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Coexpression cluster:C4758: Difference between revisions

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|full_id=C4758_small_neuroblastoma_testicular_endometrial_maxillary_choriocarcinoma_cholangiocellular
|full_id=C4758_small_neuroblastoma_testicular_endometrial_maxillary_choriocarcinoma_cholangiocellular
|id=C4758
|id=C4758
|ontology_enrichment_celltype=CL:0000039!4.79e-08!7;CL:0000586!4.79e-08!7
|ontology_enrichment_celltype=CL:0000039!1.40e-09!7;CL:0000586!1.40e-09!7;CL:0002579!8.78e-08!3
|ontology_enrichment_disease=DOID:0050687!1.86e-15!143;DOID:14566!6.38e-15!239;DOID:162!1.94e-14!235;DOID:3095!4.41e-09!22;DOID:2994!4.41e-09!22;DOID:305!3.70e-08!106;DOID:5409!5.67e-07!4
|ontology_enrichment_disease=DOID:14566!8.30e-18!239;DOID:162!1.35e-17!235;DOID:0050687!1.38e-14!143;DOID:3095!7.07e-12!22;DOID:2994!7.07e-12!22;DOID:5409!1.32e-10!4;DOID:0050686!6.10e-09!137;DOID:1325!7.68e-09!7;DOID:3904!7.68e-09!7;DOID:305!5.08e-08!106;DOID:1036!7.09e-08!8;DOID:169!7.19e-07!6
|ontology_enrichment_uberon=UBERON:0003688!6.77e-09!6;UBERON:0002358!6.77e-09!6;UBERON:0003684!6.77e-09!6;UBERON:0001178!6.77e-09!6
|ontology_enrichment_uberon=UBERON:0003688!9.58e-10!6;UBERON:0002358!9.58e-10!6;UBERON:0003684!9.58e-10!6;UBERON:0001178!9.58e-10!6;UBERON:0000013!2.93e-08!5;UBERON:0002410!2.93e-08!5
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.019131494220582!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115845669101743!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324573720851754!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109311201782448!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296238647788359!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278446508594345
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.019131494220582!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115845669101743!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0324573720851754!HMGN3#9324;3:8.17854772335059:0.00182776694216421:0.0109311201782448!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296238647788359!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278446508594345
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}}
}}

Revision as of 16:13, 19 October 2012


Full id: C4758_small_neuroblastoma_testicular_endometrial_maxillary_choriocarcinoma_cholangiocellular



Phase1 CAGE Peaks

Hg19::chr8:47529219..47529232,-p@chr8:47529219..47529232
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Hg19::chr8:47529241..47529249,-p@chr8:47529241..47529249
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Hg19::chr8:47529257..47529285,-p@chr8:47529257..47529285
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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>


Cell Type
Ontology termp-valuen
germ line cell1.40e-097
germ cell1.40e-097
omentum preadipocyte8.78e-083
Uber Anatomy
Ontology termp-valuen
omentum9.58e-106
peritoneum9.58e-106
abdominal cavity9.58e-106
visceral peritoneum9.58e-106
sympathetic nervous system2.93e-085
autonomic nervous system2.93e-085
Disease
Ontology termp-valuen
disease of cellular proliferation8.30e-18239
cancer1.35e-17235
cell type cancer1.38e-14143
germ cell and embryonal cancer7.07e-1222
germ cell cancer7.07e-1222
lung small cell carcinoma1.32e-104
organ system cancer6.10e-09137
bronchus cancer7.68e-097
bronchogenic carcinoma7.68e-097
carcinoma5.08e-08106
chronic leukemia7.09e-088
neuroendocrine tumor7.19e-076


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
CCNT2#90536.336201576962630.003930750035764890.019131494220582
CEBPB#105137.971147625824820.001974187055288560.0115845669101743
E2F6#187635.017155731697390.00791769806886330.0324573720851754
HMGN3#932438.178547723350590.001827766942164210.0109311201782448
MYC#460935.22228187160940.007020843755740150.0296238647788359
SIN3A#2594235.408884726815140.006318961977991520.0278446508594345



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.