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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1589_medial_thalamus_occipital_temporal_spinal_amygdala_duodenum
|full_id=C1589_medial_thalamus_occipital_temporal_spinal_amygdala_duodenum
|id=C1589
|id=C1589

Revision as of 14:10, 12 September 2012


Full id: C1589_medial_thalamus_occipital_temporal_spinal_amygdala_duodenum



Phase1 CAGE Peaks

Hg19::chr10:61005374..61005392,+p@chr10:61005374..61005392
+
Hg19::chr19:19367894..19367904,-p8@HAPLN4
Hg19::chr3:11060284..11060322,+p@chr3:11060284..11060322
+
Hg19::chr7:128434397..128434413,+p@chr7:128434397..128434413
+
Hg19::chr7:30198187..30198200,+p@chr7:30198187..30198200
+


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 tube1.08e-3357
neural rod1.08e-3357
future spinal cord1.08e-3357
neural keel1.08e-3357
central nervous system2.14e-3082
regional part of nervous system1.40e-2994
nervous system1.40e-2994
anterior neural tube4.95e-2842
regional part of forebrain1.30e-2741
forebrain1.30e-2741
future forebrain1.30e-2741
regional part of brain2.45e-2659
brain5.99e-2569
future brain5.99e-2569
adult organism9.91e-25115
gray matter4.54e-2434
brain grey matter4.54e-2434
telencephalon5.32e-2434
regional part of telencephalon2.71e-2333
cerebral hemisphere1.45e-2232
neural plate6.62e-2186
presumptive neural plate6.62e-2186
neurectoderm2.83e-2090
cerebral cortex1.20e-1725
pallium1.20e-1725
pre-chordal neural plate1.46e-1761
regional part of cerebral cortex1.12e-1622
anterior region of body3.19e-16129
craniocervical region3.19e-16129
ectoderm-derived structure4.54e-16169
ectoderm6.70e-16173
presumptive ectoderm6.70e-16173
head1.97e-15123
neocortex3.26e-1520
basal ganglion5.61e-089
nuclear complex of neuraxis5.61e-089
aggregate regional part of brain5.61e-089
collection of basal ganglia5.61e-089
cerebral subcortex5.61e-089
nucleus of brain7.04e-089
neural nucleus7.04e-089
posterior neural tube4.64e-0715
chordal neural plate4.64e-0715
brainstem6.31e-078


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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