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Coexpression cluster:C3438

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Full id: C3438_Macrophage_CD14_Monocytederived_Dendritic_Fibroblast_mesenchymal_ductal



Phase1 CAGE Peaks

Hg19::chr14:61447901..61447926,+p3@SLC38A6
Hg19::chr14:61447927..61447983,+p1@SLC38A6
Hg19::chr14:61510434..61510438,+p@chr14:61510434..61510438
+


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>


Uber Anatomy
Ontology termp-valuen
skeletal system6.88e-15100
musculoskeletal system1.19e-13167
bone marrow5.41e-1376
skeletal element6.47e-1390
bone element1.85e-1282
organ1.17e-10503
immune system1.47e-1093
multi-cellular organism2.89e-10656
anatomical system1.20e-08624
anatomical group2.25e-08625
germ layer6.62e-07560
germ layer / neural crest6.62e-07560
embryonic tissue6.62e-07560
presumptive structure6.62e-07560
germ layer / neural crest derived structure6.62e-07560
epiblast (generic)6.62e-07560
embryonic structure6.74e-07564


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
ATF3#467214.97544968400580.005768294540793880.0259502439606277
BRCA1#672213.45615376214920.007119807716084560.0296166645979271
ELK4#2005210.8237877723120.01091284719516480.0401835788955969
FOSL2#2355211.28680040304110.0100534586973120.0376644966419831
NANOG#79923219.49651898734180.003427255648501020.0174442786039182
NR3C1#290829.982015554115360.01278474365547170.046027985888304
SIX5#147912211.3911435703060.009873820081429030.0370646213602317
THAP1#55145220.91276306856750.002983447413736940.0158633675004211
TRIM28#10155212.39368336350830.008368344129438470.032898497799233



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.