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Coexpression cluster:C2489: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!3.19e-48!81;UBERON:0001016!4.07e-48!89;UBERON:0001049!9.98e-47!56;UBERON:0005068!9.98e-47!56;UBERON:0006241!9.98e-47!56;UBERON:0007135!9.98e-47!56;UBERON:0007023!1.52e-45!114;UBERON:0000073!8.61e-44!53;UBERON:0002616!8.61e-44!53;UBERON:0000955!3.97e-42!68;UBERON:0006238!3.97e-42!68;UBERON:0002780!1.81e-40!41;UBERON:0001890!1.81e-40!41;UBERON:0003080!1.81e-40!41;UBERON:0006240!1.81e-40!41;UBERON:0002346!4.36e-37!86;UBERON:0003528!1.39e-35!34;UBERON:0002020!1.39e-35!34;UBERON:0001893!2.07e-35!34;UBERON:0003075!2.77e-35!82;UBERON:0007284!2.77e-35!82;UBERON:0002791!2.62e-33!32;UBERON:0001869!2.68e-33!32;UBERON:0003056!3.06e-29!61;UBERON:0002619!1.30e-26!22;UBERON:0011216!6.39e-26!223;UBERON:0000956!7.12e-26!25;UBERON:0000203!7.12e-26!25;UBERON:0010371!1.96e-25!104;UBERON:0001950!2.00e-24!20;UBERON:0004121!1.64e-23!171;UBERON:0000924!1.64e-23!171;UBERON:0006601!1.64e-23!171;UBERON:0010314!3.22e-18!132;UBERON:0000477!1.20e-14!373;UBERON:0000025!3.72e-12!192;UBERON:0002420!3.14e-11!9;UBERON:0007245!3.14e-11!9;UBERON:0010009!3.14e-11!9;UBERON:0010011!3.14e-11!9;UBERON:0000454!3.14e-11!9;UBERON:0000125!4.46e-11!9;UBERON:0002308!4.46e-11!9;UBERON:0004111!1.51e-09!240;UBERON:0001871!2.64e-09!6;UBERON:0009663!7.09e-09!7;UBERON:0000200!2.44e-08!6;UBERON:0003076!4.26e-08!15;UBERON:0003057!4.26e-08!15;UBERON:0002298!5.48e-08!6;UBERON:0000062!1.02e-07!503;UBERON:0000481!2.75e-07!342;UBERON:0001872!3.89e-07!5;UBERON:0000349!4.49e-07!5;UBERON:0000922!5.88e-07!592;UBERON:0002021!9.11e-07!5
|ontology_enrichment_uberon=UBERON:0001017!3.19e-48!81;UBERON:0001016!4.07e-48!89;UBERON:0001049!9.98e-47!56;UBERON:0005068!9.98e-47!56;UBERON:0006241!9.98e-47!56;UBERON:0007135!9.98e-47!56;UBERON:0007023!1.52e-45!114;UBERON:0000073!8.61e-44!53;UBERON:0002616!8.61e-44!53;UBERON:0000955!3.97e-42!68;UBERON:0006238!3.97e-42!68;UBERON:0002780!1.81e-40!41;UBERON:0001890!1.81e-40!41;UBERON:0003080!1.81e-40!41;UBERON:0006240!1.81e-40!41;UBERON:0002346!4.36e-37!86;UBERON:0003528!1.39e-35!34;UBERON:0002020!1.39e-35!34;UBERON:0001893!2.07e-35!34;UBERON:0003075!2.77e-35!82;UBERON:0007284!2.77e-35!82;UBERON:0002791!2.62e-33!32;UBERON:0001869!2.68e-33!32;UBERON:0003056!3.06e-29!61;UBERON:0002619!1.30e-26!22;UBERON:0011216!6.39e-26!223;UBERON:0000956!7.12e-26!25;UBERON:0000203!7.12e-26!25;UBERON:0010371!1.96e-25!104;UBERON:0001950!2.00e-24!20;UBERON:0004121!1.64e-23!171;UBERON:0000924!1.64e-23!171;UBERON:0006601!1.64e-23!171;UBERON:0010314!3.22e-18!132;UBERON:0000477!1.20e-14!373;UBERON:0000025!3.72e-12!192;UBERON:0002420!3.14e-11!9;UBERON:0007245!3.14e-11!9;UBERON:0010009!3.14e-11!9;UBERON:0010011!3.14e-11!9;UBERON:0000454!3.14e-11!9;UBERON:0000125!4.46e-11!9;UBERON:0002308!4.46e-11!9;UBERON:0004111!1.51e-09!240;UBERON:0001871!2.64e-09!6;UBERON:0009663!7.09e-09!7;UBERON:0000200!2.44e-08!6;UBERON:0003076!4.26e-08!15;UBERON:0003057!4.26e-08!15;UBERON:0002298!5.48e-08!6;UBERON:0000062!1.02e-07!503;UBERON:0000481!2.75e-07!342;UBERON:0001872!3.89e-07!5;UBERON:0000349!4.49e-07!5;UBERON:0000922!5.88e-07!592;UBERON:0002021!9.11e-07!5
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}}
}}

Revision as of 15:32, 26 November 2012


Full id: C2489_pituitary_small_middle_parietal_amygdala_spinal_medial



Phase1 CAGE Peaks

Hg19::chr19:415680..415713,-p@chr19:415680..415713
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Hg19::chr19:415723..415740,-p@chr19:415723..415740
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Hg19::chr19:444205..444265,-p@chr19:444205..444265
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Hg19::chr19:444276..444288,-p@chr19:444276..444288
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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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
central nervous system3.19e-4881
nervous system4.07e-4889
neural tube9.98e-4756
neural rod9.98e-4756
future spinal cord9.98e-4756
neural keel9.98e-4756
adult organism1.52e-45114
regional part of nervous system8.61e-4453
regional part of brain8.61e-4453
brain3.97e-4268
future brain3.97e-4268
regional part of forebrain1.81e-4041
forebrain1.81e-4041
anterior neural tube1.81e-4041
future forebrain1.81e-4041
neurectoderm4.36e-3786
brain grey matter1.39e-3534
gray matter1.39e-3534
telencephalon2.07e-3534
neural plate2.77e-3582
presumptive neural plate2.77e-3582
regional part of telencephalon2.62e-3332
cerebral hemisphere2.68e-3332
pre-chordal neural plate3.06e-2961
regional part of cerebral cortex1.30e-2622
organ system subdivision6.39e-26223
cerebral cortex7.12e-2625
pallium7.12e-2625
ecto-epithelium1.96e-25104
neocortex2.00e-2420
ectoderm-derived structure1.64e-23171
ectoderm1.64e-23171
presumptive ectoderm1.64e-23171
structure with developmental contribution from neural crest3.22e-18132
anatomical cluster1.20e-14373
tube3.72e-12192
basal ganglion3.14e-119
nuclear complex of neuraxis3.14e-119
aggregate regional part of brain3.14e-119
collection of basal ganglia3.14e-119
cerebral subcortex3.14e-119
neural nucleus4.46e-119
nucleus of brain4.46e-119
anatomical conduit1.51e-09240
temporal lobe2.64e-096
telencephalic nucleus7.09e-097
gyrus2.44e-086
posterior neural tube4.26e-0815
chordal neural plate4.26e-0815
brainstem5.48e-086
organ1.02e-07503
multi-tissue structure2.75e-07342
parietal lobe3.89e-075
limbic system4.49e-075
embryo5.88e-07592
occipital lobe9.11e-075


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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