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Coexpression cluster:C4825: Difference between revisions

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|tf_chipseq_enrich=FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376915379577328!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064628663052741
|tf_chipseq_enrich=FOSL2#2355;2:11.2868004030411:0.010053458697312:0.0376915379577328!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.0064628663052741
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}}
}}

Revision as of 16:59, 26 November 2012


Full id: C4825_epithelioid_mature_Lymphatic_amniotic_Preadipocyte_Endothelial_CD14



Phase1 CAGE Peaks

Hg19::chr9:686751..686812,+p5@KANK1
Hg19::chr9:686815..686838,+p18@KANK1
Hg19::chr9:686850..686877,+p17@KANK1


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
endothelial cell of vascular tree1.22e-0924
fat cell2.51e-0915
Uber Anatomy
Ontology termp-valuen
adult organism6.85e-22114
multi-cellular organism5.11e-13656
anatomical system6.07e-12624
anatomical group7.99e-12625
neural tube2.43e-1156
neural rod2.43e-1156
future spinal cord2.43e-1156
neural keel2.43e-1156
regional part of nervous system1.12e-1053
regional part of brain1.12e-1053
ecto-epithelium8.18e-09104
regional part of forebrain9.05e-0941
forebrain9.05e-0941
anterior neural tube9.05e-0941
future forebrain9.05e-0941
embryonic structure2.23e-08564
extraembryonic membrane2.93e-0814
membranous layer2.93e-0814
organ7.90e-08503
brain grey matter8.16e-0834
gray matter8.16e-0834
germ layer8.45e-08560
germ layer / neural crest8.45e-08560
embryonic tissue8.45e-08560
presumptive structure8.45e-08560
germ layer / neural crest derived structure8.45e-08560
epiblast (generic)8.45e-08560
telencephalon1.39e-0734
brain1.39e-0768
future brain1.39e-0768
developing anatomical structure3.17e-07581
neural plate4.68e-0782
presumptive neural plate4.68e-0782
cerebral hemisphere6.22e-0732
central nervous system8.41e-0781
regional part of telencephalon8.75e-0732


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)

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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
FOSL2#2355211.28680040304110.0100534586973120.0376915379577328
STAT3#6774310.51946499715420.0008589184530415310.0064628663052741



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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