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Coexpression cluster:C2392: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002204!4.62e-07!167
|ontology_enrichment_uberon=UBERON:0002204!4.62e-07!167
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}}
}}

Revision as of 15:28, 26 November 2012


Full id: C2392_Mesenchymal_CD4_CD34_Alveolar_Aortic_CD133_Smooth



Phase1 CAGE Peaks

Hg19::chr16:89627061..89627100,+p1@RPL13
Hg19::chr17:19350184..19350189,-p1@uc002gvw.2
Hg19::chr5:168043311..168043323,+p1@ENST00000406049
Hg19::chr6:34231494..34231507,-p2@RPL35P2


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
native cell1.02e-31722
animal cell7.00e-25679
eukaryotic cell7.00e-25679
somatic cell9.63e-24588
stem cell6.14e-10441
classical monocyte1.41e-0942
CD14-positive, CD16-negative classical monocyte1.41e-0942
hematopoietic lineage restricted progenitor cell3.46e-09120
nongranular leukocyte4.38e-09115
multi fate stem cell5.48e-09427
somatic stem cell5.94e-09433
hematopoietic cell8.50e-08177
lymphocyte1.01e-0753
common lymphoid progenitor1.01e-0753
lymphoid lineage restricted progenitor cell1.23e-0752
nucleate cell2.52e-0755
hematopoietic stem cell4.21e-07168
angioblastic mesenchymal cell4.21e-07168
hematopoietic oligopotent progenitor cell4.25e-07161
hematopoietic multipotent progenitor cell4.25e-07161
defensive cell4.31e-0748
phagocyte4.31e-0748
contractile cell4.47e-0759
leukocyte6.82e-07136
Uber Anatomy
Ontology termp-valuen
musculoskeletal system4.62e-07167


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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