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Coexpression cluster:C3294

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Full id: C3294_smallcell_hepatoblastoma_thyroid_hepatocellular_Melanocyte_liver_small



Phase1 CAGE Peaks

Hg19::chr12:53497240..53497249,+p3@SOAT2
Hg19::chr7:130600638..130600649,+p@chr7:130600638..130600649
+
Hg19::chr7:130600673..130600688,+p@chr7:130600673..130600688
+


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
metabolising cell1.52e-1112
endopolyploid cell1.52e-1112
parenchymal cell1.52e-1112
polyploid cell1.52e-1112
hepatocyte1.52e-1112
uterine smooth muscle cell8.03e-071
Uber Anatomy
Ontology termp-valuen
open tracheal system trachea2.23e-112
gut epithelium4.54e-1054
digestive system5.07e-09145
digestive tract5.07e-09145
primitive gut5.07e-09145
endoderm-derived structure7.04e-09160
endoderm7.04e-09160
presumptive endoderm7.04e-09160
gland1.84e-0759
liver3.54e-0719
digestive gland3.54e-0719
liver bud3.54e-0719
endo-epithelium3.73e-0782
maxillary sinus6.43e-071
paranasal sinus6.43e-071
endocrine gland6.75e-0735
Disease
Ontology termp-valuen
paranasal sinus cancer6.43e-071
maxillary sinus cancer6.43e-071


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
EP300#203336.77394172622320.003216880500103790.0167040114627524
FOXA2#3170216.42030916844350.004810682352105480.0225787728820575
HDAC2#3066313.41562023662630.0004140761399857210.0039019848402029
HNF4A#3172323.13229036295378.07584663437677e-050.00122574240175509
HNF4G#3174328.75342252644684.20470658818262e-050.000755306761890617
POU2F2#545239.106124057742520.001324165192682130.0088040799948134
RXRA#6256213.38307809275550.007196434429465730.0298190206458628
SP1#666735.69838137814090.005403962701712170.0245694336600112
USF1#739136.361499277207960.00388404057290560.0189704584667113



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.