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Coexpression cluster:C3204: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!3.78e-35!94;UBERON:0001016!3.78e-35!94;UBERON:0001017!4.36e-34!82;UBERON:0005743!1.53e-33!86;UBERON:0001049!1.59e-32!57;UBERON:0005068!1.59e-32!57;UBERON:0006241!1.59e-32!57;UBERON:0007135!1.59e-32!57;UBERON:0002616!3.96e-29!59;UBERON:0003075!8.59e-29!86;UBERON:0007284!8.59e-29!86;UBERON:0002346!2.58e-27!90;UBERON:0002780!5.35e-27!41;UBERON:0001890!5.35e-27!41;UBERON:0006240!5.35e-27!41;UBERON:0000955!7.56e-27!69;UBERON:0006238!7.56e-27!69;UBERON:0003080!6.46e-26!42;UBERON:0004121!2.66e-25!169;UBERON:0002020!8.95e-25!34;UBERON:0003528!8.95e-25!34;UBERON:0000924!1.36e-24!173;UBERON:0006601!1.36e-24!173;UBERON:0001893!1.52e-24!34;UBERON:0002791!7.61e-24!33;UBERON:0001869!1.08e-23!32;UBERON:0003056!2.70e-23!61;UBERON:0000153!6.39e-21!129;UBERON:0007811!6.39e-21!129;UBERON:0000956!1.27e-20!25;UBERON:0000203!1.27e-20!25;UBERON:0000033!1.74e-20!123;UBERON:0002619!1.98e-18!22;UBERON:0007023!1.15e-17!115;UBERON:0001950!1.02e-16!20;UBERON:0000475!9.02e-11!365;UBERON:0003076!8.44e-08!15;UBERON:0003057!8.44e-08!15;UBERON:0001871!3.04e-07!7;UBERON:0000119!9.73e-07!312
|ontology_enrichment_uberon=UBERON:0001049!1.27e-34!56;UBERON:0005068!1.27e-34!56;UBERON:0006241!1.27e-34!56;UBERON:0007135!1.27e-34!56;UBERON:0001016!2.29e-32!89;UBERON:0000073!4.18e-31!53;UBERON:0002616!4.18e-31!53;UBERON:0001017!9.74e-30!81;UBERON:0003075!1.16e-29!82;UBERON:0007284!1.16e-29!82;UBERON:0002780!8.31e-29!41;UBERON:0001890!8.31e-29!41;UBERON:0003080!8.31e-29!41;UBERON:0006240!8.31e-29!41;UBERON:0002346!1.12e-28!86;UBERON:0000955!2.21e-26!68;UBERON:0006238!2.21e-26!68;UBERON:0010371!1.00e-25!104;UBERON:0001893!1.15e-25!34;UBERON:0003528!1.22e-25!34;UBERON:0002020!1.22e-25!34;UBERON:0003056!2.77e-25!61;UBERON:0001869!3.44e-24!32;UBERON:0002791!8.95e-24!32;UBERON:0004121!1.06e-23!171;UBERON:0000924!1.06e-23!171;UBERON:0006601!1.06e-23!171;UBERON:0010314!1.19e-23!132;UBERON:0000956!2.71e-20!25;UBERON:0000203!2.71e-20!25;UBERON:0002619!3.54e-19!22;UBERON:0007023!2.90e-17!114;UBERON:0001950!1.09e-16!20;UBERON:0011216!6.75e-12!223;UBERON:0002298!8.06e-08!6;UBERON:0000349!8.36e-08!5;UBERON:0002420!2.74e-07!9;UBERON:0007245!2.74e-07!9;UBERON:0010009!2.74e-07!9;UBERON:0010011!2.74e-07!9;UBERON:0000454!2.74e-07!9;UBERON:0000064!2.87e-07!218;UBERON:0003076!3.00e-07!15;UBERON:0003057!3.00e-07!15;UBERON:0001871!3.61e-07!6;UBERON:0000922!5.29e-07!592;UBERON:0000125!8.11e-07!9;UBERON:0002308!8.11e-07!9
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}}
}}

Revision as of 14:53, 19 October 2012


Full id: C3204_brain_non_parietal_temporal_duodenum_occipital_thalamus



Phase1 CAGE Peaks

Hg19::chr11:79032682..79032686,-p@chr11:79032682..79032686
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Hg19::chr11:79081820..79081824,-p@chr11:79081820..79081824
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Hg19::chr11:79109778..79109782,-p@chr11:79109778..79109782
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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 tube1.27e-3456
neural rod1.27e-3456
future spinal cord1.27e-3456
neural keel1.27e-3456
nervous system2.29e-3289
regional part of nervous system4.18e-3153
regional part of brain4.18e-3153
central nervous system9.74e-3081
neural plate1.16e-2982
presumptive neural plate1.16e-2982
regional part of forebrain8.31e-2941
forebrain8.31e-2941
anterior neural tube8.31e-2941
future forebrain8.31e-2941
neurectoderm1.12e-2886
brain2.21e-2668
future brain2.21e-2668
ecto-epithelium1.00e-25104
telencephalon1.15e-2534
brain grey matter1.22e-2534
gray matter1.22e-2534
pre-chordal neural plate2.77e-2561
cerebral hemisphere3.44e-2432
regional part of telencephalon8.95e-2432
ectoderm-derived structure1.06e-23171
ectoderm1.06e-23171
presumptive ectoderm1.06e-23171
structure with developmental contribution from neural crest1.19e-23132
cerebral cortex2.71e-2025
pallium2.71e-2025
regional part of cerebral cortex3.54e-1922
adult organism2.90e-17114
neocortex1.09e-1620
organ system subdivision6.75e-12223
brainstem8.06e-086
limbic system8.36e-085
basal ganglion2.74e-079
nuclear complex of neuraxis2.74e-079
aggregate regional part of brain2.74e-079
collection of basal ganglia2.74e-079
cerebral subcortex2.74e-079
organ part2.87e-07218
posterior neural tube3.00e-0715
chordal neural plate3.00e-0715
temporal lobe3.61e-076
embryo5.29e-07592
neural nucleus8.11e-079
nucleus of brain8.11e-079


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

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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