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Coexpression cluster:C3062: Difference between revisions

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|full_id=C3062_stomach_thymus_skin_pancreas_eye_vagina_globus
|full_id=C3062_stomach_thymus_skin_pancreas_eye_vagina_globus
|id=C3062
|id=C3062
|ontology_enrichment_celltype=CL:0000623!4.73e-10!3;CL:0000825!4.73e-10!3
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!9.29e-10!7;UBERON:0007029!1.22e-08!1;UBERON:0000996!1.52e-08!1;UBERON:0002370!2.79e-08!4;UBERON:0005058!2.79e-08!4;UBERON:0009113!2.79e-08!4;UBERON:0003295!2.79e-08!4;UBERON:0005562!2.79e-08!4;UBERON:0007190!6.68e-08!1;UBERON:0000974!4.65e-07!10
|ontology_enrichment_uberon=UBERON:0004177!2.08e-32!7;UBERON:0005057!2.08e-32!7;UBERON:0002370!6.73e-26!4;UBERON:0005058!6.73e-26!4;UBERON:0009113!6.73e-26!4;UBERON:0003295!6.73e-26!4;UBERON:0005562!6.73e-26!4;UBERON:0000974!4.42e-23!10;UBERON:0003351!1.22e-17!6;UBERON:0000077!4.19e-14!29;UBERON:0000341!9.40e-14!2;UBERON:0001255!1.21e-13!2;UBERON:0001556!1.21e-13!2;UBERON:0000945!2.20e-13!8;UBERON:0010039!2.20e-13!8;UBERON:0003408!5.41e-11!10;UBERON:0001042!5.41e-11!10;UBERON:0009145!5.41e-11!10;UBERON:0006562!4.42e-10!11;UBERON:0009722!4.42e-10!11;UBERON:0007690!4.42e-10!11;UBERON:0002240!1.67e-09!3;UBERON:0005174!1.67e-09!3;UBERON:0001137!1.67e-09!3;UBERON:0002106!1.81e-09!3;UBERON:0004854!1.81e-09!3;UBERON:0009034!1.81e-09!3;UBERON:0002095!1.81e-09!3;UBERON:0004782!1.81e-09!3;UBERON:0003281!1.81e-09!3;UBERON:0009664!1.81e-09!3;UBERON:0002296!1.81e-09!3;UBERON:0005602!1.81e-09!3;UBERON:0001179!1.81e-09!3;UBERON:0006293!1.81e-09!3
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}}
}}

Revision as of 14:46, 19 October 2012


Full id: C3062_stomach_thymus_skin_pancreas_eye_vagina_globus



Phase1 CAGE Peaks

Hg19::chr10:96953963..96953971,+p2@C10orf129
Hg19::chr10:96953989..96953999,+p1@C10orf129
Hg19::chr11:3185417..3185446,+p@chr11:3185417..3185446
+


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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
hemopoietic organ2.08e-327
immune organ2.08e-327
thymus6.73e-264
hemolymphoid system gland6.73e-264
thymic region6.73e-264
pharyngeal gland6.73e-264
thymus primordium6.73e-264
neck4.42e-2310
pharyngeal epithelium1.22e-176
mixed endoderm/mesoderm-derived structure4.19e-1429
throat9.40e-142
urinary bladder1.21e-132
lower urinary tract1.21e-132
stomach2.20e-138
food storage organ2.20e-138
gland of gut5.41e-1110
chordate pharynx5.41e-1110
pharyngeal region of foregut5.41e-1110
pharynx4.42e-1011
entire pharyngeal arch endoderm4.42e-1011
early pharyngeal endoderm4.42e-1011
spinal cord1.67e-093
dorsal region element1.67e-093
dorsum1.67e-093
spleen1.81e-093
gastrointestinal system mesentery1.81e-093
stomach region1.81e-093
mesentery1.81e-093
gastrointestinal system serosa1.81e-093
mesentery of stomach1.81e-093
gut mesentery1.81e-093
dorsal mesentery1.81e-093
dorsal mesogastrium1.81e-093
peritoneal cavity1.81e-093
spleen primordium1.81e-093


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.

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