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Coexpression cluster:C4507: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.27e-66!115;UBERON:0001049!1.21e-36!57;UBERON:0005068!1.21e-36!57;UBERON:0006241!1.21e-36!57;UBERON:0007135!1.21e-36!57;UBERON:0001017!1.29e-31!82;UBERON:0005743!4.74e-30!86;UBERON:0003080!2.62e-29!42;UBERON:0002616!2.84e-29!59;UBERON:0000073!3.34e-29!94;UBERON:0001016!3.34e-29!94;UBERON:0002780!1.29e-28!41;UBERON:0001890!1.29e-28!41;UBERON:0006240!1.29e-28!41;UBERON:0000955!1.58e-27!69;UBERON:0006238!1.58e-27!69;UBERON:0003075!9.88e-26!86;UBERON:0007284!9.88e-26!86;UBERON:0002346!3.33e-24!90;UBERON:0002020!2.91e-23!34;UBERON:0003528!2.91e-23!34;UBERON:0001893!8.16e-23!34;UBERON:0002791!4.87e-22!33;UBERON:0001869!9.44e-22!32;UBERON:0002619!1.17e-19!22;UBERON:0003056!6.33e-19!61;UBERON:0001950!4.80e-18!20;UBERON:0000956!4.08e-16!25;UBERON:0000203!4.08e-16!25;UBERON:0000153!2.22e-12!129;UBERON:0007811!2.22e-12!129;UBERON:0000025!2.86e-12!194;UBERON:0004121!3.25e-12!169;UBERON:0000033!6.71e-12!123;UBERON:0004111!7.90e-12!241;UBERON:0000924!9.95e-12!173;UBERON:0006601!9.95e-12!173;UBERON:0002308!9.88e-09!9;UBERON:0000125!9.88e-09!9;UBERON:0002420!1.65e-08!9;UBERON:0007245!1.65e-08!9;UBERON:0010009!1.65e-08!9;UBERON:0010011!1.65e-08!9;UBERON:0000454!1.65e-08!9;UBERON:0003076!1.71e-08!15;UBERON:0003057!1.71e-08!15;UBERON:0000477!3.14e-08!286;UBERON:0001871!9.28e-08!7;UBERON:0002298!1.23e-07!8;UBERON:0001894!2.74e-07!7;UBERON:0006222!2.74e-07!7;UBERON:0009663!6.31e-07!7
|ontology_enrichment_uberon=UBERON:0007023!3.27e-66!115;UBERON:0001049!1.21e-36!57;UBERON:0005068!1.21e-36!57;UBERON:0006241!1.21e-36!57;UBERON:0007135!1.21e-36!57;UBERON:0001017!1.29e-31!82;UBERON:0005743!4.74e-30!86;UBERON:0003080!2.62e-29!42;UBERON:0002616!2.84e-29!59;UBERON:0000073!3.34e-29!94;UBERON:0001016!3.34e-29!94;UBERON:0002780!1.29e-28!41;UBERON:0001890!1.29e-28!41;UBERON:0006240!1.29e-28!41;UBERON:0000955!1.58e-27!69;UBERON:0006238!1.58e-27!69;UBERON:0003075!9.88e-26!86;UBERON:0007284!9.88e-26!86;UBERON:0002346!3.33e-24!90;UBERON:0002020!2.91e-23!34;UBERON:0003528!2.91e-23!34;UBERON:0001893!8.16e-23!34;UBERON:0002791!4.87e-22!33;UBERON:0001869!9.44e-22!32;UBERON:0002619!1.17e-19!22;UBERON:0003056!6.33e-19!61;UBERON:0001950!4.80e-18!20;UBERON:0000956!4.08e-16!25;UBERON:0000203!4.08e-16!25;UBERON:0000153!2.22e-12!129;UBERON:0007811!2.22e-12!129;UBERON:0000025!2.86e-12!194;UBERON:0004121!3.25e-12!169;UBERON:0000033!6.71e-12!123;UBERON:0004111!7.90e-12!241;UBERON:0000924!9.95e-12!173;UBERON:0006601!9.95e-12!173;UBERON:0002308!9.88e-09!9;UBERON:0000125!9.88e-09!9;UBERON:0002420!1.65e-08!9;UBERON:0007245!1.65e-08!9;UBERON:0010009!1.65e-08!9;UBERON:0010011!1.65e-08!9;UBERON:0000454!1.65e-08!9;UBERON:0003076!1.71e-08!15;UBERON:0003057!1.71e-08!15;UBERON:0000477!3.14e-08!286;UBERON:0001871!9.28e-08!7;UBERON:0002298!1.23e-07!8;UBERON:0001894!2.74e-07!7;UBERON:0006222!2.74e-07!7;UBERON:0009663!6.31e-07!7
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}}
}}

Revision as of 20:05, 8 August 2012


Full id: C4507_large_thalamus_small_pituitary_medial_Mast_locus



Phase1 CAGE Peaks

Hg19::chr5:57877892..57877903,+p6@RAB3C
Hg19::chr5:57877953..57877971,+p5@RAB3C
Hg19::chr5:57877973..57878025,+p2@RAB3C


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
adult organism3.27e-66115
neural tube1.21e-3657
neural rod1.21e-3657
future spinal cord1.21e-3657
neural keel1.21e-3657
central nervous system1.29e-3182
anterior neural tube2.62e-2942
regional part of brain2.84e-2959
regional part of nervous system3.34e-2994
nervous system3.34e-2994
regional part of forebrain1.29e-2841
forebrain1.29e-2841
future forebrain1.29e-2841
brain1.58e-2769
future brain1.58e-2769
neural plate9.88e-2686
presumptive neural plate9.88e-2686
neurectoderm3.33e-2490
gray matter2.91e-2334
brain grey matter2.91e-2334
telencephalon8.16e-2334
regional part of telencephalon4.87e-2233
cerebral hemisphere9.44e-2232
regional part of cerebral cortex1.17e-1922
pre-chordal neural plate6.33e-1961
neocortex4.80e-1820
cerebral cortex4.08e-1625
pallium4.08e-1625
anterior region of body2.22e-12129
craniocervical region2.22e-12129
tube2.86e-12194
ectoderm-derived structure3.25e-12169
head6.71e-12123
anatomical conduit7.90e-12241
ectoderm9.95e-12173
presumptive ectoderm9.95e-12173
nucleus of brain9.88e-099
neural nucleus9.88e-099
basal ganglion1.65e-089
nuclear complex of neuraxis1.65e-089
aggregate regional part of brain1.65e-089
collection of basal ganglia1.65e-089
cerebral subcortex1.65e-089
posterior neural tube1.71e-0815
chordal neural plate1.71e-0815
anatomical cluster3.14e-08286
temporal lobe9.28e-087
brainstem1.23e-078
diencephalon2.74e-077
future diencephalon2.74e-077
telencephalic nucleus6.31e-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.

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