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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C2491_placenta_chorionic_mesothelioma_choriocarcinoma_amniotic_Alveolar_rectal
|full_id=C2491_placenta_chorionic_mesothelioma_choriocarcinoma_amniotic_Alveolar_rectal
|gostat_on_coexpression_clusters=GO:0004769!steroid delta-isomerase activity!0.00558016317052942!3283$GO:0030868!smooth endoplasmic reticulum membrane!0.00558016317052942!3283$GO:0004849!uridine kinase activity!0.00558016317052942!7371$GO:0006702!androgen biosynthetic process!0.00558016317052942!3283$GO:0006703!estrogen biosynthetic process!0.00558016317052942!3283$GO:0008209!androgen metabolic process!0.00558016317052942!3283$GO:0003854!3-beta-hydroxy-delta5-steroid dehydrogenase activity!0.00558016317052942!3283$GO:0006700!C21-steroid hormone biosynthetic process!0.00558016317052942!3283$GO:0005790!smooth endoplasmic reticulum!0.00558016317052942!3283$GO:0008210!estrogen metabolic process!0.00558016317052942!3283$GO:0019206!nucleoside kinase activity!0.00591818063176459!7371$GO:0008207!C21-steroid hormone metabolic process!0.00658720775069912!3283$GO:0016863!intramolecular oxidoreductase activity, transposing C=C bonds!0.00858334990095579!3283$GO:0005758!mitochondrial intermembrane space!0.0092975337983597!3283$GO:0031970!organelle envelope lumen!0.0092975337983597!3283$GO:0016229!steroid dehydrogenase activity!0.0092975337983597!3283$GO:0042446!hormone biosynthetic process!0.0117567410594796!3283$GO:0016860!intramolecular oxidoreductase activity!0.0178105640810361!3283$GO:0042445!hormone metabolic process!0.0201271552049052!3283$GO:0006694!steroid biosynthetic process!0.0201271552049052!3283$GO:0019205!nucleobase, nucleoside, nucleotide kinase activity!0.0201271552049052!7371$GO:0016616!oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor!0.0313622677930984!3283$GO:0005792!microsome!0.0313622677930984!3283$GO:0016614!oxidoreductase activity, acting on CH-OH group of donors!0.0313622677930984!3283$GO:0042598!vesicular fraction!0.0313622677930984!3283$GO:0008202!steroid metabolic process!0.0397599755868135!3283
|id=C2491
|id=C2491
}}
}}

Revision as of 17:37, 18 May 2012


Full id: C2491_placenta_chorionic_mesothelioma_choriocarcinoma_amniotic_Alveolar_rectal



Phase1 CAGE Peaks

Hg19::chr19:4233239..4233253,+p@chr19:4233239..4233253
+
Hg19::chr1:120049826..120049843,+p1@HSD3B1
Hg19::chr1:165864821..165864850,+p11@UCK2
Hg19::chr6:168720425..168720437,-p6@DACT2


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:0004769steroid delta-isomerase activity0.00558016317052942
GO:0030868smooth endoplasmic reticulum membrane0.00558016317052942
GO:0004849uridine kinase activity0.00558016317052942
GO:0006702androgen biosynthetic process0.00558016317052942
GO:0006703estrogen biosynthetic process0.00558016317052942
GO:0008209androgen metabolic process0.00558016317052942
GO:00038543-beta-hydroxy-delta5-steroid dehydrogenase activity0.00558016317052942
GO:0006700C21-steroid hormone biosynthetic process0.00558016317052942
GO:0005790smooth endoplasmic reticulum0.00558016317052942
GO:0008210estrogen metabolic process0.00558016317052942
GO:0019206nucleoside kinase activity0.00591818063176459
GO:0008207C21-steroid hormone metabolic process0.00658720775069912
GO:0016863intramolecular oxidoreductase activity, transposing C=C bonds0.00858334990095579
GO:0005758mitochondrial intermembrane space0.0092975337983597
GO:0031970organelle envelope lumen0.0092975337983597
GO:0016229steroid dehydrogenase activity0.0092975337983597
GO:0042446hormone biosynthetic process0.0117567410594796
GO:0016860intramolecular oxidoreductase activity0.0178105640810361
GO:0042445hormone metabolic process0.0201271552049052
GO:0006694steroid biosynthetic process0.0201271552049052
GO:0019205nucleobase, nucleoside, nucleotide kinase activity0.0201271552049052
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0313622677930984
GO:0005792microsome0.0313622677930984
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0313622677930984
GO:0042598vesicular fraction0.0313622677930984
GO:0008202steroid metabolic process0.0397599755868135



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>disease_data<br>


Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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.