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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3721_Macrophage_fibrous_anaplastic_Renal_serous_Monocytederived_small
|full_id=C3721_Macrophage_fibrous_anaplastic_Renal_serous_Monocytederived_small
|id=C3721
|id=C3721

Revision as of 16:41, 12 September 2012


Full id: C3721_Macrophage_fibrous_anaplastic_Renal_serous_Monocytederived_small



Phase1 CAGE Peaks

Hg19::chr18:43405525..43405545,+p3@SIGLEC15
Hg19::chr18:43405633..43405645,+p4@SIGLEC15
Hg19::chr18:43405655..43405696,+p1@SIGLEC15


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
somatic cell3.78e-18591
multi fate stem cell9.32e-16430
somatic stem cell4.20e-15436
animal cell3.65e-14679
eukaryotic cell3.65e-14679
stem cell4.33e-14444
non-terminally differentiated cell1.76e-13180
monopoietic cell1.40e-1063
monocyte1.40e-1063
monoblast1.40e-1063
promonocyte1.40e-1063
macrophage dendritic cell progenitor1.87e-1065
connective tissue cell3.09e-10365
epithelial cell of nephron5.40e-1016
kidney cell4.11e-0918
kidney epithelial cell4.11e-0918
motile cell4.29e-09390
kidney tubule cell6.04e-0912
nephron tubule epithelial cell6.04e-0912
mesenchymal cell1.58e-08358
contractile cell2.08e-0859
granulocyte monocyte progenitor cell2.10e-0871
native cell2.60e-08722
myeloid lineage restricted progenitor cell3.63e-0870
muscle precursor cell3.64e-0857
myoblast3.64e-0857
multi-potent skeletal muscle stem cell3.64e-0857
kidney cortical cell1.49e-0713
renal cortical epithelial cell1.49e-0713
fibroblast3.52e-0775
muscle cell4.94e-0754
myeloid leukocyte5.45e-0776
vascular associated smooth muscle cell5.97e-0732
Uber Anatomy
Ontology termp-valuen
musculoskeletal system1.56e-17167
lateral plate mesoderm6.25e-11216
bone marrow1.03e-1080
connective tissue3.63e-10375
nephron epithelium5.40e-1016
nephron5.40e-1016
uriniferous tubule5.40e-1016
metanephric mesenchyme5.40e-1016
nephrogenic mesenchyme5.40e-1016
skeletal element1.39e-09101
skeletal system1.39e-09101
somite1.62e-0983
paraxial mesoderm1.62e-0983
presomitic mesoderm1.62e-0983
presumptive segmental plate1.62e-0983
trunk paraxial mesoderm1.62e-0983
presumptive paraxial mesoderm1.62e-0983
bone element1.70e-0986
excretory tube4.73e-0917
mesonephric epithelium4.73e-0917
mesonephric tubule4.73e-0917
nephric duct4.73e-0917
kidney epithelium4.73e-0917
renal duct4.73e-0917
mesonephric duct4.73e-0917
pronephric duct4.73e-0917
dermomyotome5.99e-0970
renal tubule6.04e-0912
nephron tubule6.04e-0912
nephron tubule epithelium6.04e-0912
trunk mesenchyme7.94e-09143
multilaminar epithelium2.86e-0882
mesonephros3.18e-0818
pronephros3.18e-0818
nephrogenic cord3.18e-0818
pronephric mesoderm3.18e-0818
rostral part of nephrogenic cord3.18e-0818
presumptive pronephric mesoderm3.18e-0818
immune system4.23e-08115
intraembryonic coelom5.23e-0821
parenchyma1.11e-0717
cortex of kidney1.49e-0713
renal parenchyma1.49e-0713
skeletal muscle tissue2.76e-0761
striated muscle tissue2.76e-0761
myotome2.76e-0761
muscle tissue3.11e-0763
musculature3.11e-0763
musculature of body3.11e-0763
hemolymphoid system6.80e-07112
urogenital ridge7.66e-0720


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
FOS#235338.99795530889440.001372499272417130.00897180018226028



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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