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Coexpression cluster:C1456: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!8.91e-18!57;UBERON:0005068!8.91e-18!57;UBERON:0006241!8.91e-18!57;UBERON:0007135!8.91e-18!57;UBERON:0001869!1.98e-17!32;UBERON:0002020!6.18e-17!34;UBERON:0003528!6.18e-17!34;UBERON:0002616!3.97e-16!59;UBERON:0001893!4.47e-16!34;UBERON:0002791!1.73e-15!33;UBERON:0005743!2.01e-15!86;UBERON:0001017!2.07e-15!82;UBERON:0002619!6.07e-15!22;UBERON:0000956!1.92e-14!25;UBERON:0000203!1.92e-14!25;UBERON:0002780!7.02e-14!41;UBERON:0001890!7.02e-14!41;UBERON:0006240!7.02e-14!41;UBERON:0001950!1.01e-13!20;UBERON:0003075!1.20e-13!86;UBERON:0007284!1.20e-13!86;UBERON:0003080!1.91e-13!42;UBERON:0000955!4.43e-13!69;UBERON:0006238!4.43e-13!69;UBERON:0002346!2.41e-12!90;UBERON:0000119!6.81e-12!312;UBERON:0000483!1.16e-11!309;UBERON:0007023!1.62e-11!115;UBERON:0000073!2.60e-11!94;UBERON:0001016!2.60e-11!94;UBERON:0003056!4.26e-11!61;UBERON:0000477!1.99e-09!286;UBERON:0000025!5.51e-09!194;UBERON:0000475!5.70e-09!365;UBERON:0004111!1.42e-08!241;UBERON:0000033!5.20e-08!123;UBERON:0000153!2.02e-07!129;UBERON:0007811!2.02e-07!129
|ontology_enrichment_uberon=UBERON:0001049!1.08e-17!56;UBERON:0005068!1.08e-17!56;UBERON:0006241!1.08e-17!56;UBERON:0007135!1.08e-17!56;UBERON:0000073!1.45e-17!53;UBERON:0002616!1.45e-17!53;UBERON:0001869!3.21e-17!32;UBERON:0003528!1.13e-16!34;UBERON:0002020!1.13e-16!34;UBERON:0001893!7.71e-16!34;UBERON:0002791!9.66e-16!32;UBERON:0001017!2.68e-15!81;UBERON:0002619!8.15e-15!22;UBERON:0003075!3.70e-14!82;UBERON:0007284!3.70e-14!82;UBERON:0000956!4.75e-14!25;UBERON:0000203!4.75e-14!25;UBERON:0001950!1.25e-13!20;UBERON:0002780!1.57e-13!41;UBERON:0001890!1.57e-13!41;UBERON:0003080!1.57e-13!41;UBERON:0006240!1.57e-13!41;UBERON:0000955!7.24e-13!68;UBERON:0006238!7.24e-13!68;UBERON:0002346!8.77e-13!86;UBERON:0010371!1.39e-11!104;UBERON:0007023!3.16e-11!114;UBERON:0001016!4.31e-11!89;UBERON:0000119!9.48e-11!309;UBERON:0003056!1.08e-10!61;UBERON:0000483!1.81e-10!306;UBERON:0010314!3.10e-10!132;UBERON:0000477!1.00e-07!373;UBERON:0004111!1.03e-07!240;UBERON:0000025!1.13e-07!192;UBERON:0000481!3.87e-07!342;UBERON:0004121!7.72e-07!171;UBERON:0000924!7.72e-07!171;UBERON:0006601!7.72e-07!171
|tf_chipseq_enrich=POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380350556923406
|tf_chipseq_enrich=POLR2A#5430;6:2.14745317655807:0.0101957067681878:0.0380350556923406
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}}
}}

Revision as of 11:18, 19 October 2012


Full id: C1456_medial_amygdala_brain_hippocampus_occipital_putamen_parietal



Phase1 CAGE Peaks

Hg19::chr19:47113203..47113232,+p@chr19:47113203..47113232
+
Hg19::chr19:47113300..47113328,+p@chr19:47113300..47113328
+
Hg19::chr19:47113368..47113396,+p@chr19:47113368..47113396
+
Hg19::chr19:47113445..47113466,+p@chr19:47113445..47113466
+
Hg19::chr19:47113473..47113571,+p@chr19:47113473..47113571
+
Hg19::chr19:47113683..47113695,+p@chr19:47113683..47113695
+


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
neural tube1.08e-1756
neural rod1.08e-1756
future spinal cord1.08e-1756
neural keel1.08e-1756
regional part of nervous system1.45e-1753
regional part of brain1.45e-1753
cerebral hemisphere3.21e-1732
brain grey matter1.13e-1634
gray matter1.13e-1634
telencephalon7.71e-1634
regional part of telencephalon9.66e-1632
central nervous system2.68e-1581
regional part of cerebral cortex8.15e-1522
neural plate3.70e-1482
presumptive neural plate3.70e-1482
cerebral cortex4.75e-1425
pallium4.75e-1425
neocortex1.25e-1320
regional part of forebrain1.57e-1341
forebrain1.57e-1341
anterior neural tube1.57e-1341
future forebrain1.57e-1341
brain7.24e-1368
future brain7.24e-1368
neurectoderm8.77e-1386
ecto-epithelium1.39e-11104
adult organism3.16e-11114
nervous system4.31e-1189
cell layer9.48e-11309
pre-chordal neural plate1.08e-1061
epithelium1.81e-10306
structure with developmental contribution from neural crest3.10e-10132
anatomical cluster1.00e-07373
anatomical conduit1.03e-07240
tube1.13e-07192
multi-tissue structure3.87e-07342
ectoderm-derived structure7.72e-07171
ectoderm7.72e-07171
presumptive ectoderm7.72e-07171


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
POLR2A#543062.147453176558070.01019570676818780.0380350556923406



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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