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{{Coexpression_clusters
{{Coexpression_clusters
|full_id=C1808_thalamus_substantia_Eosinophils_globus_CD14_optic_Neutrophils
|full_id=C1808_thalamus_substantia_Eosinophils_globus_CD14_optic_Neutrophils
|gostat_on_coexpression_clusters=GO:0006417!regulation of translation!0.000758142443290168!9444;132864$GO:0031326!regulation of cellular biosynthetic process!0.000758142443290168!9444;132864$GO:0009889!regulation of biosynthetic process!0.000758142443290168!9444;132864$GO:0051246!regulation of protein metabolic process!0.00215522757872212!9444;132864$GO:0003723!RNA binding!0.0092540737721995!9444;132864$GO:0006412!translation!0.0117723159075332!9444;132864$GO:0009059!macromolecule biosynthetic process!0.016945573322919!9444;132864$GO:0044249!cellular biosynthetic process!0.0216358830215907!9444;132864$GO:0051028!mRNA transport!0.0216358830215907!9444$GO:0009058!biosynthetic process!0.0216358830215907!9444;132864$GO:0050658!RNA transport!0.0216358830215907!9444$GO:0051236!establishment of RNA localization!0.0216358830215907!9444$GO:0050657!nucleic acid transport!0.0216358830215907!9444$GO:0006403!RNA localization!0.0216358830215907!9444$GO:0015931!nucleobase, nucleoside, nucleotide and nucleic acid transport!0.0228233871901247!9444$GO:0010468!regulation of gene expression!0.0416891970694574!9444;132864$GO:0008380!RNA splicing!0.0416891970694574!9444$GO:0031323!regulation of cellular metabolic process!0.0416891970694574!9444;132864$GO:0019222!regulation of metabolic process!0.0439740545531343!9444;132864$GO:0006397!mRNA processing!0.0448216054292201!9444
|id=C1808
|id=C1808
}}
}}

Revision as of 17:36, 18 May 2012


Full id: C1808_thalamus_substantia_Eosinophils_globus_CD14_optic_Neutrophils



Phase1 CAGE Peaks

Hg19::chr19:11457233..11457257,+p2@CCDC159
Hg19::chr4:15004067..15004113,+p1@CPEB2
Hg19::chr5:65221552..65221616,+p@chr5:65221552..65221616
+
Hg19::chr6:163835167..163835226,+p7@QKI
Hg19::chr6:163835734..163835758,+p1@QKI


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:0006417regulation of translation0.000758142443290168
GO:0031326regulation of cellular biosynthetic process0.000758142443290168
GO:0009889regulation of biosynthetic process0.000758142443290168
GO:0051246regulation of protein metabolic process0.00215522757872212
GO:0003723RNA binding0.0092540737721995
GO:0006412translation0.0117723159075332
GO:0009059macromolecule biosynthetic process0.016945573322919
GO:0044249cellular biosynthetic process0.0216358830215907
GO:0051028mRNA transport0.0216358830215907
GO:0009058biosynthetic process0.0216358830215907
GO:0050658RNA transport0.0216358830215907
GO:0051236establishment of RNA localization0.0216358830215907
GO:0050657nucleic acid transport0.0216358830215907
GO:0006403RNA localization0.0216358830215907
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0228233871901247
GO:0010468regulation of gene expression0.0416891970694574
GO:0008380RNA splicing0.0416891970694574
GO:0031323regulation of cellular metabolic process0.0416891970694574
GO:0019222regulation of metabolic process0.0439740545531343
GO:0006397mRNA processing0.0448216054292201



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.