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Coexpression cluster:C2753: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!5.12e-32!89;UBERON:0001017!1.37e-31!81;UBERON:0001049!2.95e-27!56;UBERON:0005068!2.95e-27!56;UBERON:0006241!2.95e-27!56;UBERON:0007135!2.95e-27!56;UBERON:0000073!1.26e-25!53;UBERON:0002616!1.26e-25!53;UBERON:0011216!3.53e-25!223;UBERON:0004121!4.51e-25!171;UBERON:0000924!4.51e-25!171;UBERON:0006601!4.51e-25!171;UBERON:0000955!6.82e-24!68;UBERON:0006238!6.82e-24!68;UBERON:0002346!2.00e-23!86;UBERON:0002780!7.88e-21!41;UBERON:0001890!7.88e-21!41;UBERON:0003080!7.88e-21!41;UBERON:0006240!7.88e-21!41;UBERON:0003528!2.69e-20!34;UBERON:0002020!2.69e-20!34;UBERON:0001869!2.87e-20!32;UBERON:0001893!3.10e-20!34;UBERON:0003075!1.38e-19!82;UBERON:0007284!1.38e-19!82;UBERON:0002791!1.83e-18!32;UBERON:0010371!7.22e-18!104;UBERON:0007023!2.06e-16!114;UBERON:0003056!1.21e-14!61;UBERON:0010314!5.52e-14!132;UBERON:0000956!3.66e-13!25;UBERON:0000203!3.66e-13!25;UBERON:0002619!3.72e-12!22;UBERON:0001950!4.00e-12!20;UBERON:0000477!1.26e-10!373;UBERON:0000125!5.56e-09!9;UBERON:0002308!5.56e-09!9;UBERON:0000064!1.82e-08!218;UBERON:0003076!1.33e-07!15;UBERON:0003057!1.33e-07!15;UBERON:0002420!3.63e-07!9;UBERON:0007245!3.63e-07!9;UBERON:0010009!3.63e-07!9;UBERON:0010011!3.63e-07!9;UBERON:0000454!3.63e-07!9;UBERON:0009663!4.56e-07!7
|ontology_enrichment_uberon=UBERON:0001016!5.12e-32!89;UBERON:0001017!1.37e-31!81;UBERON:0001049!2.95e-27!56;UBERON:0005068!2.95e-27!56;UBERON:0006241!2.95e-27!56;UBERON:0007135!2.95e-27!56;UBERON:0000073!1.26e-25!53;UBERON:0002616!1.26e-25!53;UBERON:0011216!3.53e-25!223;UBERON:0004121!4.51e-25!171;UBERON:0000924!4.51e-25!171;UBERON:0006601!4.51e-25!171;UBERON:0000955!6.82e-24!68;UBERON:0006238!6.82e-24!68;UBERON:0002346!2.00e-23!86;UBERON:0002780!7.88e-21!41;UBERON:0001890!7.88e-21!41;UBERON:0003080!7.88e-21!41;UBERON:0006240!7.88e-21!41;UBERON:0003528!2.69e-20!34;UBERON:0002020!2.69e-20!34;UBERON:0001869!2.87e-20!32;UBERON:0001893!3.10e-20!34;UBERON:0003075!1.38e-19!82;UBERON:0007284!1.38e-19!82;UBERON:0002791!1.83e-18!32;UBERON:0010371!7.22e-18!104;UBERON:0007023!2.06e-16!114;UBERON:0003056!1.21e-14!61;UBERON:0010314!5.52e-14!132;UBERON:0000956!3.66e-13!25;UBERON:0000203!3.66e-13!25;UBERON:0002619!3.72e-12!22;UBERON:0001950!4.00e-12!20;UBERON:0000477!1.26e-10!373;UBERON:0000125!5.56e-09!9;UBERON:0002308!5.56e-09!9;UBERON:0000064!1.82e-08!218;UBERON:0003076!1.33e-07!15;UBERON:0003057!1.33e-07!15;UBERON:0002420!3.63e-07!9;UBERON:0007245!3.63e-07!9;UBERON:0010009!3.63e-07!9;UBERON:0010011!3.63e-07!9;UBERON:0000454!3.63e-07!9;UBERON:0009663!4.56e-07!7
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}}
}}

Revision as of 15:42, 26 November 2012


Full id: C2753_parietal_acute_occipital_temporal_small_duodenum_gastric



Phase1 CAGE Peaks

Hg19::chr3:77088920..77088929,+p19@ROBO2
Hg19::chr3:77088946..77088957,+p11@ROBO2
Hg19::chr3:77088958..77088982,+p2@ROBO2
Hg19::chr3:77245493..77245496,+p@chr3:77245493..77245496
+


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>disease_data<br>

Cell Type
Ontology termp-valuen
neuronal stem cell2.62e-078
Uber Anatomy
Ontology termp-valuen
nervous system5.12e-3289
central nervous system1.37e-3181
neural tube2.95e-2756
neural rod2.95e-2756
future spinal cord2.95e-2756
neural keel2.95e-2756
regional part of nervous system1.26e-2553
regional part of brain1.26e-2553
organ system subdivision3.53e-25223
ectoderm-derived structure4.51e-25171
ectoderm4.51e-25171
presumptive ectoderm4.51e-25171
brain6.82e-2468
future brain6.82e-2468
neurectoderm2.00e-2386
regional part of forebrain7.88e-2141
forebrain7.88e-2141
anterior neural tube7.88e-2141
future forebrain7.88e-2141
brain grey matter2.69e-2034
gray matter2.69e-2034
cerebral hemisphere2.87e-2032
telencephalon3.10e-2034
neural plate1.38e-1982
presumptive neural plate1.38e-1982
regional part of telencephalon1.83e-1832
ecto-epithelium7.22e-18104
adult organism2.06e-16114
pre-chordal neural plate1.21e-1461
structure with developmental contribution from neural crest5.52e-14132
cerebral cortex3.66e-1325
pallium3.66e-1325
regional part of cerebral cortex3.72e-1222
neocortex4.00e-1220
anatomical cluster1.26e-10373
neural nucleus5.56e-099
nucleus of brain5.56e-099
organ part1.82e-08218
posterior neural tube1.33e-0715
chordal neural plate1.33e-0715
basal ganglion3.63e-079
nuclear complex of neuraxis3.63e-079
aggregate regional part of brain3.63e-079
collection of basal ganglia3.63e-079
cerebral subcortex3.63e-079
telencephalic nucleus4.56e-077
Disease
Ontology termp-valuen
neuroectodermal tumor5.60e-0810


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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