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Coexpression cluster:C2474: Difference between revisions

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|tf_chipseq_enrich=EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101431346476904!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00107095299579288!FOXA2#3170;4:24.6304637526652:2.71504128667089e-06:9.43300721685365e-05!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000626654409877571!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186038449736945!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000743360518820861!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391725233699306!MAFK#7975;4:27.1007331378299:1.85228494563408e-06:6.85024034833846e-05!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322210349668774!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244204848615188
|tf_chipseq_enrich=EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101431346476904!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00107095299579288!FOXA2#3170;4:24.6304637526652:2.71504128667089e-06:9.43300721685365e-05!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000626654409877571!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186038449736945!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000743360518820861!JUND#3727;4:6.99466394187103:0.00041768421781858:0.00391725233699306!MAFK#7975;4:27.1007331378299:1.85228494563408e-06:6.85024034833846e-05!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0322210349668774!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0244204848615188
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}}
}}

Revision as of 15:31, 26 November 2012


Full id: C2474_mesothelioma_Hep2_clear_Renal_nonsmall_renal_lung



Phase1 CAGE Peaks

Hg19::chr19:10687983..10687998,-p@chr19:10687983..10687998
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Hg19::chr19:10688000..10688029,-p@chr19:10688000..10688029
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Hg19::chr19:10688031..10688042,-p@chr19:10688031..10688042
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Hg19::chr19:10688044..10688070,-p@chr19:10688044..10688070
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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
larynx6.21e-159
nephron tubule epithelium1.06e-1410
abdomen element7.32e-1354
abdominal segment element7.32e-1354
kidney1.97e-1126
kidney mesenchyme1.97e-1126
upper urinary tract1.97e-1126
kidney rudiment1.97e-1126
kidney field1.97e-1126
abdominal segment of trunk9.63e-1160
abdomen9.63e-1160
nephron epithelium1.24e-1015
renal tubule1.24e-1015
nephron tubule1.24e-1015
nephron1.24e-1015
uriniferous tubule1.24e-1015
nephrogenic mesenchyme1.24e-1015
cortex1.48e-1015
excretory tube9.08e-1016
kidney epithelium9.08e-1016
cavitated compound organ8.30e-0931
primordium1.83e-07160
cortex of kidney3.06e-0712
renal parenchyma3.06e-0712
upper respiratory tract6.96e-0719
Disease
Ontology termp-valuen
disease of cellular proliferation1.81e-17239
cancer1.43e-15235
carcinoma6.63e-14106
cell type cancer4.43e-13143
reproductive organ cancer2.02e-1029
female reproductive organ cancer7.77e-0927
ovarian cancer1.38e-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
EGR1#195844.988179094810140.001615011500076050.0101431346476904
FOXA1#3169411.08141974938556.62943068949433e-050.00107095299579288
FOXA2#3170424.63046375266522.71504128667089e-069.43300721685365e-05
HDAC2#3066413.41562023662633.0859005065161e-050.000626654409877571
HEY1#2346244.040111043105710.00375304636917980.0186038449736945
JUN#3725412.51282919233634.07770316866756e-050.000743360518820861
JUND#372746.994663941871030.000417684217818580.00391725233699306
MAFK#7975427.10073313782991.85228494563408e-066.85024034833846e-05
TAF1#687243.343046285745290.008005664898701650.0322210349668774
TBP#690843.706770687096390.005296377814784350.0244204848615188



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.