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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3875_CD14_Whole_CD14CD16_small_Neutrophils_Macrophage_esophagus
|full_id=C3875_CD14_Whole_CD14CD16_small_Neutrophils_Macrophage_esophagus
|id=C3875
|id=C3875

Revision as of 16:52, 12 September 2012


Full id: C3875_CD14_Whole_CD14CD16_small_Neutrophils_Macrophage_esophagus



Phase1 CAGE Peaks

Hg19::chr1:154980607..154980631,+p@chr1:154980607..154980631
+
Hg19::chr1:154981054..154981102,+p@chr1:154981054..154981102
+
Hg19::chr2:32490859..32490889,-p2@NLRC4


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
myeloid leukocyte2.36e-4376
macrophage dendritic cell progenitor1.54e-4165
monopoietic cell1.70e-4063
monocyte1.70e-4063
monoblast1.70e-4063
promonocyte1.70e-4063
granulocyte monocyte progenitor cell4.71e-4071
myeloid cell6.31e-39112
common myeloid progenitor6.31e-39112
myeloid lineage restricted progenitor cell1.08e-3670
CD14-positive, CD16-negative classical monocyte1.65e-3342
classical monocyte4.84e-3245
hematopoietic stem cell3.50e-28172
angioblastic mesenchymal cell3.50e-28172
leukocyte5.73e-28140
hematopoietic oligopotent progenitor cell1.43e-26165
hematopoietic multipotent progenitor cell1.43e-26165
hematopoietic cell2.01e-24182
nongranular leukocyte7.16e-24119
hematopoietic lineage restricted progenitor cell1.54e-21124
intermediate monocyte2.75e-099
CD14-positive, CD16-positive monocyte2.75e-099
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.01e-40102
blood island2.01e-40102
hemolymphoid system4.33e-36112
bone marrow3.29e-3380
bone element6.69e-2986
adult organism1.35e-25115
immune system4.31e-23115
skeletal element7.77e-22101
skeletal system7.77e-22101
lateral plate mesoderm3.18e-11216
blood7.70e-0815
haemolymphatic fluid7.70e-0815
organism substance7.70e-0815
organ7.73e-07511
musculoskeletal system7.82e-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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ESRRA#21011161.2801047120420.006187620080219560.0273512868141554



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.