Personal tools

Coexpression cluster:C3620: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{Coexpression_clusters |full_id=C3620_small_salivary_colon_seminal_submaxillary_duodenum_rectum |id=C3620 }}")
 
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C3620_small_salivary_colon_seminal_submaxillary_duodenum_rectum
|full_id=C3620_small_salivary_colon_seminal_submaxillary_duodenum_rectum
|gostat_on_coexpression_clusters=GO:0015361!low affinity sodium:dicarboxylate symporter activity!0.00323796067349582!9058$GO:0017153!sodium:dicarboxylate symporter activity!0.0183441228500482!9058$GO:0005310!dicarboxylic acid transmembrane transporter activity!0.0183441228500482!9058$GO:0005343!organic acid:sodium symporter activity!0.0252419675056647!9058$GO:0015296!anion:cation symporter activity!0.0252419675056647!9058$GO:0015370!solute:sodium symporter activity!0.0320095731496459!9058$GO:0008033!tRNA processing!0.0320095731496459!113179$GO:0031402!sodium ion binding!0.0320095731496459!9058$GO:0046943!carboxylic acid transmembrane transporter activity!0.0320095731496459!9058$GO:0005342!organic acid transmembrane transporter activity!0.0320095731496459!9058$GO:0015294!solute:cation symporter activity!0.0335012354596173!9058$GO:0006814!sodium ion transport!0.0465624244549352!9058$GO:0008509!anion transmembrane transporter activity!0.0477659391038415!9058$GO:0006399!tRNA metabolic process!0.0477659391038415!113179$GO:0031420!alkali metal ion binding!0.0477659391038415!9058$GO:0015293!symporter activity!0.0488004368474531!9058
|id=C3620
|id=C3620
}}
}}

Revision as of 17:39, 18 May 2012


Full id: C3620_small_salivary_colon_seminal_submaxillary_duodenum_rectum



Phase1 CAGE Peaks

Hg19::chr17:26800693..26800705,+p2@SLC13A2
Hg19::chr17:26800716..26800725,+p8@SLC13A2
Hg19::chr19:1907961..1907987,+p2@ADAT3


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:0015361low affinity sodium:dicarboxylate symporter activity0.00323796067349582
GO:0017153sodium:dicarboxylate symporter activity0.0183441228500482
GO:0005310dicarboxylic acid transmembrane transporter activity0.0183441228500482
GO:0005343organic acid:sodium symporter activity0.0252419675056647
GO:0015296anion:cation symporter activity0.0252419675056647
GO:0015370solute:sodium symporter activity0.0320095731496459
GO:0008033tRNA processing0.0320095731496459
GO:0031402sodium ion binding0.0320095731496459
GO:0046943carboxylic acid transmembrane transporter activity0.0320095731496459
GO:0005342organic acid transmembrane transporter activity0.0320095731496459
GO:0015294solute:cation symporter activity0.0335012354596173
GO:0006814sodium ion transport0.0465624244549352
GO:0008509anion transmembrane transporter activity0.0477659391038415
GO:0006399tRNA metabolic process0.0477659391038415
GO:0031420alkali metal ion binding0.0477659391038415
GO:0015293symporter activity0.0488004368474531



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.