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Coexpression cluster:C4296: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4296_Monocytederived_CD14_Macrophage_ductal_Basophils_cervical_Urothelial
|full_id=C4296_Monocytederived_CD14_Macrophage_ductal_Basophils_cervical_Urothelial
|id=C4296
|id=C4296

Revision as of 17:21, 12 September 2012


Full id: C4296_Monocytederived_CD14_Macrophage_ductal_Basophils_cervical_Urothelial



Phase1 CAGE Peaks

Hg19::chr3:152879985..152880038,+p1@RAP2B
Hg19::chr3:152881467..152881482,+p@chr3:152881467..152881482
+
Hg19::chr3:152881859..152881877,+p@chr3:152881859..152881877
+


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 cell6.21e-27722
macrophage dendritic cell progenitor4.52e-2565
CD14-positive, CD16-negative classical monocyte9.88e-2542
monopoietic cell2.84e-2463
monocyte2.84e-2463
monoblast2.84e-2463
promonocyte2.84e-2463
myeloid lineage restricted progenitor cell1.23e-2370
animal cell2.01e-23679
eukaryotic cell2.01e-23679
granulocyte monocyte progenitor cell2.01e-2271
classical monocyte5.29e-2245
somatic cell1.81e-21591
myeloid leukocyte1.28e-2076
hematopoietic lineage restricted progenitor cell7.58e-19124
nongranular leukocyte2.31e-18119
leukocyte7.19e-18140
myeloid cell7.93e-18112
common myeloid progenitor7.93e-18112
hematopoietic stem cell6.03e-16172
angioblastic mesenchymal cell6.03e-16172
hematopoietic cell1.14e-15182
hematopoietic oligopotent progenitor cell1.37e-15165
hematopoietic multipotent progenitor cell1.37e-15165
epithelial cell4.15e-10254
Uber Anatomy
Ontology termp-valuen
hemolymphoid system7.69e-22112
hematopoietic system2.60e-21102
blood island2.60e-21102
bone marrow6.08e-2180
bone element3.72e-1986
lateral plate mesoderm2.01e-16216
skeletal element1.13e-15101
skeletal system1.13e-15101
immune system2.86e-13115
musculoskeletal system5.27e-10167


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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