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Coexpression cluster:C4184: Difference between revisions

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|tf_chipseq_enrich=FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243477723968757
|tf_chipseq_enrich=FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243477723968757
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}}
}}

Revision as of 16:36, 26 November 2012


Full id: C4184_mesenchymal_Mesenchymal_aorta_lung_CD14_Adipocyte_Preadipocyte



Phase1 CAGE Peaks

Hg19::chr2:218766600..218766625,-p10@TNS1
Hg19::chr2:218766633..218766644,-p20@TNS1
Hg19::chr2:218766650..218766670,-p9@TNS1


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>

Cell Type
Ontology termp-valuen
multi fate stem cell2.70e-11427
somatic stem cell1.13e-10433
stem cell7.03e-10441
defensive cell2.37e-0948
phagocyte2.37e-0948
classical monocyte5.49e-0942
CD14-positive, CD16-negative classical monocyte5.49e-0942
preadipocyte1.65e-0812
fat cell2.37e-0815
muscle precursor cell2.73e-0858
myoblast2.73e-0858
multi-potent skeletal muscle stem cell2.73e-0858
stuff accumulating cell3.76e-0887
Uber Anatomy
Ontology termp-valuen
mesoderm1.30e-16315
mesoderm-derived structure1.30e-16315
presumptive mesoderm1.30e-16315
muscle tissue1.16e-0964
musculature1.16e-0964
musculature of body1.16e-0964
skeletal muscle tissue8.44e-0962
striated muscle tissue8.44e-0962
myotome8.44e-0962
primary circulatory organ3.11e-0827
omentum3.91e-086
peritoneum3.91e-086
abdominal cavity3.91e-086
visceral peritoneum3.91e-086
musculoskeletal system5.62e-08167
trunk1.36e-07199
lateral plate mesoderm1.44e-07203
heart2.85e-0724
primitive heart tube2.85e-0724
primary heart field2.85e-0724
anterior lateral plate mesoderm2.85e-0724
heart tube2.85e-0724
heart primordium2.85e-0724
cardiac mesoderm2.85e-0724
cardiogenic plate2.85e-0724
heart rudiment2.85e-0724
trunk mesenchyme3.14e-07122
Disease
Ontology termp-valuen
ovarian cancer1.87e-0714


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
FOSL2#2355316.93020060456170.0002060162053171620.00243477723968757



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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