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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3935_Wilms_pituitary_pineal_cerebellum_serous_gastrointestinal_neuroblastoma
|full_id=C3935_Wilms_pituitary_pineal_cerebellum_serous_gastrointestinal_neuroblastoma
|id=C3935
|id=C3935

Revision as of 16:56, 12 September 2012


Full id: C3935_Wilms_pituitary_pineal_cerebellum_serous_gastrointestinal_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr1:210111553..210111569,+p2@SYT14
Hg19::chr1:210111570..210111603,+p1@SYT14
Hg19::chr4:68928985..68929002,-p1@ENST00000481459


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
regional part of nervous system9.37e-4794
nervous system9.37e-4794
central nervous system6.41e-4182
ectoderm6.81e-36173
presumptive ectoderm6.81e-36173
ectoderm-derived structure3.90e-35169
brain1.18e-3369
future brain1.18e-3369
neural tube1.37e-3257
neural rod1.37e-3257
future spinal cord1.37e-3257
neural keel1.37e-3257
regional part of brain2.68e-3159
neurectoderm5.37e-3190
neural plate1.67e-3086
presumptive neural plate1.67e-3086
head5.67e-27123
regional part of forebrain1.26e-2641
forebrain1.26e-2641
future forebrain1.26e-2641
anterior region of body5.57e-26129
craniocervical region5.57e-26129
pre-chordal neural plate1.28e-2561
anterior neural tube1.89e-2542
telencephalon5.72e-2234
gray matter7.32e-2234
brain grey matter7.32e-2234
regional part of telencephalon2.76e-2133
cerebral hemisphere6.69e-2132
cell layer2.60e-17312
epithelium4.41e-17309
cerebral cortex1.03e-1625
pallium1.03e-1625
regional part of cerebral cortex2.03e-1622
organism subdivision1.99e-15365
neocortex2.21e-1520
tube2.89e-13194
multi-cellular organism1.88e-12659
anatomical cluster3.76e-12286
anatomical conduit9.75e-12241
anatomical system9.49e-11625
anatomical group1.38e-10626
embryo1.23e-09612
adult organism8.21e-09115
multi-tissue structure1.65e-08347
posterior neural tube2.89e-0815
chordal neural plate2.89e-0815
germ layer5.81e-08604
embryonic tissue5.81e-08604
presumptive structure5.81e-08604
epiblast (generic)5.81e-08604
embryonic structure8.01e-08605
developing anatomical structure8.01e-08605
basal ganglion7.96e-079
nuclear complex of neuraxis7.96e-079
aggregate regional part of brain7.96e-079
collection of basal ganglia7.96e-079
cerebral subcortex7.96e-079
segmental subdivision of nervous system9.41e-0713
organ9.95e-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
NANOG#79923219.49651898734180.003427255648501020.0174502317021157



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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