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Coexpression cluster:C4485: Difference between revisions

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|tf_chipseq_enrich=ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109915963813136
|tf_chipseq_enrich=ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0109915963813136
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}}
}}

Revision as of 16:46, 26 November 2012


Full id: C4485_Ciliary_mesothelioma_Fibroblast_neuroblastoma_leiomyoblastoma_Hair_Iris



Phase1 CAGE Peaks

Hg19::chr5:167182003..167182014,+p12@ODZ2
Hg19::chr5:167182034..167182046,+p8@ODZ2
Hg19::chr5:167182112..167182116,+p32@ODZ2


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
skin of body1.45e-1641
integument2.76e-1446
integumental system2.76e-1446
atypical epithelium2.28e-134
anterior segment of eyeball1.17e-1214
surface structure1.26e-1299
ciliary epithelium1.67e-103
ciliary body1.67e-103
pigment epithelium of eye9.86e-1011
vasculature of eye7.00e-096
uvea7.00e-096
vasculature of head7.00e-096
sense organ1.87e-0824
sensory system1.87e-0824
entire sense organ system1.87e-0824
camera-type eye2.06e-0820
simple eye2.06e-0820
immature eye2.06e-0820
ocular region2.06e-0820
eyeball of camera-type eye2.06e-0820
optic cup2.06e-0820
optic vesicle2.06e-0820
eye primordium2.06e-0820
eye6.08e-0821
visual system6.08e-0821
ectodermal placode7.42e-0831
face1.62e-0722
vasculature of organ7.59e-0711
head8.46e-0756
Disease
Ontology termp-valuen
musculoskeletal system disease8.38e-155
myotonic disease8.38e-155
muscle tissue disease8.38e-155
myopathy8.38e-155
muscular disease8.38e-155
myotonic dystrophy8.38e-155
disease of anatomical entity5.34e-0839
neuroectodermal tumor4.62e-0710


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
ZNF263#1012738.221841637010680.001799043925565870.0109915963813136



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.