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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3567_CD14_Dendritic_CD14CD16_Monocytederived_Basophils_blood_Macrophage
|full_id=C3567_CD14_Dendritic_CD14CD16_Monocytederived_Basophils_blood_Macrophage
|id=C3567
|id=C3567

Revision as of 16:30, 12 September 2012


Full id: C3567_CD14_Dendritic_CD14CD16_Monocytederived_Basophils_blood_Macrophage



Phase1 CAGE Peaks

Hg19::chr16:50313395..50313406,+p@chr16:50313395..50313406
+
Hg19::chr16:50313426..50313459,+p@chr16:50313426..50313459
+
Hg19::chr9:137266563..137266578,+p@chr9:137266563..137266578
+


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
granulocyte monocyte progenitor cell6.37e-6671
macrophage dendritic cell progenitor5.10e-6465
myeloid leukocyte1.19e-6276
myeloid lineage restricted progenitor cell1.38e-6270
monopoietic cell6.02e-6263
monocyte6.02e-6263
monoblast6.02e-6263
promonocyte6.02e-6263
myeloid cell1.75e-58112
common myeloid progenitor1.75e-58112
CD14-positive, CD16-negative classical monocyte5.53e-5342
hematopoietic stem cell1.21e-50172
angioblastic mesenchymal cell1.21e-50172
hematopoietic cell7.65e-50182
leukocyte1.09e-48140
hematopoietic oligopotent progenitor cell2.19e-48165
hematopoietic multipotent progenitor cell2.19e-48165
classical monocyte2.81e-4845
hematopoietic lineage restricted progenitor cell5.16e-47124
nongranular leukocyte1.64e-45119
intermediate monocyte1.73e-129
CD14-positive, CD16-positive monocyte1.73e-129
mesenchymal cell8.70e-11358
connective tissue cell4.59e-10365
immature conventional dendritic cell4.67e-085
common dendritic progenitor4.67e-085
motile cell5.78e-08390
circulating cell2.43e-076
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.88e-74102
blood island1.88e-74102
hemolymphoid system1.12e-68112
bone marrow8.72e-5680
bone element1.14e-5186
immune system1.68e-43115
skeletal element9.29e-42101
skeletal system9.29e-42101
lateral plate mesoderm2.78e-26216
musculoskeletal system6.39e-20167
blood5.65e-1615
haemolymphatic fluid5.65e-1615
organism substance5.65e-1615
adult organism8.40e-11115
connective tissue7.10e-10375
mesoderm3.33e-07448
mesoderm-derived structure3.33e-07448
presumptive mesoderm3.33e-07448


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
FOSL1#8061226.47571981091530.001869833702590980.0110242498625324
STAT2#6773243.50918079096040.0006968990898868230.00560778519521457
TAL1#6886219.91241111829350.003287176608740550.0170106747517716



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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