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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C801_substantia_spinal_medulla_retina_pineal_penis_tongue
|full_id=C801_substantia_spinal_medulla_retina_pineal_penis_tongue
|id=C801
|id=C801

Revision as of 18:32, 12 September 2012


Full id: C801_substantia_spinal_medulla_retina_pineal_penis_tongue



Phase1 CAGE Peaks

Hg19::chr11:58390132..58390156,+p1@CNTF
Hg19::chr11:58390160..58390175,+p2@CNTF
Hg19::chr17:79106634..79106641,-p@chr17:79106634..79106641
-
Hg19::chr1:161274636..161274641,-p@chr1:161274636..161274641
-
Hg19::chr1:24915935..24915949,+p2@C1orf130
Hg19::chr1:24915966..24915971,+p5@C1orf130
Hg19::chr1:24915973..24915984,+p3@C1orf130
Hg19::chr20:52612624..52612642,-p5@BCAS1
Hg19::chrX:100489564..100489583,+p@chrX:100489564..100489583
+
Hg19::chrX:100489588..100489605,+p@chrX:100489588..100489605
+


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 organism4.92e-40115
neural tube8.82e-2157
neural rod8.82e-2157
future spinal cord8.82e-2157
neural keel8.82e-2157
central nervous system1.22e-1782
regional part of brain2.60e-1659
regional part of nervous system5.15e-1694
nervous system5.15e-1694
regional part of forebrain6.53e-1641
forebrain6.53e-1641
future forebrain6.53e-1641
anterior neural tube3.19e-1542
brain7.88e-1469
future brain7.88e-1469
neural plate5.11e-1386
presumptive neural plate5.11e-1386
gray matter1.69e-1234
brain grey matter1.69e-1234
telencephalon2.43e-1234
neurectoderm3.85e-1290
regional part of telencephalon8.95e-1233
cerebral hemisphere7.51e-1132
regional part of cerebral cortex2.47e-0822
pre-chordal neural plate2.55e-0861
anterior region of body5.27e-08129
craniocervical region5.27e-08129
ectoderm-derived structure1.37e-07169
nucleus of brain1.98e-079
neural nucleus1.98e-079
cerebral cortex2.56e-0725
pallium2.56e-0725
neocortex2.92e-0720
ectoderm3.06e-07173
presumptive ectoderm3.06e-07173
head5.90e-07123
posterior neural tube8.01e-0715
chordal neural plate8.01e-0715


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.