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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3383_pineal_optic_corpus_substantia_thalamus_retinoblastoma_globus
|full_id=C3383_pineal_optic_corpus_substantia_thalamus_retinoblastoma_globus
|id=C3383
|id=C3383

Revision as of 16:17, 12 September 2012


Full id: C3383_pineal_optic_corpus_substantia_thalamus_retinoblastoma_globus



Phase1 CAGE Peaks

Hg19::chr13:51796497..51796517,+p1@FAM124A
Hg19::chr13:51796528..51796540,+p2@FAM124A
Hg19::chr13:51800146..51800150,+p@chr13:51800146..51800150
+


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>

Uber Anatomy
Ontology termp-valuen
adult organism6.61e-35115
regional part of nervous system1.16e-3294
nervous system1.16e-3294
central nervous system5.04e-3182
neural tube1.80e-2957
neural rod1.80e-2957
future spinal cord1.80e-2957
neural keel1.80e-2957
neural plate1.73e-2786
presumptive neural plate1.73e-2786
neurectoderm3.04e-2790
regional part of brain1.42e-2459
brain6.57e-2469
future brain6.57e-2469
anterior neural tube1.05e-2342
regional part of forebrain2.08e-2341
forebrain2.08e-2341
future forebrain2.08e-2341
pre-chordal neural plate4.78e-2161
telencephalon1.07e-1934
gray matter1.08e-1934
brain grey matter1.08e-1934
regional part of telencephalon4.51e-1933
cerebral hemisphere2.72e-1832
tube3.61e-16194
anatomical conduit9.01e-16241
ectoderm2.22e-15173
presumptive ectoderm2.22e-15173
ectoderm-derived structure3.45e-15169
head1.82e-14123
anterior region of body2.98e-14129
craniocervical region2.98e-14129
cerebral cortex3.03e-1425
pallium3.03e-1425
regional part of cerebral cortex3.16e-1422
anatomical cluster3.35e-14286
multi-cellular organism1.10e-13659
neocortex4.48e-1320
embryo7.28e-13612
anatomical system3.25e-12625
anatomical group3.91e-12626
embryonic structure1.48e-10605
developing anatomical structure1.48e-10605
germ layer2.12e-10604
embryonic tissue2.12e-10604
presumptive structure2.12e-10604
epiblast (generic)2.12e-10604
cell layer6.29e-10312
epithelium9.13e-10309
organ2.40e-09511
organ part6.15e-08219
posterior neural tube5.03e-0715
chordal neural plate5.03e-0715
endothelium5.15e-0718
blood vessel endothelium5.15e-0718
cardiovascular system endothelium5.15e-0718
nucleus of brain5.97e-079
neural nucleus5.97e-079
basal ganglion9.50e-079
nuclear complex of neuraxis9.50e-079
aggregate regional part of brain9.50e-079
collection of basal ganglia9.50e-079
cerebral subcortex9.50e-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)

{{{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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