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Coexpression cluster:C3248: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004177!2.91e-26!7;UBERON:0005057!2.91e-26!7;UBERON:0002370!4.68e-21!4;UBERON:0005058!4.68e-21!4;UBERON:0009113!4.68e-21!4;UBERON:0003295!4.68e-21!4;UBERON:0005562!4.68e-21!4;UBERON:0002022!9.43e-21!1;UBERON:0003351!2.18e-14!6;UBERON:0001950!4.95e-09!20;UBERON:0000974!5.15e-09!10;UBERON:0003408!5.15e-09!10;UBERON:0001042!5.15e-09!10;UBERON:0009145!5.15e-09!10;UBERON:0002619!2.68e-08!22;UBERON:0006562!2.82e-08!11;UBERON:0009722!2.82e-08!11;UBERON:0007690!2.82e-08!11;UBERON:0002106!6.78e-08!3;UBERON:0004854!6.78e-08!3;UBERON:0009034!6.78e-08!3;UBERON:0002095!6.78e-08!3;UBERON:0004782!6.78e-08!3;UBERON:0003281!6.78e-08!3;UBERON:0009664!6.78e-08!3;UBERON:0002296!6.78e-08!3;UBERON:0005602!6.78e-08!3;UBERON:0001179!6.78e-08!3;UBERON:0006293!6.78e-08!3;UBERON:0001870!7.76e-08!3;UBERON:0000956!2.09e-07!25;UBERON:0000203!2.09e-07!25;UBERON:0000077!7.93e-07!29
|ontology_enrichment_uberon=UBERON:0004177!2.91e-26!7;UBERON:0005057!2.91e-26!7;UBERON:0002370!4.68e-21!4;UBERON:0005058!4.68e-21!4;UBERON:0009113!4.68e-21!4;UBERON:0003295!4.68e-21!4;UBERON:0005562!4.68e-21!4;UBERON:0002022!9.43e-21!1;UBERON:0003351!2.18e-14!6;UBERON:0001950!4.95e-09!20;UBERON:0000974!5.15e-09!10;UBERON:0003408!5.15e-09!10;UBERON:0001042!5.15e-09!10;UBERON:0009145!5.15e-09!10;UBERON:0002619!2.68e-08!22;UBERON:0006562!2.82e-08!11;UBERON:0009722!2.82e-08!11;UBERON:0007690!2.82e-08!11;UBERON:0002106!6.78e-08!3;UBERON:0004854!6.78e-08!3;UBERON:0009034!6.78e-08!3;UBERON:0002095!6.78e-08!3;UBERON:0004782!6.78e-08!3;UBERON:0003281!6.78e-08!3;UBERON:0009664!6.78e-08!3;UBERON:0002296!6.78e-08!3;UBERON:0005602!6.78e-08!3;UBERON:0001179!6.78e-08!3;UBERON:0006293!6.78e-08!3;UBERON:0001870!7.76e-08!3;UBERON:0000956!2.09e-07!25;UBERON:0000203!2.09e-07!25;UBERON:0000077!7.93e-07!29
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}}
}}

Revision as of 16:01, 26 November 2012


Full id: C3248_Eosinophils_thymus_Neutrophils_acute_liposarcoma_CD34_hepatocellular



Phase1 CAGE Peaks

Hg19::chr12:123634401..123634410,-p26@PITPNM2
Hg19::chr21:42742070..42742082,+p4@MX2
Hg19::chr6:44193696..44193705,+p@chr6:44193696..44193705
+


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

No GOStat results

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><br>

Cell Type
Ontology termp-valuen
eosinophil1.82e-112
Uber Anatomy
Ontology termp-valuen
hemopoietic organ2.91e-267
immune organ2.91e-267
thymus4.68e-214
hemolymphoid system gland4.68e-214
thymic region4.68e-214
pharyngeal gland4.68e-214
thymus primordium4.68e-214
insula9.43e-211
pharyngeal epithelium2.18e-146
neocortex4.95e-0920
neck5.15e-0910
gland of gut5.15e-0910
chordate pharynx5.15e-0910
pharyngeal region of foregut5.15e-0910
regional part of cerebral cortex2.68e-0822
pharynx2.82e-0811
entire pharyngeal arch endoderm2.82e-0811
early pharyngeal endoderm2.82e-0811
spleen6.78e-083
gastrointestinal system mesentery6.78e-083
stomach region6.78e-083
mesentery6.78e-083
gastrointestinal system serosa6.78e-083
mesentery of stomach6.78e-083
gut mesentery6.78e-083
dorsal mesentery6.78e-083
dorsal mesogastrium6.78e-083
peritoneal cavity6.78e-083
spleen primordium6.78e-083
frontal cortex7.76e-083
cerebral cortex2.09e-0725
pallium2.09e-0725
mixed endoderm/mesoderm-derived structure7.93e-0729


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)

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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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