Personal tools

Coexpression cluster:C2616

From FANTOM5_SSTAR

Revision as of 15:37, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2616_Fibroblast_Keratinocyte_Keratocytes_Bronchial_Trabecular_Small_Tracheal



Phase1 CAGE Peaks

Hg19::chr20:361617..361622,+p8@TRIB3
Hg19::chr20:361623..361731,+p1@TRIB3
Hg19::chr20:361975..361996,+p6@TRIB3
Hg19::chr20:362017..362036,+p11@TRIB3


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 cell6.85e-33253
animal cell2.82e-20679
eukaryotic cell2.82e-20679
native cell1.04e-13722
endodermal cell1.38e-1258
embryonic cell1.33e-11250
endo-epithelial cell8.27e-0842
squamous epithelial cell4.25e-0763
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.10e-10160
endoderm1.10e-10160
presumptive endoderm1.10e-10160
immaterial anatomical entity4.73e-10117
endo-epithelium8.10e-1082
trunk1.56e-09199
organism subdivision3.05e-09264
subdivision of trunk3.15e-08112
trunk region element4.21e-08101
digestive system9.70e-08145
digestive tract9.70e-08145
primitive gut9.70e-08145
Disease
Ontology termp-valuen
cell type cancer1.58e-20143
cancer6.78e-20235
disease of cellular proliferation3.61e-19239
carcinoma8.27e-16106
disease of anatomical entity8.79e-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
ATF3#467316.84738089450660.0003409986823655640.00346469125280447
BHLHE40#8553444.87181354697742.46312701995675e-071.2849476665198e-05
CCNT2#90546.336201576962630.0006203100587215640.00512698339845057
CEBPB#105135.978360719368610.007153832484726970.029735696524413
E2F1#186944.907389214879320.001724022357361790.0106585669200561
EGR1#195844.988179094810140.001615011500076050.0101504595327943
ELF1#199744.258097958807540.003041525565781240.0161024934640151
GABPB1#255347.067683836182170.0004006876864423170.00390477011144435
HEY1#2346244.040111043105710.00375304636917980.0186268312384531
REST#597849.650028716128020.0001152825614219170.00157200619302045
SPI1#668848.204323508522730.000220661881527680.00249574466589445
TAF1#687243.343046285745290.008005664898701650.0322583292702458
TCF7L2#6934410.77017656313737.42969445082454e-050.00115537501302809
TFAP2C#7022410.80922860986027.32289634782688e-050.00114644876580826



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.