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Coexpression cluster:C4694: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!9.07e-26!81;UBERON:0001049!1.42e-23!56;UBERON:0005068!1.42e-23!56;UBERON:0006241!1.42e-23!56;UBERON:0007135!1.42e-23!56;UBERON:0001016!3.80e-23!89;UBERON:0000073!5.49e-22!53;UBERON:0002616!5.49e-22!53;UBERON:0004121!1.23e-20!171;UBERON:0000924!1.23e-20!171;UBERON:0006601!1.23e-20!171;UBERON:0000955!1.88e-19!68;UBERON:0006238!1.88e-19!68;UBERON:0002346!1.98e-19!86;UBERON:0003528!2.49e-19!34;UBERON:0002020!2.49e-19!34;UBERON:0003075!3.34e-19!82;UBERON:0007284!3.34e-19!82;UBERON:0002780!3.70e-19!41;UBERON:0001890!3.70e-19!41;UBERON:0003080!3.70e-19!41;UBERON:0006240!3.70e-19!41;UBERON:0001893!5.96e-19!34;UBERON:0002791!4.36e-18!32;UBERON:0001869!7.78e-18!32;UBERON:0010371!3.08e-17!104;UBERON:0007023!1.74e-16!114;UBERON:0003056!2.39e-16!61;UBERON:0000956!2.36e-13!25;UBERON:0000203!2.36e-13!25;UBERON:0002619!5.87e-13!22;UBERON:0011216!2.46e-12!223;UBERON:0001950!1.37e-11!20;UBERON:0010314!2.07e-10!132;UBERON:0002420!8.57e-08!9;UBERON:0007245!8.57e-08!9;UBERON:0010009!8.57e-08!9;UBERON:0010011!8.57e-08!9;UBERON:0000454!8.57e-08!9;UBERON:0000125!1.38e-07!9;UBERON:0002308!1.38e-07!9
|ontology_enrichment_uberon=UBERON:0001017!9.07e-26!81;UBERON:0001049!1.42e-23!56;UBERON:0005068!1.42e-23!56;UBERON:0006241!1.42e-23!56;UBERON:0007135!1.42e-23!56;UBERON:0001016!3.80e-23!89;UBERON:0000073!5.49e-22!53;UBERON:0002616!5.49e-22!53;UBERON:0004121!1.23e-20!171;UBERON:0000924!1.23e-20!171;UBERON:0006601!1.23e-20!171;UBERON:0000955!1.88e-19!68;UBERON:0006238!1.88e-19!68;UBERON:0002346!1.98e-19!86;UBERON:0003528!2.49e-19!34;UBERON:0002020!2.49e-19!34;UBERON:0003075!3.34e-19!82;UBERON:0007284!3.34e-19!82;UBERON:0002780!3.70e-19!41;UBERON:0001890!3.70e-19!41;UBERON:0003080!3.70e-19!41;UBERON:0006240!3.70e-19!41;UBERON:0001893!5.96e-19!34;UBERON:0002791!4.36e-18!32;UBERON:0001869!7.78e-18!32;UBERON:0010371!3.08e-17!104;UBERON:0007023!1.74e-16!114;UBERON:0003056!2.39e-16!61;UBERON:0000956!2.36e-13!25;UBERON:0000203!2.36e-13!25;UBERON:0002619!5.87e-13!22;UBERON:0011216!2.46e-12!223;UBERON:0001950!1.37e-11!20;UBERON:0010314!2.07e-10!132;UBERON:0002420!8.57e-08!9;UBERON:0007245!8.57e-08!9;UBERON:0010009!8.57e-08!9;UBERON:0010011!8.57e-08!9;UBERON:0000454!8.57e-08!9;UBERON:0000125!1.38e-07!9;UBERON:0002308!1.38e-07!9
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}}
}}

Revision as of 16:54, 26 November 2012


Full id: C4694_Mast_Neurons_parietal_small_medulloblastoma_occipital_temporal



Phase1 CAGE Peaks

Hg19::chr7:70228182..70228210,+p@chr7:70228182..70228210
+
Hg19::chr7:70228238..70228275,+p@chr7:70228238..70228275
+
Hg19::chr7:70231159..70231182,+p7@AUTS2


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
neural cell7.12e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system9.07e-2681
neural tube1.42e-2356
neural rod1.42e-2356
future spinal cord1.42e-2356
neural keel1.42e-2356
nervous system3.80e-2389
regional part of nervous system5.49e-2253
regional part of brain5.49e-2253
ectoderm-derived structure1.23e-20171
ectoderm1.23e-20171
presumptive ectoderm1.23e-20171
brain1.88e-1968
future brain1.88e-1968
neurectoderm1.98e-1986
brain grey matter2.49e-1934
gray matter2.49e-1934
neural plate3.34e-1982
presumptive neural plate3.34e-1982
regional part of forebrain3.70e-1941
forebrain3.70e-1941
anterior neural tube3.70e-1941
future forebrain3.70e-1941
telencephalon5.96e-1934
regional part of telencephalon4.36e-1832
cerebral hemisphere7.78e-1832
ecto-epithelium3.08e-17104
adult organism1.74e-16114
pre-chordal neural plate2.39e-1661
cerebral cortex2.36e-1325
pallium2.36e-1325
regional part of cerebral cortex5.87e-1322
organ system subdivision2.46e-12223
neocortex1.37e-1120
structure with developmental contribution from neural crest2.07e-10132
basal ganglion8.57e-089
nuclear complex of neuraxis8.57e-089
aggregate regional part of brain8.57e-089
collection of basal ganglia8.57e-089
cerebral subcortex8.57e-089
neural nucleus1.38e-079
nucleus of brain1.38e-079


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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