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Coexpression cluster:C2863: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003076!1.11e-18!15;UBERON:0003057!1.11e-18!15;UBERON:0000924!1.08e-15!173;UBERON:0006601!1.08e-15!173;UBERON:0004733!1.35e-15!12;UBERON:0002028!1.35e-15!12;UBERON:0007277!1.35e-15!12;UBERON:0004121!6.78e-15!169;UBERON:0004732!3.93e-14!13;UBERON:0000489!4.27e-13!32;UBERON:0002680!5.92e-12!9;UBERON:0001895!5.92e-12!9;UBERON:0010092!5.92e-12!9;UBERON:0004876!8.05e-12!20;UBERON:0000080!9.87e-12!18;UBERON:0002120!9.87e-12!18;UBERON:0004875!9.87e-12!18;UBERON:0005721!9.87e-12!18;UBERON:0005754!9.87e-12!18;UBERON:0007297!9.87e-12!18;UBERON:0006555!8.32e-11!17;UBERON:0005103!8.32e-11!17;UBERON:0000083!8.32e-11!17;UBERON:0009201!8.32e-11!17;UBERON:0004819!8.32e-11!17;UBERON:0006553!8.32e-11!17;UBERON:0003074!8.32e-11!17;UBERON:0003060!8.32e-11!17;UBERON:0002113!2.15e-10!27;UBERON:0003918!2.15e-10!27;UBERON:0005095!2.15e-10!27;UBERON:0007687!2.15e-10!27;UBERON:0009773!1.42e-09!12;UBERON:0001231!1.42e-09!12;UBERON:0004810!1.42e-09!12;UBERON:0004211!1.53e-09!16;UBERON:0001285!1.53e-09!16;UBERON:0007684!1.53e-09!16;UBERON:0003220!1.53e-09!16;UBERON:0004208!1.53e-09!16;UBERON:0003887!1.59e-09!21;UBERON:0001444!5.23e-09!48;UBERON:0002298!9.75e-09!8;UBERON:0002037!1.84e-08!6;UBERON:0006215!1.84e-08!6;UBERON:0000058!2.23e-08!26;UBERON:0003064!5.83e-08!37;UBERON:0000153!7.83e-08!129;UBERON:0007811!7.83e-08!129;UBERON:0000033!1.14e-07!123;UBERON:0002346!1.48e-07!90;UBERON:0001008!1.82e-07!45;UBERON:0003075!6.81e-07!86;UBERON:0007284!6.81e-07!86;UBERON:0006554!6.84e-07!44
|ontology_enrichment_uberon=UBERON:0003076!1.11e-18!15;UBERON:0003057!1.11e-18!15;UBERON:0000924!1.08e-15!173;UBERON:0006601!1.08e-15!173;UBERON:0004733!1.35e-15!12;UBERON:0002028!1.35e-15!12;UBERON:0007277!1.35e-15!12;UBERON:0004121!6.78e-15!169;UBERON:0004732!3.93e-14!13;UBERON:0000489!4.27e-13!32;UBERON:0002680!5.92e-12!9;UBERON:0001895!5.92e-12!9;UBERON:0010092!5.92e-12!9;UBERON:0004876!8.05e-12!20;UBERON:0000080!9.87e-12!18;UBERON:0002120!9.87e-12!18;UBERON:0004875!9.87e-12!18;UBERON:0005721!9.87e-12!18;UBERON:0005754!9.87e-12!18;UBERON:0007297!9.87e-12!18;UBERON:0006555!8.32e-11!17;UBERON:0005103!8.32e-11!17;UBERON:0000083!8.32e-11!17;UBERON:0009201!8.32e-11!17;UBERON:0004819!8.32e-11!17;UBERON:0006553!8.32e-11!17;UBERON:0003074!8.32e-11!17;UBERON:0003060!8.32e-11!17;UBERON:0002113!2.15e-10!27;UBERON:0003918!2.15e-10!27;UBERON:0005095!2.15e-10!27;UBERON:0007687!2.15e-10!27;UBERON:0009773!1.42e-09!12;UBERON:0001231!1.42e-09!12;UBERON:0004810!1.42e-09!12;UBERON:0004211!1.53e-09!16;UBERON:0001285!1.53e-09!16;UBERON:0007684!1.53e-09!16;UBERON:0003220!1.53e-09!16;UBERON:0004208!1.53e-09!16;UBERON:0003887!1.59e-09!21;UBERON:0001444!5.23e-09!48;UBERON:0002298!9.75e-09!8;UBERON:0002037!1.84e-08!6;UBERON:0006215!1.84e-08!6;UBERON:0000058!2.23e-08!26;UBERON:0003064!5.83e-08!37;UBERON:0000153!7.83e-08!129;UBERON:0007811!7.83e-08!129;UBERON:0000033!1.14e-07!123;UBERON:0002346!1.48e-07!90;UBERON:0001008!1.82e-07!45;UBERON:0003075!6.81e-07!86;UBERON:0007284!6.81e-07!86;UBERON:0006554!6.84e-07!44
|tf_chipseq_enrich=EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435212281958445!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000724295606409489!REST#5978;4:9.65002871612802:0.000115282561421917:0.00157509097754364!YY1#7528;4:4.91117074985386:0.0017187183805544:0.0107049874133302
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}}
}}

