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Coexpression cluster:C4543: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!2.78e-23!89;UBERON:0001017!2.07e-22!81;UBERON:0001049!4.98e-20!56;UBERON:0005068!4.98e-20!56;UBERON:0006241!4.98e-20!56;UBERON:0007135!4.98e-20!56;UBERON:0000073!8.18e-19!53;UBERON:0002616!8.18e-19!53;UBERON:0004121!7.90e-18!171;UBERON:0000924!7.90e-18!171;UBERON:0006601!7.90e-18!171;UBERON:0002346!3.49e-17!86;UBERON:0000955!6.88e-17!68;UBERON:0006238!6.88e-17!68;UBERON:0001893!1.32e-16!34;UBERON:0003528!3.14e-16!34;UBERON:0002020!3.14e-16!34;UBERON:0002780!5.32e-16!41;UBERON:0001890!5.32e-16!41;UBERON:0003080!5.32e-16!41;UBERON:0006240!5.32e-16!41;UBERON:0001869!1.01e-15!32;UBERON:0002791!1.17e-15!32;UBERON:0010371!3.68e-15!104;UBERON:0003075!4.41e-15!82;UBERON:0007284!4.41e-15!82;UBERON:0002619!2.14e-14!22;UBERON:0000956!9.80e-14!25;UBERON:0000203!9.80e-14!25;UBERON:0001950!4.36e-13!20;UBERON:0003056!1.84e-12!61;UBERON:0011216!3.31e-11!223;UBERON:0010314!9.71e-11!132;UBERON:0000477!3.17e-07!373
|ontology_enrichment_uberon=UBERON:0001016!2.78e-23!89;UBERON:0001017!2.07e-22!81;UBERON:0001049!4.98e-20!56;UBERON:0005068!4.98e-20!56;UBERON:0006241!4.98e-20!56;UBERON:0007135!4.98e-20!56;UBERON:0000073!8.18e-19!53;UBERON:0002616!8.18e-19!53;UBERON:0004121!7.90e-18!171;UBERON:0000924!7.90e-18!171;UBERON:0006601!7.90e-18!171;UBERON:0002346!3.49e-17!86;UBERON:0000955!6.88e-17!68;UBERON:0006238!6.88e-17!68;UBERON:0001893!1.32e-16!34;UBERON:0003528!3.14e-16!34;UBERON:0002020!3.14e-16!34;UBERON:0002780!5.32e-16!41;UBERON:0001890!5.32e-16!41;UBERON:0003080!5.32e-16!41;UBERON:0006240!5.32e-16!41;UBERON:0001869!1.01e-15!32;UBERON:0002791!1.17e-15!32;UBERON:0010371!3.68e-15!104;UBERON:0003075!4.41e-15!82;UBERON:0007284!4.41e-15!82;UBERON:0002619!2.14e-14!22;UBERON:0000956!9.80e-14!25;UBERON:0000203!9.80e-14!25;UBERON:0001950!4.36e-13!20;UBERON:0003056!1.84e-12!61;UBERON:0011216!3.31e-11!223;UBERON:0010314!9.71e-11!132;UBERON:0000477!3.17e-07!373
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}}
}}

Revision as of 16:48, 26 November 2012


Full id: C4543_peripheral_neuroectodermal_parietal_medial_temporal_occipital_amygdala



Phase1 CAGE Peaks

Hg19::chr6:110423031..110423054,-p2@AK056044
Hg19::chr6:110423315..110423359,-p1@AK056044
Hg19::chr6:110424638..110424673,-p@chr6:110424638..110424673
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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
nervous system2.78e-2389
central nervous system2.07e-2281
neural tube4.98e-2056
neural rod4.98e-2056
future spinal cord4.98e-2056
neural keel4.98e-2056
regional part of nervous system8.18e-1953
regional part of brain8.18e-1953
ectoderm-derived structure7.90e-18171
ectoderm7.90e-18171
presumptive ectoderm7.90e-18171
neurectoderm3.49e-1786
brain6.88e-1768
future brain6.88e-1768
telencephalon1.32e-1634
brain grey matter3.14e-1634
gray matter3.14e-1634
regional part of forebrain5.32e-1641
forebrain5.32e-1641
anterior neural tube5.32e-1641
future forebrain5.32e-1641
cerebral hemisphere1.01e-1532
regional part of telencephalon1.17e-1532
ecto-epithelium3.68e-15104
neural plate4.41e-1582
presumptive neural plate4.41e-1582
regional part of cerebral cortex2.14e-1422
cerebral cortex9.80e-1425
pallium9.80e-1425
neocortex4.36e-1320
pre-chordal neural plate1.84e-1261
organ system subdivision3.31e-11223
structure with developmental contribution from neural crest9.71e-11132
anatomical cluster3.17e-07373


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)

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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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