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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1564_heart_spinal_left_locus_cerebellum_brain_breast
|full_id=C1564_heart_spinal_left_locus_cerebellum_brain_breast
|id=C1564
|id=C1564

Revision as of 14:09, 12 September 2012


Full id: C1564_heart_spinal_left_locus_cerebellum_brain_breast



Phase1 CAGE Peaks

Hg19::chr10:116527977..116528075,-p3@ABLIM1
Hg19::chr10:116528079..116528090,-p17@ABLIM1
Hg19::chr10:116528118..116528130,-p12@ABLIM1
Hg19::chr10:116528142..116528153,-p16@ABLIM1
Hg19::chr10:116528240..116528280,-p11@ABLIM1


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 organism6.86e-41115
neural tube5.79e-3157
neural rod5.79e-3157
future spinal cord5.79e-3157
neural keel5.79e-3157
neural plate1.84e-2886
presumptive neural plate1.84e-2886
central nervous system6.65e-2782
regional part of brain1.05e-2659
neurectoderm5.77e-2590
brain5.30e-2469
future brain5.30e-2469
regional part of nervous system1.22e-2394
nervous system1.22e-2394
anterior neural tube1.15e-2242
regional part of forebrain4.26e-2241
forebrain4.26e-2241
future forebrain4.26e-2241
anterior region of body4.40e-20129
craniocervical region4.40e-20129
head6.59e-20123
ectoderm-derived structure6.99e-20169
anatomical conduit3.19e-19241
telencephalon3.46e-1934
gray matter3.53e-1934
brain grey matter3.53e-1934
pre-chordal neural plate6.18e-1961
regional part of telencephalon1.61e-1833
ectoderm5.24e-18173
presumptive ectoderm5.24e-18173
cerebral hemisphere5.90e-1832
anatomical cluster2.38e-16286
cell layer5.50e-16312
epithelium6.91e-16309
organism subdivision1.45e-15365
tube1.73e-15194
regional part of cerebral cortex2.40e-1522
neocortex4.65e-1420
cerebral cortex1.00e-1325
pallium1.00e-1325
organ1.48e-13511
multi-tissue structure3.58e-13347
organ part2.90e-12219
multi-cellular organism4.00e-11659
anatomical system9.32e-11625
anatomical group1.58e-10626
posterior neural tube2.21e-0915
chordal neural plate2.21e-0915
segmental subdivision of nervous system1.03e-0713
segmental subdivision of hindbrain1.89e-0712
hindbrain1.89e-0712
presumptive hindbrain1.89e-0712
nucleus of brain5.59e-079
neural nucleus5.59e-079
basal ganglion7.30e-079
nuclear complex of neuraxis7.30e-079
aggregate regional part of brain7.30e-079
collection of basal ganglia7.30e-079
cerebral subcortex7.30e-079
embryo8.69e-07612


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.

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