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Coexpression cluster:C3979: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3979_Mast_acute_chronic_granulocyte_Fibroblast_mesodermal_epithelioid
|full_id=C3979_Mast_acute_chronic_granulocyte_Fibroblast_mesodermal_epithelioid
|id=C3979
|id=C3979

Revision as of 16:59, 12 September 2012


Full id: C3979_Mast_acute_chronic_granulocyte_Fibroblast_mesodermal_epithelioid



Phase1 CAGE Peaks

Hg19::chr1:39670444..39670458,+p5@MACF1
Hg19::chr1:39670475..39670506,+p4@MACF1
Hg19::chr1:39670514..39670534,+p11@MACF1


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
lateral plate mesoderm3.64e-10216
musculoskeletal system4.13e-09167
circulatory system4.41e-09113
cardiovascular system8.12e-09110
splanchnic layer of lateral plate mesoderm2.18e-0884
vasculature8.85e-0879
vascular system8.85e-0879
blood vessel1.01e-0760
epithelial tube open at both ends1.01e-0760
blood vasculature1.01e-0760
vascular cord1.01e-0760
artery2.00e-0742
arterial blood vessel2.00e-0742
arterial system2.00e-0742
adult organism8.73e-07115
Disease
Ontology termp-valuen
myeloid leukemia3.42e-0931
leukemia1.86e-0739


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
CTCF#1066435.360256373075030.0064925092527670.0279720792809593
ELF1#199734.258097958807540.01295179875054610.0462800365987506
FOS#235338.99795530889440.001372499272417130.0089830451533479
GATA2#2624312.7449317335540.0004829527704283790.00437118505856396
JUN#3725312.51282919233630.0005103313992726250.00444598773845793
JUND#372736.994663941871030.002921845042734990.0156924084345469
REST#597839.650028716128020.001112636247114590.00768332564218465
TRIM28#10155318.59052504526250.0001555969297255280.00197213443490344



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.

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