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Coexpression cluster:C1245: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001016!2.78e-41!89;UBERON:0001017!4.27e-40!81;UBERON:0001049!1.16e-36!56;UBERON:0005068!1.16e-36!56;UBERON:0006241!1.16e-36!56;UBERON:0007135!1.16e-36!56;UBERON:0000073!2.19e-34!53;UBERON:0002616!2.19e-34!53;UBERON:0000955!2.01e-30!68;UBERON:0006238!2.01e-30!68;UBERON:0002780!7.14e-29!41;UBERON:0001890!7.14e-29!41;UBERON:0003080!7.14e-29!41;UBERON:0006240!7.14e-29!41;UBERON:0002346!1.72e-28!86;UBERON:0003075!1.51e-25!82;UBERON:0007284!1.51e-25!82;UBERON:0003528!1.77e-25!34;UBERON:0002020!1.77e-25!34;UBERON:0001893!9.21e-25!34;UBERON:0001869!5.03e-24!32;UBERON:0002791!7.15e-24!32;UBERON:0004121!1.33e-21!171;UBERON:0000924!1.33e-21!171;UBERON:0006601!1.33e-21!171;UBERON:0000956!1.08e-19!25;UBERON:0000203!1.08e-19!25;UBERON:0010371!3.99e-19!104;UBERON:0003056!1.39e-18!61;UBERON:0007023!1.47e-18!114;UBERON:0002619!1.39e-17!22;UBERON:0001950!4.70e-16!20;UBERON:0011216!3.68e-15!223;UBERON:0010314!4.98e-15!132;UBERON:0003076!6.58e-09!15;UBERON:0003057!6.58e-09!15;UBERON:0004732!1.85e-07!13;UBERON:0002420!2.55e-07!9;UBERON:0007245!2.55e-07!9;UBERON:0010009!2.55e-07!9;UBERON:0010011!2.55e-07!9;UBERON:0000454!2.55e-07!9;UBERON:0000125!3.17e-07!9;UBERON:0002308!3.17e-07!9;UBERON:0001871!7.48e-07!6;UBERON:0004733!7.63e-07!12;UBERON:0002028!7.63e-07!12;UBERON:0007277!7.63e-07!12
|ontology_enrichment_uberon=UBERON:0001016!2.78e-41!89;UBERON:0001017!4.27e-40!81;UBERON:0001049!1.16e-36!56;UBERON:0005068!1.16e-36!56;UBERON:0006241!1.16e-36!56;UBERON:0007135!1.16e-36!56;UBERON:0000073!2.19e-34!53;UBERON:0002616!2.19e-34!53;UBERON:0000955!2.01e-30!68;UBERON:0006238!2.01e-30!68;UBERON:0002780!7.14e-29!41;UBERON:0001890!7.14e-29!41;UBERON:0003080!7.14e-29!41;UBERON:0006240!7.14e-29!41;UBERON:0002346!1.72e-28!86;UBERON:0003075!1.51e-25!82;UBERON:0007284!1.51e-25!82;UBERON:0003528!1.77e-25!34;UBERON:0002020!1.77e-25!34;UBERON:0001893!9.21e-25!34;UBERON:0001869!5.03e-24!32;UBERON:0002791!7.15e-24!32;UBERON:0004121!1.33e-21!171;UBERON:0000924!1.33e-21!171;UBERON:0006601!1.33e-21!171;UBERON:0000956!1.08e-19!25;UBERON:0000203!1.08e-19!25;UBERON:0010371!3.99e-19!104;UBERON:0003056!1.39e-18!61;UBERON:0007023!1.47e-18!114;UBERON:0002619!1.39e-17!22;UBERON:0001950!4.70e-16!20;UBERON:0011216!3.68e-15!223;UBERON:0010314!4.98e-15!132;UBERON:0003076!6.58e-09!15;UBERON:0003057!6.58e-09!15;UBERON:0004732!1.85e-07!13;UBERON:0002420!2.55e-07!9;UBERON:0007245!2.55e-07!9;UBERON:0010009!2.55e-07!9;UBERON:0010011!2.55e-07!9;UBERON:0000454!2.55e-07!9;UBERON:0000125!3.17e-07!9;UBERON:0002308!3.17e-07!9;UBERON:0001871!7.48e-07!6;UBERON:0004733!7.63e-07!12;UBERON:0002028!7.63e-07!12;UBERON:0007277!7.63e-07!12
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}}
}}

Revision as of 14:46, 26 November 2012


Full id: C1245_normal_Neurons_parietal_temporal_neuroectodermal_occipital_basal



Phase1 CAGE Peaks

Hg19::chr19:9964647..9964684,-p@chr19:9964647..9964684
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Hg19::chr19:9964687..9964698,-p@chr19:9964687..9964698
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Hg19::chr19:9964700..9964741,-p@chr19:9964700..9964741
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Hg19::chr19:9964743..9964754,-p@chr19:9964743..9964754
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Hg19::chr19:9964757..9964786,-p@chr19:9964757..9964786
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Hg19::chr19:9964795..9964828,-p@chr19:9964795..9964828
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Hg19::chr19:9965051..9965063,-p@chr19:9965051..9965063
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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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
neuronal stem cell3.96e-088
fat cell1.56e-0715
neuron7.28e-076
neuroblast7.28e-076
electrically signaling cell7.28e-076
Uber Anatomy
Ontology termp-valuen
nervous system2.78e-4189
central nervous system4.27e-4081
neural tube1.16e-3656
neural rod1.16e-3656
future spinal cord1.16e-3656
neural keel1.16e-3656
regional part of nervous system2.19e-3453
regional part of brain2.19e-3453
brain2.01e-3068
future brain2.01e-3068
regional part of forebrain7.14e-2941
forebrain7.14e-2941
anterior neural tube7.14e-2941
future forebrain7.14e-2941
neurectoderm1.72e-2886
neural plate1.51e-2582
presumptive neural plate1.51e-2582
brain grey matter1.77e-2534
gray matter1.77e-2534
telencephalon9.21e-2534
cerebral hemisphere5.03e-2432
regional part of telencephalon7.15e-2432
ectoderm-derived structure1.33e-21171
ectoderm1.33e-21171
presumptive ectoderm1.33e-21171
cerebral cortex1.08e-1925
pallium1.08e-1925
ecto-epithelium3.99e-19104
pre-chordal neural plate1.39e-1861
adult organism1.47e-18114
regional part of cerebral cortex1.39e-1722
neocortex4.70e-1620
organ system subdivision3.68e-15223
structure with developmental contribution from neural crest4.98e-15132
posterior neural tube6.58e-0915
chordal neural plate6.58e-0915
segmental subdivision of nervous system1.85e-0713
basal ganglion2.55e-079
nuclear complex of neuraxis2.55e-079
aggregate regional part of brain2.55e-079
collection of basal ganglia2.55e-079
cerebral subcortex2.55e-079
neural nucleus3.17e-079
nucleus of brain3.17e-079
temporal lobe7.48e-076
segmental subdivision of hindbrain7.63e-0712
hindbrain7.63e-0712
presumptive hindbrain7.63e-0712


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.