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Coexpression cluster:C4274: Difference between revisions

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|ontology_enrichment_disease=DOID:3095!4.13e-09!22;DOID:2994!4.13e-09!22;DOID:171!6.32e-08!10
|ontology_enrichment_disease=DOID:3095!4.13e-09!22;DOID:2994!4.13e-09!22;DOID:171!6.32e-08!10
|ontology_enrichment_uberon=UBERON:0001017!4.63e-38!82;UBERON:0000073!6.97e-38!94;UBERON:0001016!6.97e-38!94;UBERON:0005743!1.39e-36!86;UBERON:0007023!3.55e-35!115;UBERON:0001049!7.26e-35!57;UBERON:0005068!7.26e-35!57;UBERON:0006241!7.26e-35!57;UBERON:0007135!7.26e-35!57;UBERON:0002780!1.84e-30!41;UBERON:0001890!1.84e-30!41;UBERON:0006240!1.84e-30!41;UBERON:0003080!2.39e-29!42;UBERON:0001893!8.28e-29!34;UBERON:0002616!2.19e-28!59;UBERON:0002020!2.85e-28!34;UBERON:0003528!2.85e-28!34;UBERON:0002791!6.11e-28!33;UBERON:0002346!9.78e-28!90;UBERON:0001869!1.18e-27!32;UBERON:0000955!1.62e-27!69;UBERON:0006238!1.62e-27!69;UBERON:0000924!2.12e-26!173;UBERON:0006601!2.12e-26!173;UBERON:0003075!8.92e-25!86;UBERON:0007284!8.92e-25!86;UBERON:0004121!6.74e-24!169;UBERON:0000956!2.12e-22!25;UBERON:0000203!2.12e-22!25;UBERON:0002619!1.19e-19!22;UBERON:0003056!5.18e-19!61;UBERON:0001950!2.36e-18!20;UBERON:0000153!2.86e-18!129;UBERON:0007811!2.86e-18!129;UBERON:0000033!3.59e-17!123;UBERON:0000922!6.85e-11!612;UBERON:0000468!1.01e-08!659;UBERON:0000025!3.47e-08!194;UBERON:0002050!4.26e-08!605;UBERON:0005423!4.26e-08!605;UBERON:0004111!6.20e-08!241;UBERON:0001871!8.11e-08!7;UBERON:0002420!8.60e-08!9;UBERON:0007245!8.60e-08!9;UBERON:0010009!8.60e-08!9;UBERON:0010011!8.60e-08!9;UBERON:0000454!8.60e-08!9;UBERON:0000923!9.95e-08!604;UBERON:0005291!9.95e-08!604;UBERON:0006598!9.95e-08!604;UBERON:0002532!9.95e-08!604;UBERON:0000481!1.11e-07!347;UBERON:0002308!2.44e-07!9;UBERON:0000125!2.44e-07!9;UBERON:0000477!2.89e-07!286;UBERON:0003076!5.39e-07!15;UBERON:0003057!5.39e-07!15;UBERON:0000064!5.81e-07!219;UBERON:0000483!6.57e-07!309
|ontology_enrichment_uberon=UBERON:0001017!4.63e-38!82;UBERON:0000073!6.97e-38!94;UBERON:0001016!6.97e-38!94;UBERON:0005743!1.39e-36!86;UBERON:0007023!3.55e-35!115;UBERON:0001049!7.26e-35!57;UBERON:0005068!7.26e-35!57;UBERON:0006241!7.26e-35!57;UBERON:0007135!7.26e-35!57;UBERON:0002780!1.84e-30!41;UBERON:0001890!1.84e-30!41;UBERON:0006240!1.84e-30!41;UBERON:0003080!2.39e-29!42;UBERON:0001893!8.28e-29!34;UBERON:0002616!2.19e-28!59;UBERON:0002020!2.85e-28!34;UBERON:0003528!2.85e-28!34;UBERON:0002791!6.11e-28!33;UBERON:0002346!9.78e-28!90;UBERON:0001869!1.18e-27!32;UBERON:0000955!1.62e-27!69;UBERON:0006238!1.62e-27!69;UBERON:0000924!2.12e-26!173;UBERON:0006601!2.12e-26!173;UBERON:0003075!8.92e-25!86;UBERON:0007284!8.92e-25!86;UBERON:0004121!6.74e-24!169;UBERON:0000956!2.12e-22!25;UBERON:0000203!2.12e-22!25;UBERON:0002619!1.19e-19!22;UBERON:0003056!5.18e-19!61;UBERON:0001950!2.36e-18!20;UBERON:0000153!2.86e-18!129;UBERON:0007811!2.86e-18!129;UBERON:0000033!3.59e-17!123;UBERON:0000922!6.85e-11!612;UBERON:0000468!1.01e-08!659;UBERON:0000025!3.47e-08!194;UBERON:0002050!4.26e-08!605;UBERON:0005423!4.26e-08!605;UBERON:0004111!6.20e-08!241;UBERON:0001871!8.11e-08!7;UBERON:0002420!8.60e-08!9;UBERON:0007245!8.60e-08!9;UBERON:0010009!8.60e-08!9;UBERON:0010011!8.60e-08!9;UBERON:0000454!8.60e-08!9;UBERON:0000923!9.95e-08!604;UBERON:0005291!9.95e-08!604;UBERON:0006598!9.95e-08!604;UBERON:0002532!9.95e-08!604;UBERON:0000481!1.11e-07!347;UBERON:0002308!2.44e-07!9;UBERON:0000125!2.44e-07!9;UBERON:0000477!2.89e-07!286;UBERON:0003076!5.39e-07!15;UBERON:0003057!5.39e-07!15;UBERON:0000064!5.81e-07!219;UBERON:0000483!6.57e-07!309
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}}
}}

