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Coexpression cluster:C3579: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002346!1.66e-49!86;UBERON:0001049!5.01e-48!56;UBERON:0005068!5.01e-48!56;UBERON:0006241!5.01e-48!56;UBERON:0007135!5.01e-48!56;UBERON:0003075!1.45e-44!82;UBERON:0007284!1.45e-44!82;UBERON:0000073!2.04e-44!53;UBERON:0002616!2.04e-44!53;UBERON:0001017!2.34e-44!81;UBERON:0001016!1.11e-43!89;UBERON:0002780!1.81e-42!41;UBERON:0001890!1.81e-42!41;UBERON:0003080!1.81e-42!41;UBERON:0006240!1.81e-42!41;UBERON:0003528!7.08e-42!34;UBERON:0002020!7.08e-42!34;UBERON:0001893!1.67e-41!34;UBERON:0003056!4.76e-41!61;UBERON:0002791!2.81e-39!32;UBERON:0001869!3.51e-39!32;UBERON:0000955!3.39e-36!68;UBERON:0006238!3.39e-36!68;UBERON:0010371!1.14e-32!104;UBERON:0000956!1.07e-29!25;UBERON:0000203!1.07e-29!25;UBERON:0004121!4.84e-29!171;UBERON:0000924!4.84e-29!171;UBERON:0006601!4.84e-29!171;UBERON:0010314!3.92e-27!132;UBERON:0002619!1.00e-26!22;UBERON:0001950!8.03e-24!20;UBERON:0007023!4.22e-18!114;UBERON:0002420!4.66e-14!9;UBERON:0007245!4.66e-14!9;UBERON:0010009!4.66e-14!9;UBERON:0010011!4.66e-14!9;UBERON:0000454!4.66e-14!9;UBERON:0000125!1.53e-13!9;UBERON:0002308!1.53e-13!9;UBERON:0011216!1.79e-12!223;UBERON:0009663!4.82e-11!7;UBERON:0000025!5.50e-11!192;UBERON:0000200!1.90e-09!6;UBERON:0000349!5.97e-09!5;UBERON:0000477!7.19e-09!373;UBERON:0001871!2.22e-08!6;UBERON:0004111!5.20e-08!240;UBERON:0001872!5.40e-08!5;UBERON:0003076!1.07e-07!15;UBERON:0003057!1.07e-07!15;UBERON:0000369!1.67e-07!4;UBERON:0002435!1.67e-07!4;UBERON:0000204!1.67e-07!4;UBERON:0010082!1.67e-07!4
|ontology_enrichment_uberon=UBERON:0002346!1.66e-49!86;UBERON:0001049!5.01e-48!56;UBERON:0005068!5.01e-48!56;UBERON:0006241!5.01e-48!56;UBERON:0007135!5.01e-48!56;UBERON:0003075!1.45e-44!82;UBERON:0007284!1.45e-44!82;UBERON:0000073!2.04e-44!53;UBERON:0002616!2.04e-44!53;UBERON:0001017!2.34e-44!81;UBERON:0001016!1.11e-43!89;UBERON:0002780!1.81e-42!41;UBERON:0001890!1.81e-42!41;UBERON:0003080!1.81e-42!41;UBERON:0006240!1.81e-42!41;UBERON:0003528!7.08e-42!34;UBERON:0002020!7.08e-42!34;UBERON:0001893!1.67e-41!34;UBERON:0003056!4.76e-41!61;UBERON:0002791!2.81e-39!32;UBERON:0001869!3.51e-39!32;UBERON:0000955!3.39e-36!68;UBERON:0006238!3.39e-36!68;UBERON:0010371!1.14e-32!104;UBERON:0000956!1.07e-29!25;UBERON:0000203!1.07e-29!25;UBERON:0004121!4.84e-29!171;UBERON:0000924!4.84e-29!171;UBERON:0006601!4.84e-29!171;UBERON:0010314!3.92e-27!132;UBERON:0002619!1.00e-26!22;UBERON:0001950!8.03e-24!20;UBERON:0007023!4.22e-18!114;UBERON:0002420!4.66e-14!9;UBERON:0007245!4.66e-14!9;UBERON:0010009!4.66e-14!9;UBERON:0010011!4.66e-14!9;UBERON:0000454!4.66e-14!9;UBERON:0000125!1.53e-13!9;UBERON:0002308!1.53e-13!9;UBERON:0011216!1.79e-12!223;UBERON:0009663!4.82e-11!7;UBERON:0000025!5.50e-11!192;UBERON:0000200!1.90e-09!6;UBERON:0000349!5.97e-09!5;UBERON:0000477!7.19e-09!373;UBERON:0001871!2.22e-08!6;UBERON:0004111!5.20e-08!240;UBERON:0001872!5.40e-08!5;UBERON:0003076!1.07e-07!15;UBERON:0003057!1.07e-07!15;UBERON:0000369!1.67e-07!4;UBERON:0002435!1.67e-07!4;UBERON:0000204!1.67e-07!4;UBERON:0010082!1.67e-07!4
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}}
}}

Revision as of 16:13, 26 November 2012


Full id: C3579_neuroectodermal_basal_amygdala_putamen_mesodermal_caudate_brain



Phase1 CAGE Peaks

Hg19::chr16:62070305..62070310,-p4@CDH8
Hg19::chr16:62070317..62070352,-p1@CDH8
Hg19::chr16:62070355..62070364,-p3@CDH8


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
neurectoderm1.66e-4986
neural tube5.01e-4856
neural rod5.01e-4856
future spinal cord5.01e-4856
neural keel5.01e-4856
neural plate1.45e-4482
presumptive neural plate1.45e-4482
regional part of nervous system2.04e-4453
regional part of brain2.04e-4453
central nervous system2.34e-4481
nervous system1.11e-4389
regional part of forebrain1.81e-4241
forebrain1.81e-4241
anterior neural tube1.81e-4241
future forebrain1.81e-4241
brain grey matter7.08e-4234
gray matter7.08e-4234
telencephalon1.67e-4134
pre-chordal neural plate4.76e-4161
regional part of telencephalon2.81e-3932
cerebral hemisphere3.51e-3932
brain3.39e-3668
future brain3.39e-3668
ecto-epithelium1.14e-32104
cerebral cortex1.07e-2925
pallium1.07e-2925
ectoderm-derived structure4.84e-29171
ectoderm4.84e-29171
presumptive ectoderm4.84e-29171
structure with developmental contribution from neural crest3.92e-27132
regional part of cerebral cortex1.00e-2622
neocortex8.03e-2420
adult organism4.22e-18114
basal ganglion4.66e-149
nuclear complex of neuraxis4.66e-149
aggregate regional part of brain4.66e-149
collection of basal ganglia4.66e-149
cerebral subcortex4.66e-149
neural nucleus1.53e-139
nucleus of brain1.53e-139
organ system subdivision1.79e-12223
telencephalic nucleus4.82e-117
tube5.50e-11192
gyrus1.90e-096
limbic system5.97e-095
anatomical cluster7.19e-09373
temporal lobe2.22e-086
anatomical conduit5.20e-08240
parietal lobe5.40e-085
posterior neural tube1.07e-0715
chordal neural plate1.07e-0715
corpus striatum1.67e-074
striatum1.67e-074
ventral part of telencephalon1.67e-074
future corpus striatum1.67e-074


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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