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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}

Revision as of 18:43, 8 August 2012


Full id: C2916_pineal_neuroectodermal_cerebellum_small_neuroepithelioma_thyroid_neuroblastoma



Phase1 CAGE Peaks

Hg19::chr8:12809093..12809143,+p1@KIAA1456
Hg19::chr8:12809536..12809544,+p15@KIAA1456
Hg19::chr8:12809553..12809567,+p11@KIAA1456
Hg19::chr8:12809591..12809598,+p13@KIAA1456


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 organism7.19e-37115
neural tube1.17e-2757
neural rod1.17e-2757
future spinal cord1.17e-2757
neural keel1.17e-2757
central nervous system3.64e-2682
ectoderm3.43e-24173
presumptive ectoderm3.43e-24173
neurectoderm6.14e-2490
regional part of nervous system1.32e-2394
nervous system1.32e-2394
regional part of brain4.04e-2359
brain8.80e-2369
future brain8.80e-2369
anterior neural tube2.61e-2242
regional part of forebrain6.08e-2241
forebrain6.08e-2241
future forebrain6.08e-2241
ectoderm-derived structure6.12e-22169
neural plate2.45e-2186
presumptive neural plate2.45e-2186
head1.27e-20123
anterior region of body2.11e-20129
craniocervical region2.11e-20129
telencephalon3.65e-1934
gray matter5.35e-1934
brain grey matter5.35e-1934
regional part of telencephalon1.62e-1833
cerebral hemisphere1.77e-1832
pre-chordal neural plate3.73e-1661
cerebral cortex3.97e-1525
pallium3.97e-1525
regional part of cerebral cortex5.60e-1522
organ5.28e-14511
neocortex5.33e-1420
multi-cellular organism3.11e-12659
organism subdivision2.53e-10365
anatomical system1.35e-08625
anatomical group1.95e-08626
organ part2.86e-08219


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.