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Coexpression cluster:C4615: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000466!2.67e-12!117;UBERON:0001007!6.94e-12!145;UBERON:0001555!6.94e-12!145;UBERON:0007026!6.94e-12!145;UBERON:0004119!3.18e-11!160;UBERON:0000925!3.18e-11!160;UBERON:0006595!3.18e-11!160;UBERON:0002048!8.83e-11!22;UBERON:0000117!8.83e-11!22;UBERON:0000171!8.83e-11!22;UBERON:0000170!8.83e-11!22;UBERON:0005597!8.83e-11!22;UBERON:0000118!8.83e-11!22;UBERON:0005177!1.11e-10!101;UBERON:0004921!1.26e-10!118;UBERON:0001041!1.85e-10!87;UBERON:0005178!4.36e-10!34;UBERON:0002224!4.36e-10!34;UBERON:0005911!5.60e-10!82;UBERON:0005181!9.65e-10!35;UBERON:0004802!9.66e-10!19;UBERON:0000115!9.66e-10!19;UBERON:0000464!2.63e-09!95;UBERON:0005153!5.62e-09!37;UBERON:0001004!1.27e-07!74;UBERON:0008947!3.24e-07!38;UBERON:0003258!3.24e-07!38;UBERON:0009569!3.75e-07!112;UBERON:0000065!7.30e-07!54;UBERON:0009497!9.12e-07!25;UBERON:0000015!9.12e-07!25;UBERON:0002423!9.12e-07!25;UBERON:0006235!9.12e-07!25;UBERON:0004161!9.12e-07!25
|ontology_enrichment_uberon=UBERON:0000466!2.67e-12!117;UBERON:0001007!6.94e-12!145;UBERON:0001555!6.94e-12!145;UBERON:0007026!6.94e-12!145;UBERON:0004119!3.18e-11!160;UBERON:0000925!3.18e-11!160;UBERON:0006595!3.18e-11!160;UBERON:0002048!8.83e-11!22;UBERON:0000117!8.83e-11!22;UBERON:0000171!8.83e-11!22;UBERON:0000170!8.83e-11!22;UBERON:0005597!8.83e-11!22;UBERON:0000118!8.83e-11!22;UBERON:0005177!1.11e-10!101;UBERON:0004921!1.26e-10!118;UBERON:0001041!1.85e-10!87;UBERON:0005178!4.36e-10!34;UBERON:0002224!4.36e-10!34;UBERON:0005911!5.60e-10!82;UBERON:0005181!9.65e-10!35;UBERON:0004802!9.66e-10!19;UBERON:0000115!9.66e-10!19;UBERON:0000464!2.63e-09!95;UBERON:0005153!5.62e-09!37;UBERON:0001004!1.27e-07!74;UBERON:0008947!3.24e-07!38;UBERON:0003258!3.24e-07!38;UBERON:0009569!3.75e-07!112;UBERON:0000065!7.30e-07!54;UBERON:0009497!9.12e-07!25;UBERON:0000015!9.12e-07!25;UBERON:0002423!9.12e-07!25;UBERON:0006235!9.12e-07!25;UBERON:0004161!9.12e-07!25
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}}
}}

Revision as of 16:51, 26 November 2012


Full id: C4615_maxillary_bile_mucinous_small_lung_oral_squamous



Phase1 CAGE Peaks

Hg19::chr6:53481796..53481815,-p1@ENST00000502390
p1@ENST00000506206
p1@ENST00000510846
Hg19::chr6:53481847..53481854,-p2@ENST00000506206
p2@ENST00000510846
Hg19::chr8:63077406..63077421,-p@chr8:63077406..63077421
-


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 cell5.76e-16253
endodermal cell4.12e-1358
epithelial cell of lung9.66e-1019
seromucus secreting cell5.85e-092
endo-epithelial cell2.90e-0742
Uber Anatomy
Ontology termp-valuen
immaterial anatomical entity2.67e-12117
digestive system6.94e-12145
digestive tract6.94e-12145
primitive gut6.94e-12145
endoderm-derived structure3.18e-11160
endoderm3.18e-11160
presumptive endoderm3.18e-11160
lung8.83e-1122
respiratory tube8.83e-1122
respiration organ8.83e-1122
pair of lungs8.83e-1122
lung primordium8.83e-1122
lung bud8.83e-1122
trunk region element1.11e-10101
subdivision of digestive tract1.26e-10118
foregut1.85e-1087
thoracic cavity element4.36e-1034
thoracic cavity4.36e-1034
endo-epithelium5.60e-1082
thoracic segment organ9.65e-1035
respiratory tract epithelium9.66e-1019
lung epithelium9.66e-1019
anatomical space2.63e-0995
epithelial bud5.62e-0937
respiratory system1.27e-0774
respiratory primordium3.24e-0738
endoderm of foregut3.24e-0738
subdivision of trunk3.75e-07112
respiratory tract7.30e-0754
epithelium of foregut-midgut junction9.12e-0725
anatomical boundary9.12e-0725
hepatobiliary system9.12e-0725
foregut-midgut junction9.12e-0725
septum transversum9.12e-0725
Disease
Ontology termp-valuen
carcinoma3.64e-35106
cell type cancer1.64e-27143
cancer8.05e-18235
squamous cell carcinoma2.04e-1714
disease of cellular proliferation2.92e-17239
respiratory system cancer2.00e-1516
adenocarcinoma7.31e-1425
lung cancer1.28e-1215
signet ring cell adenocarcinoma8.35e-092


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)

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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

No analysis results for this cluster

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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