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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2200_left_heart_epitheloid_Hep2_cervical_small_large
|full_id=C2200_left_heart_epitheloid_Hep2_cervical_small_large
|gostat_on_coexpression_clusters=GO:0004119!cGMP-inhibited cyclic-nucleotide phosphodiesterase activity!0.000941952195926057!5139$GO:0004114!3',5'-cyclic-nucleotide phosphodiesterase activity!0.00737862553475411!5139$GO:0004112!cyclic-nucleotide phosphodiesterase activity!0.00737862553475411!5139$GO:0008081!phosphoric diester hydrolase activity!0.0162486753797245!5139
|gostat_on_coexpression_clusters=GO:0004119!cGMP-inhibited cyclic-nucleotide phosphodiesterase activity!0.000941952195926057!5139$GO:0004114!3',5'-cyclic-nucleotide phosphodiesterase activity!0.00737862553475411!5139$GO:0004112!cyclic-nucleotide phosphodiesterase activity!0.00737862553475411!5139$GO:0008081!phosphoric diester hydrolase activity!0.0162486753797245!5139

Revision as of 14:54, 12 September 2012


Full id: C2200_left_heart_epitheloid_Hep2_cervical_small_large



Phase1 CAGE Peaks

Hg19::chr12:20521255..20521275,+p@chr12:20521255..20521275
+
Hg19::chr12:20522183..20522203,+p9@PDE3A
Hg19::chr12:20522208..20522233,+p3@PDE3A
Hg19::chr12:20523184..20523195,-p1@ENST00000535755


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:0004119cGMP-inhibited cyclic-nucleotide phosphodiesterase activity0.000941952195926057
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.00737862553475411
GO:0004112cyclic-nucleotide phosphodiesterase activity0.00737862553475411
GO:0008081phosphoric diester hydrolase activity0.0162486753797245



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism2.19e-20115
anatomical cluster5.79e-15286
multi-cellular organism1.80e-13659
tube5.58e-13194
splanchnic layer of lateral plate mesoderm1.47e-1184
embryo4.79e-11612
multi-tissue structure9.23e-11347
embryonic structure4.21e-10605
developing anatomical structure4.21e-10605
anatomical system6.44e-10625
anatomical group8.71e-10626
germ layer9.12e-10604
embryonic tissue9.12e-10604
presumptive structure9.12e-10604
epiblast (generic)9.12e-10604
central nervous system1.23e-0982
regional part of brain1.34e-0959
anatomical conduit2.24e-09241
neurectoderm3.19e-0990
larynx3.25e-099
regional part of nervous system5.30e-0994
nervous system5.30e-0994
neural plate8.98e-0986
presumptive neural plate8.98e-0986
circulatory system1.71e-08113
neural tube1.87e-0857
neural rod1.87e-0857
future spinal cord1.87e-0857
neural keel1.87e-0857
brain2.18e-0869
future brain2.18e-0869
primary circulatory organ2.21e-0827
cell layer2.28e-08312
epithelium3.90e-08309
blood vessel6.16e-0860
epithelial tube open at both ends6.16e-0860
blood vasculature6.16e-0860
vascular cord6.16e-0860
vasculature9.25e-0879
vascular system9.25e-0879
cardiovascular system3.08e-07110
epithelial tube3.60e-07118


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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