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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0000475!1.75e-15!365;UBERON:0000468!3.62e-13!659;UBERON:0004923!2.29e-11!57;UBERON:0000467!5.38e-11!625;UBERON:0000480!1.02e-10!626;UBERON:0000481!1.10e-09!347;UBERON:0007023!2.79e-09!115;UBERON:0003102!8.71e-09!95;UBERON:0000062!1.62e-08!511;UBERON:0000064!2.29e-08!219;UBERON:0000477!4.23e-08!286;UBERON:0000119!6.81e-08!312;UBERON:0004290!9.36e-08!70;UBERON:0000914!1.01e-07!83;UBERON:0002329!1.01e-07!83;UBERON:0003077!1.01e-07!83;UBERON:0003059!1.01e-07!83;UBERON:0007282!1.01e-07!83;UBERON:0009618!1.01e-07!83;UBERON:0007285!1.01e-07!83;UBERON:0002385!1.48e-07!63;UBERON:0001015!1.48e-07!63;UBERON:0000383!1.48e-07!63;UBERON:0000483!1.87e-07!309;UBERON:0005631!2.23e-07!14;UBERON:0000158!2.23e-07!14;UBERON:0004872!2.43e-07!84;UBERON:0000486!2.81e-07!82;UBERON:0001134!3.16e-07!61;UBERON:0002036!3.16e-07!61;UBERON:0003082!3.16e-07!61;UBERON:0004111!3.90e-07!241;UBERON:0002199!5.13e-07!45;UBERON:0002416!5.13e-07!45;UBERON:0005256!5.61e-07!143
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}}
}}

Revision as of 17:20, 8 August 2012


Full id: C1492_chorionic_amniotic_Smooth_basal_spindle_placenta_mesenchymal



Phase1 CAGE Peaks

Hg19::chr22:33197683..33197698,+p1@TIMP3
Hg19::chr22:33253227..33253256,+p@chr22:33253227..33253256
+
Hg19::chr22:33255260..33255310,-p2@CU676956
Hg19::chr22:33255345..33255482,-p1@CU676956
Hg19::chr22:33256226..33256238,-p4@ENST00000327661
Hg19::chr22:33256911..33256925,+p3@TIMP3


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:0008191metalloendopeptidase inhibitor activity0.00900741787354292
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0227077761517889
GO:0050953sensory perception of light stimulus0.0227077761517889
GO:0007601visual perception0.0227077761517889
GO:0004866endopeptidase inhibitor activity0.0227077761517889
GO:0030414protease inhibitor activity0.0227077761517889
GO:0007167enzyme linked receptor protein signaling pathway0.0227077761517889
GO:0004857enzyme inhibitor activity0.0247851171553044
GO:0005578proteinaceous extracellular matrix0.0247851171553044
GO:0044421extracellular region part0.0457596095179988
GO:0007600sensory perception0.0457596095179988



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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell2.27e-17180
fibroblast1.21e-1175
preadipocyte4.15e-0812
muscle cell4.21e-0754
contractile cell4.43e-0759
smooth muscle cell4.53e-0742
smooth muscle myoblast4.53e-0742
vascular associated smooth muscle cell7.82e-0732
fat cell8.15e-0715
Uber Anatomy
Ontology termp-valuen
organism subdivision1.75e-15365
multi-cellular organism3.62e-13659
organ component layer2.29e-1157
anatomical system5.38e-11625
anatomical group1.02e-10626
multi-tissue structure1.10e-09347
adult organism2.79e-09115
surface structure8.71e-0995
organ1.62e-08511
organ part2.29e-08219
anatomical cluster4.23e-08286
cell layer6.81e-08312
dermomyotome9.36e-0870
somite1.01e-0783
paraxial mesoderm1.01e-0783
presomitic mesoderm1.01e-0783
presumptive segmental plate1.01e-0783
trunk paraxial mesoderm1.01e-0783
presumptive paraxial mesoderm1.01e-0783
muscle tissue1.48e-0763
musculature1.48e-0763
musculature of body1.48e-0763
epithelium1.87e-07309
extraembryonic membrane2.23e-0714
membranous layer2.23e-0714
splanchnic layer of lateral plate mesoderm2.43e-0784
multilaminar epithelium2.81e-0782
skeletal muscle tissue3.16e-0761
striated muscle tissue3.16e-0761
myotome3.16e-0761
anatomical conduit3.90e-07241
integument5.13e-0745
integumental system5.13e-0745
trunk mesenchyme5.61e-07143


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)

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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.