Revision as of 19:52, 8 August 2012


Full id: C4274_neuroectodermal_neuroepithelioma_neuroblastoma_Astrocyte_peripheral_Neural_parietal



Phase1 CAGE Peaks

Hg19::chr3:122746538..122746562,-p2@SEMA5B
Hg19::chr3:122746566..122746623,-p1@SEMA5B
Hg19::chr3:122746628..122746635,-p8@SEMA5B


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 cell3.43e-098
neural cell2.78e-0725
neuron3.28e-076
neuroblast3.28e-076
electrically signaling cell3.28e-076
neurectodermal cell7.12e-0759
Uber Anatomy
Ontology termp-valuen
central nervous system4.63e-3882
regional part of nervous system6.97e-3894
nervous system6.97e-3894
adult organism3.55e-35115
neural tube7.26e-3557
neural rod7.26e-3557
future spinal cord7.26e-3557
neural keel7.26e-3557
regional part of forebrain1.84e-3041
forebrain1.84e-3041
future forebrain1.84e-3041
anterior neural tube2.39e-2942
telencephalon8.28e-2934
regional part of brain2.19e-2859
gray matter2.85e-2834
brain grey matter2.85e-2834
regional part of telencephalon6.11e-2833
neurectoderm9.78e-2890
cerebral hemisphere1.18e-2732
brain1.62e-2769
future brain1.62e-2769
ectoderm2.12e-26173
presumptive ectoderm2.12e-26173
neural plate8.92e-2586
presumptive neural plate8.92e-2586
ectoderm-derived structure6.74e-24169
cerebral cortex2.12e-2225
pallium2.12e-2225
regional part of cerebral cortex1.19e-1922
pre-chordal neural plate5.18e-1961
neocortex2.36e-1820
anterior region of body2.86e-18129
craniocervical region2.86e-18129
head3.59e-17123
embryo6.85e-11612
multi-cellular organism1.01e-08659
tube3.47e-08194
embryonic structure4.26e-08605
developing anatomical structure4.26e-08605
anatomical conduit6.20e-08241
temporal lobe8.11e-087
basal ganglion8.60e-089
nuclear complex of neuraxis8.60e-089
aggregate regional part of brain8.60e-089
collection of basal ganglia8.60e-089
cerebral subcortex8.60e-089
germ layer9.95e-08604
embryonic tissue9.95e-08604
presumptive structure9.95e-08604
epiblast (generic)9.95e-08604
multi-tissue structure1.11e-07347
nucleus of brain2.44e-079
neural nucleus2.44e-079
anatomical cluster2.89e-07286
posterior neural tube5.39e-0715
chordal neural plate5.39e-0715
organ part5.81e-07219
epithelium6.57e-07309
Disease
Ontology termp-valuen
germ cell and embryonal cancer4.13e-0922
germ cell cancer4.13e-0922
neuroectodermal tumor6.32e-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)

{{{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.