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Coexpression cluster:C1909: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.21e-56!115;UBERON:0001017!2.77e-43!82;UBERON:0001049!5.69e-43!57;UBERON:0005068!5.69e-43!57;UBERON:0006241!5.69e-43!57;UBERON:0007135!5.69e-43!57;UBERON:0005743!3.70e-42!86;UBERON:0000073!4.38e-41!94;UBERON:0001016!4.38e-41!94;UBERON:0002616!8.95e-36!59;UBERON:0000955!2.64e-35!69;UBERON:0006238!2.64e-35!69;UBERON:0003080!6.45e-33!42;UBERON:0002780!1.10e-32!41;UBERON:0001890!1.10e-32!41;UBERON:0006240!1.10e-32!41;UBERON:0003075!1.58e-32!86;UBERON:0007284!1.58e-32!86;UBERON:0002346!4.67e-32!90;UBERON:0002020!3.13e-27!34;UBERON:0003528!3.13e-27!34;UBERON:0001893!3.84e-27!34;UBERON:0002791!1.91e-26!33;UBERON:0001869!1.16e-25!32;UBERON:0000924!3.36e-25!173;UBERON:0006601!3.36e-25!173;UBERON:0004121!4.12e-25!169;UBERON:0003056!4.99e-23!61;UBERON:0000153!2.03e-21!129;UBERON:0007811!2.03e-21!129;UBERON:0000033!6.27e-21!123;UBERON:0000956!2.57e-20!25;UBERON:0000203!2.57e-20!25;UBERON:0002619!5.39e-18!22;UBERON:0001950!2.57e-16!20;UBERON:0003076!5.93e-11!15;UBERON:0003057!5.93e-11!15;UBERON:0004732!2.10e-09!13;UBERON:0004733!9.62e-09!12;UBERON:0002028!9.62e-09!12;UBERON:0007277!9.62e-09!12;UBERON:0002308!2.47e-08!9;UBERON:0000125!2.47e-08!9;UBERON:0002420!3.70e-08!9;UBERON:0007245!3.70e-08!9;UBERON:0010009!3.70e-08!9;UBERON:0010011!3.70e-08!9;UBERON:0000454!3.70e-08!9;UBERON:0004111!3.53e-07!241;UBERON:0001894!6.49e-07!7;UBERON:0006222!6.49e-07!7;UBERON:0001871!7.76e-07!7;UBERON:0002298!8.01e-07!8;UBERON:0009663!8.63e-07!7
|ontology_enrichment_uberon=UBERON:0007023!3.21e-56!115;UBERON:0001017!2.77e-43!82;UBERON:0001049!5.69e-43!57;UBERON:0005068!5.69e-43!57;UBERON:0006241!5.69e-43!57;UBERON:0007135!5.69e-43!57;UBERON:0005743!3.70e-42!86;UBERON:0000073!4.38e-41!94;UBERON:0001016!4.38e-41!94;UBERON:0002616!8.95e-36!59;UBERON:0000955!2.64e-35!69;UBERON:0006238!2.64e-35!69;UBERON:0003080!6.45e-33!42;UBERON:0002780!1.10e-32!41;UBERON:0001890!1.10e-32!41;UBERON:0006240!1.10e-32!41;UBERON:0003075!1.58e-32!86;UBERON:0007284!1.58e-32!86;UBERON:0002346!4.67e-32!90;UBERON:0002020!3.13e-27!34;UBERON:0003528!3.13e-27!34;UBERON:0001893!3.84e-27!34;UBERON:0002791!1.91e-26!33;UBERON:0001869!1.16e-25!32;UBERON:0000924!3.36e-25!173;UBERON:0006601!3.36e-25!173;UBERON:0004121!4.12e-25!169;UBERON:0003056!4.99e-23!61;UBERON:0000153!2.03e-21!129;UBERON:0007811!2.03e-21!129;UBERON:0000033!6.27e-21!123;UBERON:0000956!2.57e-20!25;UBERON:0000203!2.57e-20!25;UBERON:0002619!5.39e-18!22;UBERON:0001950!2.57e-16!20;UBERON:0003076!5.93e-11!15;UBERON:0003057!5.93e-11!15;UBERON:0004732!2.10e-09!13;UBERON:0004733!9.62e-09!12;UBERON:0002028!9.62e-09!12;UBERON:0007277!9.62e-09!12;UBERON:0002308!2.47e-08!9;UBERON:0000125!2.47e-08!9;UBERON:0002420!3.70e-08!9;UBERON:0007245!3.70e-08!9;UBERON:0010009!3.70e-08!9;UBERON:0010011!3.70e-08!9;UBERON:0000454!3.70e-08!9;UBERON:0004111!3.53e-07!241;UBERON:0001894!6.49e-07!7;UBERON:0006222!6.49e-07!7;UBERON:0001871!7.76e-07!7;UBERON:0002298!8.01e-07!8;UBERON:0009663!8.63e-07!7
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}}
}}

Revision as of 17:46, 8 August 2012


Full id: C1909_anaplastic_cerebellum_pineal_parietal_temporal_occipital_duodenum



Phase1 CAGE Peaks

Hg19::chr2:50246776..50246779,-p24@NRXN1
Hg19::chr3:114173558..114173571,-p19@ZBTB20
Hg19::chr3:114173654..114173696,-p12@ZBTB20
Hg19::chr3:114173720..114173794,-p6@ZBTB20
Hg19::chr3:114173859..114173873,-p15@ZBTB20


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
B cell2.66e-0714
lymphocyte of B lineage4.42e-0724
pro-B cell4.42e-0724
Uber Anatomy
Ontology termp-valuen
adult organism3.21e-56115
central nervous system2.77e-4382
neural tube5.69e-4357
neural rod5.69e-4357
future spinal cord5.69e-4357
neural keel5.69e-4357
regional part of nervous system4.38e-4194
nervous system4.38e-4194
regional part of brain8.95e-3659
brain2.64e-3569
future brain2.64e-3569
anterior neural tube6.45e-3342
regional part of forebrain1.10e-3241
forebrain1.10e-3241
future forebrain1.10e-3241
neural plate1.58e-3286
presumptive neural plate1.58e-3286
neurectoderm4.67e-3290
gray matter3.13e-2734
brain grey matter3.13e-2734
telencephalon3.84e-2734
regional part of telencephalon1.91e-2633
cerebral hemisphere1.16e-2532
ectoderm3.36e-25173
presumptive ectoderm3.36e-25173
ectoderm-derived structure4.12e-25169
pre-chordal neural plate4.99e-2361
anterior region of body2.03e-21129
craniocervical region2.03e-21129
head6.27e-21123
cerebral cortex2.57e-2025
pallium2.57e-2025
regional part of cerebral cortex5.39e-1822
neocortex2.57e-1620
posterior neural tube5.93e-1115
chordal neural plate5.93e-1115
segmental subdivision of nervous system2.10e-0913
segmental subdivision of hindbrain9.62e-0912
hindbrain9.62e-0912
presumptive hindbrain9.62e-0912
nucleus of brain2.47e-089
neural nucleus2.47e-089
basal ganglion3.70e-089
nuclear complex of neuraxis3.70e-089
aggregate regional part of brain3.70e-089
collection of basal ganglia3.70e-089
cerebral subcortex3.70e-089
anatomical conduit3.53e-07241
diencephalon6.49e-077
future diencephalon6.49e-077
temporal lobe7.76e-077
brainstem8.01e-078
telencephalic nucleus8.63e-077


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.