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Coexpression cluster:C4356

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Full id: C4356_small_umbilical_carcinoid_neuroblastoma_eye_skin_Trabecular



Phase1 CAGE Peaks

Hg19::chr4:107956900..107956907,-p7@DKK2
Hg19::chr4:107956922..107956939,-p4@DKK2
Hg19::chr4:107956965..107956995,-p2@DKK2


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 organism3.45e-26115
neurectoderm2.15e-1590
neural plate7.37e-1386
presumptive neural plate7.37e-1386
ectoderm5.62e-12173
presumptive ectoderm5.62e-12173
anterior region of body1.18e-10129
craniocervical region1.18e-10129
neural tube2.96e-1057
neural rod2.96e-1057
future spinal cord2.96e-1057
neural keel2.96e-1057
ectoderm-derived structure3.84e-10169
pre-chordal neural plate7.09e-1061
regional part of nervous system7.59e-1094
nervous system7.59e-1094
head9.99e-10123
regional part of brain1.60e-0959
central nervous system2.52e-0982
umbilical cord3.73e-0910
blastocyst3.73e-0910
blastula3.73e-0910
bilaminar disc3.73e-0910
inner cell mass3.73e-0910
connecting stalk3.73e-0910
inner cell mass derived epiblast3.73e-0910
extraembryonic mesoderm3.73e-0910
anterior neural tube1.16e-0842
organism subdivision2.97e-08365
brain4.22e-0869
future brain4.22e-0869
regional part of forebrain4.47e-0841
forebrain4.47e-0841
future forebrain4.47e-0841
multi-cellular organism1.96e-07659
tissue3.75e-07787


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)

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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.