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Coexpression cluster:C2033: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00510999859779314!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101200087632113!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160479887119646!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00247666651742204!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321022705454215
|tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00510999859779314!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101200087632113!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0160479887119646!HMGN3#9324;4:8.17854772335059:0.000223457028444047:0.00247666651742204!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321022705454215
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}}
}}

Revision as of 15:15, 26 November 2012


Full id: C2033_Preadipocyte_Adipocyte_hepatic_Mesenchymal_Ewing_skeletal_Fibroblast



Phase1 CAGE Peaks

Hg19::chr10:105428458..105428467,-p13@SH3PXD2A
Hg19::chr10:105428481..105428540,-p5@SH3PXD2A
Hg19::chr10:105428550..105428555,-p25@SH3PXD2A
Hg19::chr10:105428632..105428639,-p26@SH3PXD2A


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
fat cell3.09e-1515
fibroblast9.73e-1476
multi fate stem cell1.70e-12427
preadipocyte3.74e-1212
somatic stem cell7.46e-12433
stem cell4.93e-11441
mesenchymal cell4.73e-10354
connective tissue cell2.43e-09361
cardiocyte1.28e-0816
skin fibroblast2.55e-0823
motile cell1.21e-07386
Uber Anatomy
Ontology termp-valuen
connective tissue2.79e-09371
omentum3.32e-096
peritoneum3.32e-096
abdominal cavity3.32e-096
visceral peritoneum3.32e-096
cavity lining7.33e-0812
serous membrane7.33e-0812
adipose tissue1.12e-0714
primary circulatory organ2.68e-0727
integument6.72e-0746
integumental system6.72e-0746
Disease
Ontology termp-valuen
ovarian cancer4.40e-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)

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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
CCNT2#90546.336201576962630.0006203100587215640.00510999859779314
EGR1#195844.988179094810140.001615011500076050.0101200087632113
ELF1#199744.258097958807540.003041525565781240.0160479887119646
HMGN3#932448.178547723350590.0002234570284440470.00247666651742204
TAF1#687243.343046285745290.008005664898701650.0321022705454215



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.