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Coexpression cluster:C2957: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!3.29e-27!56;UBERON:0005068!3.29e-27!56;UBERON:0006241!3.29e-27!56;UBERON:0007135!3.29e-27!56;UBERON:0001017!1.32e-25!81;UBERON:0000073!2.11e-25!53;UBERON:0002616!2.11e-25!53;UBERON:0001016!5.81e-23!89;UBERON:0000955!3.25e-21!68;UBERON:0006238!3.25e-21!68;UBERON:0002780!9.36e-21!41;UBERON:0001890!9.36e-21!41;UBERON:0003080!9.36e-21!41;UBERON:0006240!9.36e-21!41;UBERON:0002346!7.58e-19!86;UBERON:0003528!3.47e-18!34;UBERON:0002020!3.47e-18!34;UBERON:0001893!3.81e-18!34;UBERON:0003075!4.00e-18!82;UBERON:0007284!4.00e-18!82;UBERON:0002791!3.59e-17!32;UBERON:0001869!4.08e-17!32;UBERON:0010371!1.35e-15!104;UBERON:0004121!4.55e-14!171;UBERON:0000924!4.55e-14!171;UBERON:0006601!4.55e-14!171;UBERON:0000956!2.14e-13!25;UBERON:0000203!2.14e-13!25;UBERON:0002619!4.75e-13!22;UBERON:0010314!4.96e-13!132;UBERON:0003056!9.96e-13!61;UBERON:0007023!2.56e-12!114;UBERON:0001950!6.90e-12!20;UBERON:0000025!1.03e-10!192;UBERON:0004111!5.29e-09!240;UBERON:0000468!7.14e-08!656;UBERON:0003076!1.25e-07!15;UBERON:0003057!1.25e-07!15;UBERON:0000923!1.27e-07!560;UBERON:0010316!1.27e-07!560;UBERON:0005291!1.27e-07!560;UBERON:0006598!1.27e-07!560;UBERON:0010317!1.27e-07!560;UBERON:0002532!1.27e-07!560;UBERON:0002050!2.43e-07!564;UBERON:0011216!5.70e-07!223;UBERON:0005423!6.35e-07!581;UBERON:0000483!7.01e-07!306;UBERON:0000922!7.97e-07!592;UBERON:0000119!8.79e-07!309
|ontology_enrichment_uberon=UBERON:0001049!3.29e-27!56;UBERON:0005068!3.29e-27!56;UBERON:0006241!3.29e-27!56;UBERON:0007135!3.29e-27!56;UBERON:0001017!1.32e-25!81;UBERON:0000073!2.11e-25!53;UBERON:0002616!2.11e-25!53;UBERON:0001016!5.81e-23!89;UBERON:0000955!3.25e-21!68;UBERON:0006238!3.25e-21!68;UBERON:0002780!9.36e-21!41;UBERON:0001890!9.36e-21!41;UBERON:0003080!9.36e-21!41;UBERON:0006240!9.36e-21!41;UBERON:0002346!7.58e-19!86;UBERON:0003528!3.47e-18!34;UBERON:0002020!3.47e-18!34;UBERON:0001893!3.81e-18!34;UBERON:0003075!4.00e-18!82;UBERON:0007284!4.00e-18!82;UBERON:0002791!3.59e-17!32;UBERON:0001869!4.08e-17!32;UBERON:0010371!1.35e-15!104;UBERON:0004121!4.55e-14!171;UBERON:0000924!4.55e-14!171;UBERON:0006601!4.55e-14!171;UBERON:0000956!2.14e-13!25;UBERON:0000203!2.14e-13!25;UBERON:0002619!4.75e-13!22;UBERON:0010314!4.96e-13!132;UBERON:0003056!9.96e-13!61;UBERON:0007023!2.56e-12!114;UBERON:0001950!6.90e-12!20;UBERON:0000025!1.03e-10!192;UBERON:0004111!5.29e-09!240;UBERON:0000468!7.14e-08!656;UBERON:0003076!1.25e-07!15;UBERON:0003057!1.25e-07!15;UBERON:0000923!1.27e-07!560;UBERON:0010316!1.27e-07!560;UBERON:0005291!1.27e-07!560;UBERON:0006598!1.27e-07!560;UBERON:0010317!1.27e-07!560;UBERON:0002532!1.27e-07!560;UBERON:0002050!2.43e-07!564;UBERON:0011216!5.70e-07!223;UBERON:0005423!6.35e-07!581;UBERON:0000483!7.01e-07!306;UBERON:0000922!7.97e-07!592;UBERON:0000119!8.79e-07!309
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}}
}}

Revision as of 15:50, 26 November 2012


Full id: C2957_medial_occipital_Neurons_amygdala_brain_duodenum_temporal



Phase1 CAGE Peaks

Hg19::chrX:153667431..153667445,+p@chrX:153667431..153667445
+
Hg19::chrX:153669457..153669479,+p9@GDI1
Hg19::chrX:153669960..153670004,+p6@GDI1
Hg19::chrX:153670019..153670061,+p11@GDI1


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
neural tube3.29e-2756
neural rod3.29e-2756
future spinal cord3.29e-2756
neural keel3.29e-2756
central nervous system1.32e-2581
regional part of nervous system2.11e-2553
regional part of brain2.11e-2553
nervous system5.81e-2389
brain3.25e-2168
future brain3.25e-2168
regional part of forebrain9.36e-2141
forebrain9.36e-2141
anterior neural tube9.36e-2141
future forebrain9.36e-2141
neurectoderm7.58e-1986
brain grey matter3.47e-1834
gray matter3.47e-1834
telencephalon3.81e-1834
neural plate4.00e-1882
presumptive neural plate4.00e-1882
regional part of telencephalon3.59e-1732
cerebral hemisphere4.08e-1732
ecto-epithelium1.35e-15104
ectoderm-derived structure4.55e-14171
ectoderm4.55e-14171
presumptive ectoderm4.55e-14171
cerebral cortex2.14e-1325
pallium2.14e-1325
regional part of cerebral cortex4.75e-1322
structure with developmental contribution from neural crest4.96e-13132
pre-chordal neural plate9.96e-1361
adult organism2.56e-12114
neocortex6.90e-1220
tube1.03e-10192
anatomical conduit5.29e-09240
multi-cellular organism7.14e-08656
posterior neural tube1.25e-0715
chordal neural plate1.25e-0715
germ layer1.27e-07560
germ layer / neural crest1.27e-07560
embryonic tissue1.27e-07560
presumptive structure1.27e-07560
germ layer / neural crest derived structure1.27e-07560
epiblast (generic)1.27e-07560
embryonic structure2.43e-07564
organ system subdivision5.70e-07223
developing anatomical structure6.35e-07581
epithelium7.01e-07306
embryo7.97e-07592
cell layer8.79e-07309


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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