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Coexpression cluster:C3009: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3009_optic_substantia_thalamus_globus_spinal_mature_Mast
|full_id=C3009_optic_substantia_thalamus_globus_spinal_mature_Mast
|id=C3009
|id=C3009

Revision as of 15:51, 12 September 2012


Full id: C3009_optic_substantia_thalamus_globus_spinal_mature_Mast



Phase1 CAGE Peaks

Hg19::chr10:24914220..24914234,-p@chr10:24914220..24914234
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Hg19::chr10:25012800..25012822,-p1@ARHGAP21
Hg19::chr10:25012828..25012860,-p2@ARHGAP21


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
fibroblast4.86e-0875
Uber Anatomy
Ontology termp-valuen
neural tube2.27e-2757
neural rod2.27e-2757
future spinal cord2.27e-2757
neural keel2.27e-2757
central nervous system1.40e-2582
ectoderm-derived structure2.26e-25169
ectoderm8.29e-25173
presumptive ectoderm8.29e-25173
regional part of brain1.70e-2459
brain1.85e-2369
future brain1.85e-2369
regional part of nervous system2.53e-2394
nervous system2.53e-2394
head2.83e-23123
multi-cellular organism6.59e-23659
anterior neural tube1.56e-2242
regional part of forebrain5.35e-2241
forebrain5.35e-2241
future forebrain5.35e-2241
anterior region of body1.15e-21129
craniocervical region1.15e-21129
gray matter1.29e-2134
brain grey matter1.29e-2134
telencephalon1.55e-2134
adult organism4.01e-21115
regional part of telencephalon5.91e-2133
cerebral hemisphere3.64e-2032
anatomical system8.78e-20625
anatomical group2.40e-19626
neural plate4.51e-1986
presumptive neural plate4.51e-1986
neurectoderm3.22e-1890
organ1.86e-17511
cerebral cortex5.58e-1625
pallium5.58e-1625
embryonic structure9.70e-16605
developing anatomical structure9.70e-16605
germ layer2.29e-15604
embryonic tissue2.29e-15604
presumptive structure2.29e-15604
epiblast (generic)2.29e-15604
organism subdivision7.27e-15365
embryo1.06e-14612
regional part of cerebral cortex1.56e-1422
pre-chordal neural plate1.75e-1361
neocortex2.77e-1320
anatomical conduit1.21e-11241
anatomical cluster1.41e-11286
multi-tissue structure3.68e-09347
epithelium6.20e-09309
organ part6.64e-09219
cell layer8.40e-09312
tube1.95e-08194
nucleus of brain4.22e-079
neural nucleus4.22e-079
basal ganglion5.54e-079
nuclear complex of neuraxis5.54e-079
aggregate regional part of brain5.54e-079
collection of basal ganglia5.54e-079
cerebral subcortex5.54e-079
tissue6.07e-07787


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)

{{{tfbs_overrepresentation_jaspar}}}



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.