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Coexpression cluster:C4446: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000477!3.59e-25!373;UBERON:0000481!4.98e-20!342;UBERON:0000064!1.61e-17!218;UBERON:0000119!7.06e-17!309;UBERON:0000483!1.60e-16!306;UBERON:0004121!1.62e-13!171;UBERON:0000924!1.62e-13!171;UBERON:0006601!1.62e-13!171;UBERON:0000922!3.04e-13!592;UBERON:0000468!4.06e-13!656;UBERON:0000467!1.18e-12!624;UBERON:0000480!1.49e-12!625;UBERON:0005423!3.26e-12!581;UBERON:0004111!1.01e-10!240;UBERON:0011216!1.10e-10!223;UBERON:0010371!1.72e-09!104;UBERON:0010314!3.41e-09!132;UBERON:0000025!1.02e-08!192;UBERON:0003075!1.06e-08!82;UBERON:0007284!1.06e-08!82;UBERON:0002346!1.20e-08!86;UBERON:0000062!1.41e-08!503;UBERON:0002050!2.35e-08!564;UBERON:0003056!2.90e-08!61;UBERON:0000923!3.69e-08!560;UBERON:0010316!3.69e-08!560;UBERON:0005291!3.69e-08!560;UBERON:0006598!3.69e-08!560;UBERON:0010317!3.69e-08!560;UBERON:0002532!3.69e-08!560;UBERON:0000475!9.25e-08!264;UBERON:0002113!1.01e-07!26;UBERON:0003918!1.01e-07!26;UBERON:0011143!1.01e-07!26;UBERON:0005095!1.01e-07!26;UBERON:0007687!1.01e-07!26;UBERON:0005177!2.83e-07!101;UBERON:0001950!3.46e-07!20;UBERON:0000489!3.58e-07!31;UBERON:0003103!5.20e-07!68
|ontology_enrichment_uberon=UBERON:0000477!3.59e-25!373;UBERON:0000481!4.98e-20!342;UBERON:0000064!1.61e-17!218;UBERON:0000119!7.06e-17!309;UBERON:0000483!1.60e-16!306;UBERON:0004121!1.62e-13!171;UBERON:0000924!1.62e-13!171;UBERON:0006601!1.62e-13!171;UBERON:0000922!3.04e-13!592;UBERON:0000468!4.06e-13!656;UBERON:0000467!1.18e-12!624;UBERON:0000480!1.49e-12!625;UBERON:0005423!3.26e-12!581;UBERON:0004111!1.01e-10!240;UBERON:0011216!1.10e-10!223;UBERON:0010371!1.72e-09!104;UBERON:0010314!3.41e-09!132;UBERON:0000025!1.02e-08!192;UBERON:0003075!1.06e-08!82;UBERON:0007284!1.06e-08!82;UBERON:0002346!1.20e-08!86;UBERON:0000062!1.41e-08!503;UBERON:0002050!2.35e-08!564;UBERON:0003056!2.90e-08!61;UBERON:0000923!3.69e-08!560;UBERON:0010316!3.69e-08!560;UBERON:0005291!3.69e-08!560;UBERON:0006598!3.69e-08!560;UBERON:0010317!3.69e-08!560;UBERON:0002532!3.69e-08!560;UBERON:0000475!9.25e-08!264;UBERON:0002113!1.01e-07!26;UBERON:0003918!1.01e-07!26;UBERON:0011143!1.01e-07!26;UBERON:0005095!1.01e-07!26;UBERON:0007687!1.01e-07!26;UBERON:0005177!2.83e-07!101;UBERON:0001950!3.46e-07!20;UBERON:0000489!3.58e-07!31;UBERON:0003103!5.20e-07!68
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}}
}}

Revision as of 16:44, 26 November 2012


Full id: C4446_Lymphatic_mesothelioma_bile_Wilms_leiomyoblastoma_large_merkel



Phase1 CAGE Peaks

Hg19::chr5:106715245..106715249,-p1@EFNA5
Hg19::chr5:106716071..106716075,-p@chr5:106716071..106716075
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Hg19::chr5:106716277..106716281,-p@chr5:106716277..106716281
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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 cell1.11e-26253
embryonic cell1.13e-08250
squamous epithelial cell1.50e-0863
kidney cell5.77e-0717
kidney epithelial cell5.77e-0717
Uber Anatomy
Ontology termp-valuen
anatomical cluster3.59e-25373
multi-tissue structure4.98e-20342
organ part1.61e-17218
cell layer7.06e-17309
epithelium1.60e-16306
ectoderm-derived structure1.62e-13171
ectoderm1.62e-13171
presumptive ectoderm1.62e-13171
embryo3.04e-13592
multi-cellular organism4.06e-13656
anatomical system1.18e-12624
anatomical group1.49e-12625
developing anatomical structure3.26e-12581
anatomical conduit1.01e-10240
organ system subdivision1.10e-10223
ecto-epithelium1.72e-09104
structure with developmental contribution from neural crest3.41e-09132
tube1.02e-08192
neural plate1.06e-0882
presumptive neural plate1.06e-0882
neurectoderm1.20e-0886
organ1.41e-08503
embryonic structure2.35e-08564
pre-chordal neural plate2.90e-0861
germ layer3.69e-08560
germ layer / neural crest3.69e-08560
embryonic tissue3.69e-08560
presumptive structure3.69e-08560
germ layer / neural crest derived structure3.69e-08560
epiblast (generic)3.69e-08560
organism subdivision9.25e-08264
kidney1.01e-0726
kidney mesenchyme1.01e-0726
upper urinary tract1.01e-0726
kidney rudiment1.01e-0726
kidney field1.01e-0726
trunk region element2.83e-07101
neocortex3.46e-0720
cavitated compound organ3.58e-0731
compound organ5.20e-0768
Disease
Ontology termp-valuen
cell type cancer1.80e-12143
carcinoma1.50e-11106


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

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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