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Coexpression cluster:C54

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Full id: C54_Dendritic_Macrophage_Monocytederived_CD14_leiomyoma_adipose_immature



Phase1 CAGE Peaks


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


p.valueFDRnGenesnPathwayName
2.56514820294416e-060.00162373881246366588Hematopoietic cell lineage (KEGG):04640
0.0001963575646258050.04143144613604495217IL-4 up reg. targets (Netpath):NetPath_16
7.59372259526931e-060.00240341320140274451{HLA-A,53} (Static Module):NA



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


GO IDGO nameFDR corrected p-value
GO:0019863IgE binding5.1960847290596e-05
GO:0005886plasma membrane0.000122264959160882
GO:0019865immunoglobulin binding0.000955205006431885
GO:0016020membrane0.00119483706388099
GO:0005529sugar binding0.00824731730437619
GO:0044425membrane part0.00824731730437619
GO:0006955immune response0.00824731730437619
GO:0030318melanocyte differentiation0.00824731730437619
GO:0050931pigment cell differentiation0.00824731730437619
GO:0016021integral to membrane0.00824731730437619
GO:0031224intrinsic to membrane0.00834284437193673
GO:0005887integral to plasma membrane0.0145372615868946
GO:0031226intrinsic to plasma membrane0.0147652395785898
GO:0002376immune system process0.0166019979534477
GO:0030246carbohydrate binding0.0166019979534477
GO:0044459plasma membrane part0.0183348900050476
GO:0048066pigmentation during development0.0191821965536301
GO:0044464cell part0.0276503768469693
GO:0019370leukotriene biosynthetic process0.0311516029945749
GO:0043450alkene biosynthetic process0.0311516029945749
GO:0032403protein complex binding0.0360937359626909
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.0438007771105616
GO:0006691leukotriene metabolic process0.0438007771105616
GO:0043449alkene metabolic process0.0438007771105616
GO:0046456icosanoid biosynthetic process0.0438007771105616
GO:0008420CTD phosphatase activity0.0438007771105616
GO:0047757chondroitin-glucuronate 5-epimerase activity0.0438007771105616
GO:0042018interleukin-22 receptor activity0.0438007771105616
GO:0042017interleukin-22 binding0.0438007771105616
GO:0004642phosphoribosylformylglycinamidine synthase activity0.0438007771105616
GO:0004234macrophage elastase activity0.0438007771105616
GO:0008924malate dehydrogenase (acceptor) activity0.0438007771105616
GO:0047800cysteamine dioxygenase activity0.0438007771105616



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>


Uber Anatomy
Ontology termp-valuen
bone marrow1.47e-0976
bone element6.90e-0982
musculoskeletal system1.92e-08167
umbilical artery2.26e-084
skeletal element3.96e-0890
immune system7.07e-0893
hematopoietic system1.72e-0798
blood island1.72e-0798
skeletal system2.40e-07100
hemolymphoid system8.01e-07108


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
SPI1#6688741.85097542570331.14115300581627e-076.62484039880183e-06



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