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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1788_seminal_rhabdomyosarcoma_ductus_lung_epididymis_skeletal_tridermal
|full_id=C1788_seminal_rhabdomyosarcoma_ductus_lung_epididymis_skeletal_tridermal
|id=C1788
|id=C1788

Revision as of 14:24, 12 September 2012


Full id: C1788_seminal_rhabdomyosarcoma_ductus_lung_epididymis_skeletal_tridermal



Phase1 CAGE Peaks

Hg19::chr17:59475321..59475327,+p@chr17:59475321..59475327
+
Hg19::chr17:59475638..59475661,+p@chr17:59475638..59475661
+
Hg19::chr17:59475669..59475689,+p@chr17:59475669..59475689
+
Hg19::chr17:59475721..59475732,+p@chr17:59475721..59475732
+
Hg19::chr17:59475868..59475879,+p@chr17:59475868..59475879
+


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 organism2.22e-49115
neural tube9.59e-2257
neural rod9.59e-2257
future spinal cord9.59e-2257
neural keel9.59e-2257
neural plate6.84e-2186
presumptive neural plate6.84e-2186
neurectoderm4.30e-1990
regional part of brain7.94e-1859
anterior neural tube1.76e-1742
regional part of nervous system1.78e-1794
nervous system1.78e-1794
regional part of forebrain9.13e-1741
forebrain9.13e-1741
future forebrain9.13e-1741
anterior region of body7.67e-16129
craniocervical region7.67e-16129
head2.45e-15123
pre-chordal neural plate3.58e-1561
central nervous system5.18e-1582
gray matter6.44e-1534
brain grey matter6.44e-1534
telencephalon7.02e-1534
ectoderm-derived structure1.04e-14169
brain1.61e-1469
future brain1.61e-1469
regional part of telencephalon3.00e-1433
organism subdivision6.78e-14365
ectoderm8.15e-14173
presumptive ectoderm8.15e-14173
cerebral hemisphere2.26e-1332
multi-tissue structure2.31e-12347
regional part of cerebral cortex3.19e-1122
neocortex9.33e-1020
cerebral cortex3.38e-0925
pallium3.38e-0925
brainstem8.97e-088
basal ganglion9.13e-089
nuclear complex of neuraxis9.13e-089
aggregate regional part of brain9.13e-089
collection of basal ganglia9.13e-089
cerebral subcortex9.13e-089
nucleus of brain9.21e-089
neural nucleus9.21e-089
epithelium1.04e-07309
anatomical cluster1.10e-07286
cell layer1.19e-07312
organ part5.06e-07219
multi-cellular organism8.22e-07659
organ8.58e-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
SUZ12#23512550.11578091106293.15480790456198e-092.62328807917635e-07



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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