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Coexpression cluster:C2921: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2921_Alveolar_acute_neuroepithelioma_hepatoblastoma_embryonic_Renal_Mesenchymal
|full_id=C2921_Alveolar_acute_neuroepithelioma_hepatoblastoma_embryonic_Renal_Mesenchymal
|id=C2921
|id=C2921

Revision as of 15:43, 12 September 2012


Full id: C2921_Alveolar_acute_neuroepithelioma_hepatoblastoma_embryonic_Renal_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr8:145515072..145515134,-p1@BOP1
Hg19::chr9:137001185..137001233,+p1@WDR5
Hg19::chr9:137001235..137001260,+p2@WDR5
Hg19::chr9:140484917..140484998,-p1@ZMYND19


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
epithelial cell9.82e-25254
embryonic cell1.42e-17248
squamous epithelial cell2.12e-1162
animal cell3.17e-07679
eukaryotic cell3.17e-07679
Uber Anatomy
Ontology termp-valuen
mesenchyme1.77e-08238
entire embryonic mesenchyme1.77e-08238
Disease
Ontology termp-valuen
cancer1.40e-33235
disease of cellular proliferation1.44e-32239
cell type cancer7.14e-18143
organ system cancer3.38e-15137
carcinoma6.90e-14106
hematologic cancer8.53e-1451
immune system cancer8.53e-1451
leukemia1.95e-1339
myeloid leukemia3.91e-1331


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#186944.907389214879320.001724022357361790.0106844986340202
E2F6#187645.017155731697390.00157802193473060.00999618079949833
ETS1#211337.296570691651750.00400857377511390.0192156532105898
IRF1#365947.63716375356390.0002938853996185490.00308101759192548
NRF1#4899412.21027944771094.49717228915276e-050.000795798333966156
SIN3A#2594245.408884726815140.001168172384885160.00798342858951844
SP1#666745.69838137814090.0009482606065333980.0068593565234618
TAF1#687243.343046285745290.008005664898701650.0323444346752612
TBP#690843.706770687096390.005296377814784350.0245135565077892



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.