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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2426_pons_merkel_Saos2_Dendritic_locus_medulla_parietal
|full_id=C2426_pons_merkel_Saos2_Dendritic_locus_medulla_parietal
|id=C2426
|id=C2426

Revision as of 15:09, 12 September 2012


Full id: C2426_pons_merkel_Saos2_Dendritic_locus_medulla_parietal



Phase1 CAGE Peaks

Hg19::chr17:61116852..61116863,+p4@AB074278
Hg19::chr17:61116864..61116883,+p3@AB074278
Hg19::chr17:61116885..61116914,+p1@AB074278
Hg19::chr17:61116919..61116955,+p2@AB074278


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 tube9.65e-5057
neural rod9.65e-5057
future spinal cord9.65e-5057
neural keel9.65e-5057
central nervous system7.83e-4482
brain1.19e-4369
future brain1.19e-4369
regional part of brain3.58e-4259
regional part of nervous system1.13e-4094
nervous system1.13e-4094
regional part of forebrain2.42e-4041
forebrain2.42e-4041
future forebrain2.42e-4041
adult organism5.61e-40115
anterior neural tube4.74e-3942
neurectoderm4.16e-3590
neural plate8.25e-3586
presumptive neural plate8.25e-3586
gray matter6.39e-3334
brain grey matter6.39e-3334
telencephalon8.03e-3334
regional part of telencephalon1.62e-3133
cerebral hemisphere2.19e-3032
pre-chordal neural plate2.11e-2561
head9.42e-23123
regional part of cerebral cortex1.60e-2222
cerebral cortex2.23e-2225
pallium2.23e-2225
anterior region of body9.95e-22129
craniocervical region9.95e-22129
ectoderm7.67e-21173
presumptive ectoderm7.67e-21173
neocortex1.41e-2020
ectoderm-derived structure3.03e-20169
nucleus of brain3.83e-129
neural nucleus3.83e-129
posterior neural tube1.43e-1115
chordal neural plate1.43e-1115
tube7.14e-11194
telencephalic nucleus1.68e-097
segmental subdivision of nervous system3.11e-0913
basal ganglion3.70e-099
nuclear complex of neuraxis3.70e-099
aggregate regional part of brain3.70e-099
collection of basal ganglia3.70e-099
cerebral subcortex3.70e-099
brainstem4.19e-098
gyrus4.21e-096
anatomical conduit5.35e-09241
diencephalon7.39e-097
future diencephalon7.39e-097
segmental subdivision of hindbrain3.66e-0812
hindbrain3.66e-0812
presumptive hindbrain3.66e-0812
temporal lobe5.81e-087
organism subdivision1.40e-07365
anatomical cluster1.53e-07286
occipital lobe3.43e-075
organ3.81e-07511


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
MYC#460945.22228187160940.001344309395272740.0088736145198388
YY1#752844.911170749853860.00171871838055440.0106807823959729



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.