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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C499_medulla_thalamus_spinal_globus_optic_caudate_hippocampus
|full_id=C499_medulla_thalamus_spinal_globus_optic_caudate_hippocampus
|gostat_on_coexpression_clusters=GO:0016403!dimethylargininase activity!0.0259898459425752!23576$GO:0043121!neurotrophin binding!0.0259898459425752!4915$GO:0007263!nitric oxide mediated signal transduction!0.0259898459425752!23576$GO:0006527!arginine catabolic process!0.0259898459425752!23576$GO:0015250!water channel activity!0.0259898459425752!361$GO:0005372!water transporter activity!0.0297760869891295!361$GO:0009065!glutamine family amino acid catabolic process!0.0396763042251676!23576$GO:0016813!hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines!0.0396763042251676!23576$GO:0007399!nervous system development!0.0396763042251676!4915;361$GO:0006525!arginine metabolic process!0.040578659960201!23576$GO:0000051!urea cycle intermediate metabolic process!0.0472042095940519!23576
|id=C499
|id=C499
}}
}}

Revision as of 17:40, 18 May 2012


Full id: C499_medulla_thalamus_spinal_globus_optic_caudate_hippocampus



Phase1 CAGE Peaks

Hg19::chr12:41365353..41365362,+p@chr12:41365353..41365362
+
Hg19::chr15:59664884..59664903,+p4@FAM81A
Hg19::chr17:42991223..42991232,-p@chr17:42991223..42991232
-
Hg19::chr18:24434129..24434169,-p8@AQP4
Hg19::chr18:24434187..24434198,-p13@AQP4
Hg19::chr18:24435190..24435201,-p@chr18:24435190..24435201
-
Hg19::chr18:74691180..74691220,-p@chr18:74691180..74691220
-
Hg19::chr18:74691599..74691602,+p@chr18:74691599..74691602
+
Hg19::chr1:204991565..204991578,+p@chr1:204991565..204991578
+
Hg19::chr1:68849935..68849943,-p@chr1:68849935..68849943
-
Hg19::chr1:85786236..85786252,-p30@DDAH1
Hg19::chr6:164348089..164348100,+p@chr6:164348089..164348100
+
Hg19::chr8:26491964..26491967,+p@chr8:26491964..26491967
+
Hg19::chr8:28965684..28965712,-p4@KIF13B
Hg19::chr9:87426149..87426182,+p25@NTRK2
Hg19::chr9:87426979..87426990,+p54@NTRK2
Hg19::chr9:87427842..87427853,+p46@NTRK2
Hg19::chr9:87429337..87429348,+p57@NTRK2
Hg19::chrX:13792037..13792048,-p@chrX:13792037..13792048
-


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:0016403dimethylargininase activity0.0259898459425752
GO:0043121neurotrophin binding0.0259898459425752
GO:0007263nitric oxide mediated signal transduction0.0259898459425752
GO:0006527arginine catabolic process0.0259898459425752
GO:0015250water channel activity0.0259898459425752
GO:0005372water transporter activity0.0297760869891295
GO:0009065glutamine family amino acid catabolic process0.0396763042251676
GO:0016813hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines0.0396763042251676
GO:0007399nervous system development0.0396763042251676
GO:0006525arginine metabolic process0.040578659960201
GO:0000051urea cycle intermediate metabolic process0.0472042095940519



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.