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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3118_Eosinophils_CD8_CD14_Natural_CD4_Neutrophils_Dendritic
|full_id=C3118_Eosinophils_CD8_CD14_Natural_CD4_Neutrophils_Dendritic
|id=C3118
|id=C3118

Revision as of 15:59, 12 September 2012


Full id: C3118_Eosinophils_CD8_CD14_Natural_CD4_Neutrophils_Dendritic



Phase1 CAGE Peaks

Hg19::chr11:13696614..13696618,+p@chr11:13696614..13696618
+
Hg19::chr13:96356096..96356099,+p@chr13:96356096..96356099
+
Hg19::chr15:80411113..80411117,+p@chr15:80411113..80411117
+


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
hematopoietic stem cell3.43e-35172
angioblastic mesenchymal cell3.43e-35172
leukocyte4.76e-35140
hematopoietic cell4.56e-32182
hematopoietic oligopotent progenitor cell3.67e-31165
hematopoietic multipotent progenitor cell3.67e-31165
nongranular leukocyte9.89e-30119
hematopoietic lineage restricted progenitor cell1.49e-28124
myeloid leukocyte6.25e-2476
myeloid cell1.65e-23112
common myeloid progenitor1.65e-23112
CD14-positive, CD16-negative classical monocyte2.10e-2342
macrophage dendritic cell progenitor6.39e-2365
classical monocyte1.70e-2245
monopoietic cell3.56e-2263
monocyte3.56e-2263
monoblast3.56e-2263
promonocyte3.56e-2263
myeloid lineage restricted progenitor cell3.42e-2170
granulocyte monocyte progenitor cell1.89e-2071
lymphoid lineage restricted progenitor cell1.31e-0752
lymphocyte2.21e-0753
common lymphoid progenitor2.21e-0753
intermediate monocyte3.19e-079
CD14-positive, CD16-positive monocyte3.19e-079
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.83e-21102
blood island5.83e-21102
hemolymphoid system1.80e-18112
bone marrow6.14e-1880
bone element1.90e-1786
skeletal element6.44e-14101
skeletal system6.44e-14101
immune system3.60e-10115


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.