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Coexpression cluster:C4844: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032830169738458!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000680273755060296!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00585020250352164!REST#5978;3:9.65002871612802:0.00111263624711459:0.00772264351780426!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00198272178423675
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032830169738458!ESR1#2099;3:30.7686032961545:3.43136389821584e-05:0.000680273755060296!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.00585020250352164!REST#5978;3:9.65002871612802:0.00111263624711459:0.00772264351780426!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00198272178423675
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}}
}}

Revision as of 17:00, 26 November 2012


Full id: C4844_cervical_smooth_extraskeletal_argyrophil_Fibroblast_skin_rectum



Phase1 CAGE Peaks

Hg19::chrX:10851763..10851782,-p4@MID1
Hg19::chrX:10851792..10851820,-p6@MID1
Hg19::chrX:10851823..10851849,-p8@MID1


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
digestive system1.36e-11145
digestive tract1.36e-11145
primitive gut1.36e-11145
organ3.65e-11503
endoderm-derived structure1.63e-10160
endoderm1.63e-10160
presumptive endoderm1.63e-10160
intestine2.20e-0917
subdivision of digestive tract4.87e-09118
organ part2.80e-08218
gastrointestinal system4.85e-0825
organ component layer5.96e-0866
organ system subdivision2.55e-07223
multi-tissue structure3.35e-07342
multi-cellular organism4.17e-07656
large intestine4.50e-0711
adult organism7.54e-07114
hindgut9.76e-0719


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
E2F1#186934.907389214879320.008460985347239390.032830169738458
ESR1#2099330.76860329615453.43136389821584e-050.000680273755060296
FOXA1#3169311.08141974938550.000734755275698670.00585020250352164
REST#597839.650028716128020.001112636247114590.00772264351780426
TRIM28#10155318.59052504526250.0001555969297255280.00198272178423675



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.