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Coexpression cluster:C3343: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!3.87e-44!114;UBERON:0000481!5.20e-16!342;UBERON:0011216!1.69e-14!223;UBERON:0000477!2.01e-14!373;UBERON:0010314!1.05e-10!132;UBERON:0001049!1.18e-10!56;UBERON:0005068!1.18e-10!56;UBERON:0006241!1.18e-10!56;UBERON:0007135!1.18e-10!56;UBERON:0003075!2.27e-10!82;UBERON:0007284!2.27e-10!82;UBERON:0000468!2.89e-10!656;UBERON:0000062!4.48e-10!503;UBERON:0002346!8.21e-10!86;UBERON:0000073!3.21e-09!53;UBERON:0002616!3.21e-09!53;UBERON:0004111!4.15e-09!240;UBERON:0000479!7.87e-09!773;UBERON:0002050!7.89e-09!564;UBERON:0000923!8.60e-09!560;UBERON:0010316!8.60e-09!560;UBERON:0005291!8.60e-09!560;UBERON:0006598!8.60e-09!560;UBERON:0010317!8.60e-09!560;UBERON:0002532!8.60e-09!560;UBERON:0000467!4.08e-08!624;UBERON:0002780!4.15e-08!41;UBERON:0001890!4.15e-08!41;UBERON:0003080!4.15e-08!41;UBERON:0006240!4.15e-08!41;UBERON:0000480!5.16e-08!625;UBERON:0005423!6.99e-08!581;UBERON:0000922!1.12e-07!592;UBERON:0000119!2.00e-07!309;UBERON:0001007!3.10e-07!145;UBERON:0001555!3.10e-07!145;UBERON:0007026!3.10e-07!145;UBERON:0000483!3.28e-07!306;UBERON:0007100!3.33e-07!27;UBERON:0000955!6.21e-07!68;UBERON:0006238!6.21e-07!68;UBERON:0001017!6.60e-07!81;UBERON:0004921!8.25e-07!118
|ontology_enrichment_uberon=UBERON:0007023!3.87e-44!114;UBERON:0000481!5.20e-16!342;UBERON:0011216!1.69e-14!223;UBERON:0000477!2.01e-14!373;UBERON:0010314!1.05e-10!132;UBERON:0001049!1.18e-10!56;UBERON:0005068!1.18e-10!56;UBERON:0006241!1.18e-10!56;UBERON:0007135!1.18e-10!56;UBERON:0003075!2.27e-10!82;UBERON:0007284!2.27e-10!82;UBERON:0000468!2.89e-10!656;UBERON:0000062!4.48e-10!503;UBERON:0002346!8.21e-10!86;UBERON:0000073!3.21e-09!53;UBERON:0002616!3.21e-09!53;UBERON:0004111!4.15e-09!240;UBERON:0000479!7.87e-09!773;UBERON:0002050!7.89e-09!564;UBERON:0000923!8.60e-09!560;UBERON:0010316!8.60e-09!560;UBERON:0005291!8.60e-09!560;UBERON:0006598!8.60e-09!560;UBERON:0010317!8.60e-09!560;UBERON:0002532!8.60e-09!560;UBERON:0000467!4.08e-08!624;UBERON:0002780!4.15e-08!41;UBERON:0001890!4.15e-08!41;UBERON:0003080!4.15e-08!41;UBERON:0006240!4.15e-08!41;UBERON:0000480!5.16e-08!625;UBERON:0005423!6.99e-08!581;UBERON:0000922!1.12e-07!592;UBERON:0000119!2.00e-07!309;UBERON:0001007!3.10e-07!145;UBERON:0001555!3.10e-07!145;UBERON:0007026!3.10e-07!145;UBERON:0000483!3.28e-07!306;UBERON:0007100!3.33e-07!27;UBERON:0000955!6.21e-07!68;UBERON:0006238!6.21e-07!68;UBERON:0001017!6.60e-07!81;UBERON:0004921!8.25e-07!118
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}}
}}

Revision as of 16:04, 26 November 2012


Full id: C3343_heart_aorta_cervix_prostate_penis_rectum_smooth



Phase1 CAGE Peaks

Hg19::chr12:91576750..91576805,-p7@DCN
Hg19::chr16:49698178..49698209,-p1@ZNF423
Hg19::chr19:41107249..41107295,+p1@LTBP4


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

GO IDGO nameFDR corrected p-value
GO:0005578proteinaceous extracellular matrix0.0337609163535741
GO:0030162regulation of proteolysis0.0337609163535741
GO:0004675transmembrane receptor protein serine/threonine kinase activity0.0337609163535741
GO:0005024transforming growth factor beta receptor activity0.0337609163535741
GO:0044421extracellular region part0.0359035381252379



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism3.87e-44114
multi-tissue structure5.20e-16342
organ system subdivision1.69e-14223
anatomical cluster2.01e-14373
structure with developmental contribution from neural crest1.05e-10132
neural tube1.18e-1056
neural rod1.18e-1056
future spinal cord1.18e-1056
neural keel1.18e-1056
neural plate2.27e-1082
presumptive neural plate2.27e-1082
multi-cellular organism2.89e-10656
organ4.48e-10503
neurectoderm8.21e-1086
regional part of nervous system3.21e-0953
regional part of brain3.21e-0953
anatomical conduit4.15e-09240
tissue7.87e-09773
embryonic structure7.89e-09564
germ layer8.60e-09560
germ layer / neural crest8.60e-09560
embryonic tissue8.60e-09560
presumptive structure8.60e-09560
germ layer / neural crest derived structure8.60e-09560
epiblast (generic)8.60e-09560
anatomical system4.08e-08624
regional part of forebrain4.15e-0841
forebrain4.15e-0841
anterior neural tube4.15e-0841
future forebrain4.15e-0841
anatomical group5.16e-08625
developing anatomical structure6.99e-08581
embryo1.12e-07592
cell layer2.00e-07309
digestive system3.10e-07145
digestive tract3.10e-07145
primitive gut3.10e-07145
epithelium3.28e-07306
primary circulatory organ3.33e-0727
brain6.21e-0768
future brain6.21e-0768
central nervous system6.60e-0781
subdivision of digestive tract8.25e-07118


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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