Revision as of 13:13, 5 September 2012


Full id: C2863_neuroepithelioma_breast_neuroblastoma_merkel_epididymis_neuroectodermal_Trabecular



Phase1 CAGE Peaks

Hg19::chr6:50786547..50786564,+p3@TFAP2B
Hg19::chr6:50786571..50786590,+p2@TFAP2B
Hg19::chr6:50786591..50786614,+p1@TFAP2B
Hg19::chr6:50786631..50786635,+p11@TFAP2B


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
posterior neural tube1.11e-1815
chordal neural plate1.11e-1815
ectoderm1.08e-15173
presumptive ectoderm1.08e-15173
segmental subdivision of hindbrain1.35e-1512
hindbrain1.35e-1512
presumptive hindbrain1.35e-1512
ectoderm-derived structure6.78e-15169
segmental subdivision of nervous system3.93e-1413
cavitated compound organ4.27e-1332
regional part of metencephalon5.92e-129
metencephalon5.92e-129
future metencephalon5.92e-129
urogenital ridge8.05e-1220
mesonephros9.87e-1218
pronephros9.87e-1218
nephrogenic cord9.87e-1218
pronephric mesoderm9.87e-1218
rostral part of nephrogenic cord9.87e-1218
presumptive pronephric mesoderm9.87e-1218
excretory tube8.32e-1117
mesonephric epithelium8.32e-1117
mesonephric tubule8.32e-1117
nephric duct8.32e-1117
kidney epithelium8.32e-1117
renal duct8.32e-1117
mesonephric duct8.32e-1117
pronephric duct8.32e-1117
kidney2.15e-1027
kidney mesenchyme2.15e-1027
kidney rudiment2.15e-1027
kidney field2.15e-1027
renal tubule1.42e-0912
nephron tubule1.42e-0912
nephron tubule epithelium1.42e-0912
nephron epithelium1.53e-0916
nephron1.53e-0916
uriniferous tubule1.53e-0916
metanephric mesenchyme1.53e-0916
nephrogenic mesenchyme1.53e-0916
intraembryonic coelom1.59e-0921
subdivision of head5.23e-0948
brainstem9.75e-098
cerebellum1.84e-086
rhombic lip1.84e-086
duct2.23e-0826
intermediate mesoderm5.83e-0837
anterior region of body7.83e-08129
craniocervical region7.83e-08129
head1.14e-07123
neurectoderm1.48e-0790
renal system1.82e-0745
neural plate6.81e-0786
presumptive neural plate6.81e-0786
urinary system structure6.84e-0744


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#203346.77394172622320.0004748459821442640.00435212281958445
GATA2#2624412.7449317335543.78864877853583e-050.000724295606409489
REST#597849.650028716128020.0001152825614219170.00157509097754364
YY1#752844.911170749853860.00171871838055440.0107049874133302



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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