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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3165_Dendritic_CD14_Monocytederived_Macrophage_splenic_CD14CD16_spleen
|full_id=C3165_Dendritic_CD14_Monocytederived_Macrophage_splenic_CD14CD16_spleen
|id=C3165
|id=C3165

Revision as of 16:02, 12 September 2012


Full id: C3165_Dendritic_CD14_Monocytederived_Macrophage_splenic_CD14CD16_spleen



Phase1 CAGE Peaks

Hg19::chr11:58979658..58979676,-p3@MPEG1
Hg19::chr11:58980437..58980460,-p2@MPEG1
Hg19::chr12:75875067..75875110,+p4@GLIPR1


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
leukocyte2.38e-52140
nongranular leukocyte3.84e-47119
hematopoietic stem cell1.57e-43172
angioblastic mesenchymal cell1.57e-43172
hematopoietic lineage restricted progenitor cell4.43e-42124
hematopoietic oligopotent progenitor cell5.63e-40165
hematopoietic multipotent progenitor cell5.63e-40165
hematopoietic cell1.28e-38182
myeloid leukocyte5.53e-3876
macrophage dendritic cell progenitor3.69e-3765
monopoietic cell6.85e-3663
monocyte6.85e-3663
monoblast6.85e-3663
promonocyte6.85e-3663
granulocyte monocyte progenitor cell1.39e-3471
CD14-positive, CD16-negative classical monocyte2.06e-3342
myeloid lineage restricted progenitor cell4.34e-3170
classical monocyte1.29e-2945
myeloid cell1.11e-27112
common myeloid progenitor1.11e-27112
lymphocyte5.85e-1153
common lymphoid progenitor5.85e-1153
lymphocyte of B lineage1.40e-1024
pro-B cell1.40e-1024
lymphoid lineage restricted progenitor cell1.70e-1052
B cell1.75e-0814
intermediate monocyte9.10e-089
CD14-positive, CD16-positive monocyte9.10e-089
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.04e-38102
blood island1.04e-38102
hemolymphoid system2.89e-34112
adult organism3.53e-30115
bone marrow2.99e-2980
bone element1.07e-2586
immune system7.91e-23115
skeletal element8.31e-19101
skeletal system8.31e-19101
lateral plate mesoderm1.87e-13216
musculoskeletal system1.64e-08167
blood5.97e-0715
haemolymphatic fluid5.97e-0715
organism substance5.97e-0715
tissue8.83e-07787


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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