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Coexpression cluster:C2465: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.57e-37!115;UBERON:0001049!9.85e-26!57;UBERON:0005068!9.85e-26!57;UBERON:0006241!9.85e-26!57;UBERON:0007135!9.85e-26!57;UBERON:0000073!1.66e-24!94;UBERON:0001016!1.66e-24!94;UBERON:0001017!9.41e-24!82;UBERON:0000924!4.98e-22!173;UBERON:0006601!4.98e-22!173;UBERON:0005743!7.45e-22!86;UBERON:0004121!5.07e-21!169;UBERON:0000955!3.33e-20!69;UBERON:0006238!3.33e-20!69;UBERON:0002616!6.21e-20!59;UBERON:0003080!1.27e-19!42;UBERON:0002780!4.81e-19!41;UBERON:0001890!4.81e-19!41;UBERON:0006240!4.81e-19!41;UBERON:0002346!8.48e-19!90;UBERON:0003075!8.06e-18!86;UBERON:0007284!8.06e-18!86;UBERON:0000153!9.23e-18!129;UBERON:0007811!9.23e-18!129;UBERON:0000033!1.03e-16!123;UBERON:0001893!2.13e-16!34;UBERON:0002020!5.36e-16!34;UBERON:0003528!5.36e-16!34;UBERON:0002791!7.42e-16!33;UBERON:0001869!2.90e-15!32;UBERON:0000475!3.64e-13!365;UBERON:0000956!2.50e-12!25;UBERON:0000203!2.50e-12!25;UBERON:0002619!2.62e-12!22;UBERON:0001950!1.06e-11!20;UBERON:0004111!1.94e-11!241;UBERON:0003056!2.12e-11!61;UBERON:0000468!2.23e-10!659;UBERON:0000467!2.72e-09!625;UBERON:0000480!3.86e-09!626;UBERON:0000477!1.13e-08!286;UBERON:0003076!2.68e-07!15;UBERON:0003057!2.68e-07!15;UBERON:0000483!3.97e-07!309;UBERON:0000025!4.64e-07!194
|ontology_enrichment_uberon=UBERON:0007023!2.18e-40!114;UBERON:0001016!4.91e-28!89;UBERON:0001049!8.80e-26!56;UBERON:0005068!8.80e-26!56;UBERON:0006241!8.80e-26!56;UBERON:0007135!8.80e-26!56;UBERON:0001017!1.77e-24!81;UBERON:0000073!5.62e-24!53;UBERON:0002616!5.62e-24!53;UBERON:0004121!1.21e-22!171;UBERON:0000924!1.21e-22!171;UBERON:0006601!1.21e-22!171;UBERON:0000955!5.71e-20!68;UBERON:0006238!5.71e-20!68;UBERON:0002346!1.51e-19!86;UBERON:0011216!2.38e-19!223;UBERON:0002780!2.97e-19!41;UBERON:0001890!2.97e-19!41;UBERON:0003080!2.97e-19!41;UBERON:0006240!2.97e-19!41;UBERON:0003075!2.20e-18!82;UBERON:0007284!2.20e-18!82;UBERON:0010371!5.85e-17!104;UBERON:0001893!6.07e-17!34;UBERON:0003528!1.45e-16!34;UBERON:0002020!1.45e-16!34;UBERON:0002791!1.16e-15!32;UBERON:0001869!1.22e-15!32;UBERON:0010314!7.44e-14!132;UBERON:0000477!9.55e-14!373;UBERON:0002619!9.97e-13!22;UBERON:0000956!1.66e-12!25;UBERON:0000203!1.66e-12!25;UBERON:0001950!6.58e-12!20;UBERON:0003056!1.57e-11!61;UBERON:0000468!3.06e-10!656;UBERON:0004111!3.03e-09!240;UBERON:0000467!2.38e-08!624;UBERON:0000480!3.10e-08!625;UBERON:0003076!1.04e-07!15;UBERON:0003057!1.04e-07!15;UBERON:0004732!9.56e-07!13
|tf_chipseq_enrich=EP300#2033;3:5.0804562946674:0.0114429840539824:0.0418934276865379
|tf_chipseq_enrich=EP300#2033;3:5.0804562946674:0.0114429840539824:0.0418934276865379
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}}
}}

Revision as of 14:03, 19 October 2012


Full id: C2465_small_peripheral_acute_lymphoma_diffuse_Neural_merkel



Phase1 CAGE Peaks

Hg19::chr18:53089453..53089482,-p11@TCF4
Hg19::chr18:53089493..53089517,-p15@TCF4
Hg19::chr18:53089521..53089533,-p22@TCF4
Hg19::chr18:53089538..53089578,-p14@TCF4


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism2.18e-40114
nervous system4.91e-2889
neural tube8.80e-2656
neural rod8.80e-2656
future spinal cord8.80e-2656
neural keel8.80e-2656
central nervous system1.77e-2481
regional part of nervous system5.62e-2453
regional part of brain5.62e-2453
ectoderm-derived structure1.21e-22171
ectoderm1.21e-22171
presumptive ectoderm1.21e-22171
brain5.71e-2068
future brain5.71e-2068
neurectoderm1.51e-1986
organ system subdivision2.38e-19223
regional part of forebrain2.97e-1941
forebrain2.97e-1941
anterior neural tube2.97e-1941
future forebrain2.97e-1941
neural plate2.20e-1882
presumptive neural plate2.20e-1882
ecto-epithelium5.85e-17104
telencephalon6.07e-1734
brain grey matter1.45e-1634
gray matter1.45e-1634
regional part of telencephalon1.16e-1532
cerebral hemisphere1.22e-1532
structure with developmental contribution from neural crest7.44e-14132
anatomical cluster9.55e-14373
regional part of cerebral cortex9.97e-1322
cerebral cortex1.66e-1225
pallium1.66e-1225
neocortex6.58e-1220
pre-chordal neural plate1.57e-1161
multi-cellular organism3.06e-10656
anatomical conduit3.03e-09240
anatomical system2.38e-08624
anatomical group3.10e-08625
posterior neural tube1.04e-0715
chordal neural plate1.04e-0715
segmental subdivision of nervous system9.56e-0713


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#203335.08045629466740.01144298405398240.0418934276865379



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.