of lateral plate mesoderm4.08e-2084
vasculature2.84e-1979
vascular system2.84e-1979
blood vessel4.83e-1960
epithelial tube open at both ends4.83e-1960
blood vasculature4.83e-1960
vascular cord4.83e-1960
anatomical group1.88e-18626
anatomical system2.14e-18625
epithelial tube2.48e-17118
circulatory system7.53e-15113
cardiovascular system1.88e-14110
unilaminar epithelium3.07e-14138
artery1.11e-1342
arterial blood vessel1.11e-1342
arterial system1.11e-1342
mesoderm1.47e-13448
mesoderm-derived structure1.47e-13448
presumptive mesoderm1.47e-13448
trunk8.29e-13216
trunk mesenchyme1.13e-10143
systemic artery1.60e-1033
systemic arterial system1.60e-1033
somite4.88e-1083
paraxial mesoderm4.88e-1083
presomitic mesoderm4.88e-1083
presumptive segmental plate4.88e-1083
trunk paraxial mesoderm4.88e-1083
presumptive paraxial mesoderm4.88e-1083
multilaminar epithelium5.86e-1082
simple squamous epithelium7.29e-1022
endothelium7.83e-1018
blood vessel endothelium7.83e-1018
cardiovascular system endothelium7.83e-1018
embryonic structure1.90e-09605
developing anatomical structure1.90e-09605
germ layer2.25e-09604
embryonic tissue2.25e-09604
presumptive structure2.25e-09604
epiblast (generic)2.25e-09604
embryo3.96e-09612
organism subdivision8.03e-09365
squamous epithelium1.19e-0825
surface structure1.95e-0895
dermomyotome3.29e-0870
lateral plate mesoderm3.62e-08216
muscle tissue3.70e-0863
musculature3.70e-0863
musculature of body3.70e-0863
skeletal muscle tissue4.17e-0861
striated muscle tissue4.17e-0861
myotome4.17e-0861
aorta4.30e-0821
aortic system4.30e-0821
anatomical cluster7.03e-08286
mesenchyme8.07e-08238
entire embryonic mesenchyme8.07e-08238
anatomical conduit2.88e-07241
epithelium5.43e-07309


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)

{{{tfbs_overrepresentation_jaspar}}}



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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