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Revision as of 05:37, 21 May 2012

Full id: C3515_neuroblastoma_neuroectodermal_brain_pineal_Retinal_Mesothelial_amygdala

Phase1 CAGE Peaks

  Short description
Hg19::chr15:77363355..77363369,- p3@TSPAN3
Hg19::chr15:77363375..77363406,- p2@TSPAN3
Hg19::chr15:77363411..77363423,- p4@TSPAN3

Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset

No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset


Cell Type
Ontology termp-valuen
stuff accumulating cell3.02e-0739
Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.49e-3094
nervous system4.49e-3094
central nervous system2.34e-2682
future brain1.91e-2369
regional part of brain9.64e-2159
neural tube1.56e-2057
neural rod1.56e-2057
future spinal cord1.56e-2057
neural keel1.56e-2057
neural plate5.89e-1886
presumptive neural plate5.89e-1886
regional part of forebrain1.44e-1641
future forebrain1.44e-1641
presumptive ectoderm2.96e-16173
anterior neural tube3.83e-1642
pre-chordal neural plate4.59e-1661
ectoderm-derived structure1.87e-15169
anterior region of body1.40e-14129
craniocervical region1.40e-14129
cell layer7.04e-14312
gray matter1.33e-1334
brain grey matter1.33e-1334
anatomical cluster2.62e-13286
cerebral hemisphere3.70e-1332
regional part of telencephalon4.09e-1333
anatomical conduit1.15e-12241
organism subdivision2.06e-10365
cerebral cortex5.97e-1025
regional part of cerebral cortex1.63e-0922
multi-tissue structure4.01e-07347

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs

Jaspar motifs

Novel motifs

JASPAR motifs



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset


No analysis results for this cluster

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.

link to data source

This analysis result is provided for C0 - C305 clusters.