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Coexpression cluster:C4581: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!4.09e-30!115;UBERON:0000477!1.07e-18!286;UBERON:0002616!5.62e-16!59;UBERON:0001017!8.83e-16!82;UBERON:0003075!1.15e-15!86;UBERON:0007284!1.15e-15!86;UBERON:0001049!1.18e-15!57;UBERON:0005068!1.18e-15!57;UBERON:0006241!1.18e-15!57;UBERON:0007135!1.18e-15!57;UBERON:0005743!1.39e-15!86;UBERON:0002346!2.20e-14!90;UBERON:0000153!2.73e-14!129;UBERON:0007811!2.73e-14!129;UBERON:0004111!2.83e-14!241;UBERON:0000119!3.10e-14!312;UBERON:0000955!7.43e-14!69;UBERON:0006238!7.43e-14!69;UBERON:0000025!1.70e-13!194;UBERON:0000073!6.76e-13!94;UBERON:0001016!6.76e-13!94;UBERON:0000483!7.36e-13!309;UBERON:0000033!1.80e-12!123;UBERON:0003103!8.72e-11!69;UBERON:0000481!4.34e-10!347;UBERON:0004121!5.87e-10!169;UBERON:0000475!8.55e-10!365;UBERON:0003080!1.53e-09!42;UBERON:0000924!2.25e-09!173;UBERON:0006601!2.25e-09!173;UBERON:0009773!3.31e-09!12;UBERON:0001231!3.31e-09!12;UBERON:0004810!3.31e-09!12;UBERON:0002780!6.59e-09!41;UBERON:0001890!6.59e-09!41;UBERON:0006240!6.59e-09!41;UBERON:0002298!6.91e-09!8;UBERON:0003056!2.15e-08!61;UBERON:0000489!3.26e-08!32;UBERON:0003076!5.43e-08!15;UBERON:0003057!5.43e-08!15;UBERON:0004905!1.33e-07!5;UBERON:0000982!1.33e-07!5;UBERON:0004770!1.33e-07!5;UBERON:0005174!2.35e-07!5;UBERON:0001137!2.35e-07!5;UBERON:0006555!7.62e-07!17;UBERON:0005103!7.62e-07!17;UBERON:0000083!7.62e-07!17;UBERON:0009201!7.62e-07!17;UBERON:0004819!7.62e-07!17;UBERON:0006553!7.62e-07!17;UBERON:0003074!7.62e-07!17;UBERON:0003060!7.62e-07!17
|ontology_enrichment_uberon=UBERON:0007023!4.09e-30!115;UBERON:0000477!1.07e-18!286;UBERON:0002616!5.62e-16!59;UBERON:0001017!8.83e-16!82;UBERON:0003075!1.15e-15!86;UBERON:0007284!1.15e-15!86;UBERON:0001049!1.18e-15!57;UBERON:0005068!1.18e-15!57;UBERON:0006241!1.18e-15!57;UBERON:0007135!1.18e-15!57;UBERON:0005743!1.39e-15!86;UBERON:0002346!2.20e-14!90;UBERON:0000153!2.73e-14!129;UBERON:0007811!2.73e-14!129;UBERON:0004111!2.83e-14!241;UBERON:0000119!3.10e-14!312;UBERON:0000955!7.43e-14!69;UBERON:0006238!7.43e-14!69;UBERON:0000025!1.70e-13!194;UBERON:0000073!6.76e-13!94;UBERON:0001016!6.76e-13!94;UBERON:0000483!7.36e-13!309;UBERON:0000033!1.80e-12!123;UBERON:0003103!8.72e-11!69;UBERON:0000481!4.34e-10!347;UBERON:0004121!5.87e-10!169;UBERON:0000475!8.55e-10!365;UBERON:0003080!1.53e-09!42;UBERON:0000924!2.25e-09!173;UBERON:0006601!2.25e-09!173;UBERON:0009773!3.31e-09!12;UBERON:0001231!3.31e-09!12;UBERON:0004810!3.31e-09!12;UBERON:0002780!6.59e-09!41;UBERON:0001890!6.59e-09!41;UBERON:0006240!6.59e-09!41;UBERON:0002298!6.91e-09!8;UBERON:0003056!2.15e-08!61;UBERON:0000489!3.26e-08!32;UBERON:0003076!5.43e-08!15;UBERON:0003057!5.43e-08!15;UBERON:0004905!1.33e-07!5;UBERON:0000982!1.33e-07!5;UBERON:0004770!1.33e-07!5;UBERON:0005174!2.35e-07!5;UBERON:0001137!2.35e-07!5;UBERON:0006555!7.62e-07!17;UBERON:0005103!7.62e-07!17;UBERON:0000083!7.62e-07!17;UBERON:0009201!7.62e-07!17;UBERON:0004819!7.62e-07!17;UBERON:0006553!7.62e-07!17;UBERON:0003074!7.62e-07!17;UBERON:0003060!7.62e-07!17
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115696157267988!MAFK#7975;3:27.1007331378299:5.02195559325033e-05:0.000859112236205523
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}}
}}

Revision as of 13:09, 5 September 2012


Full id: C4581_Chondrocyte_salivary_submaxillary_parotid_dura_aorta_retina



Phase1 CAGE Peaks

Hg19::chr6:1626414..1626429,-p7@GMDS
Hg19::chr6:1626436..1626467,-p4@GMDS
Hg19::chr6:1626471..1626487,-p9@GMDS


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><br>

Uber Anatomy
Ontology termp-valuen
adult organism4.09e-30115
anatomical cluster1.07e-18286
regional part of brain5.62e-1659
central nervous system8.83e-1682
neural plate1.15e-1586
presumptive neural plate1.15e-1586
neural tube1.18e-1557
neural rod1.18e-1557
future spinal cord1.18e-1557
neural keel1.18e-1557
neurectoderm2.20e-1490
anterior region of body2.73e-14129
craniocervical region2.73e-14129
anatomical conduit2.83e-14241
cell layer3.10e-14312
brain7.43e-1469
future brain7.43e-1469
tube1.70e-13194
regional part of nervous system6.76e-1394
nervous system6.76e-1394
epithelium7.36e-13309
head1.80e-12123
compound organ8.72e-1169
multi-tissue structure4.34e-10347
ectoderm-derived structure5.87e-10169
organism subdivision8.55e-10365
anterior neural tube1.53e-0942
ectoderm2.25e-09173
presumptive ectoderm2.25e-09173
renal tubule3.31e-0912
nephron tubule3.31e-0912
nephron tubule epithelium3.31e-0912
regional part of forebrain6.59e-0941
forebrain6.59e-0941
future forebrain6.59e-0941
brainstem6.91e-098
pre-chordal neural plate2.15e-0861
cavitated compound organ3.26e-0832
posterior neural tube5.43e-0815
chordal neural plate5.43e-0815
articulation1.33e-075
skeletal joint1.33e-075
articular system1.33e-075
dorsal region element2.35e-075
dorsum2.35e-075
excretory tube7.62e-0717
mesonephric epithelium7.62e-0717
mesonephric tubule7.62e-0717
nephric duct7.62e-0717
kidney epithelium7.62e-0717
renal duct7.62e-0717
mesonephric duct7.62e-0717
pronephric duct7.62e-0717


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
CEBPB#105137.971147625824820.001974187055288560.0115696157267988
MAFK#7975327.10073313782995.02195559325033e-050.000859112236205523



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4581&oldid=2131944"