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Coexpression cluster:C535

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Full id: C535_medulloblastoma_small_pineal_retinoblastoma_eye_Retinal_retina



Phase1 CAGE Peaks

Hg19::chr11:67290913..67290920,-p1@CABP2
Hg19::chr14:57268994..57269015,+p@chr14:57268994..57269015
+
Hg19::chr14:57271021..57271034,-p@chr14:57271021..57271034
-
Hg19::chr14:57271062..57271079,-p@chr14:57271062..57271079
-
Hg19::chr14:57277178..57277203,-p1@OTX2
Hg19::chr14:57278918..57278927,-p@chr14:57278918..57278927
-
Hg19::chr15:75918721..75918732,-p7@SNUPN
Hg19::chr17:55952035..55952049,-p@chr17:55952035..55952049
-
Hg19::chr17:67712324..67712342,+p@chr17:67712324..67712342
+
Hg19::chr1:205426201..205426247,-p@chr1:205426201..205426247
-
Hg19::chr1:54791102..54791151,-p6@SSBP3
Hg19::chr22:29025920..29025935,-p@chr22:29025920..29025935
-
Hg19::chr2:20552002..20552029,-p7@PUM2
Hg19::chr3:52001448..52001478,-p2@PCBP4
Hg19::chr6:35480705..35480718,-p4@TULP1
Hg19::chr7:105241331..105241343,-p2@EFCAB10
Hg19::chrX:118425471..118425477,+p1@ENST00000428222


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

GO IDGO nameFDR corrected p-value
GO:0042706eye photoreceptor cell fate commitment0.0171023195572825
GO:0046552photoreceptor cell fate commitment0.0171023195572825
GO:0040036regulation of fibroblast growth factor receptor signaling pathway0.0265895153713653
GO:0003723RNA binding0.0265895153713653
GO:0008190eukaryotic initiation factor 4E binding0.0265895153713653
GO:0031369translation initiation factor binding0.0265895153713653
GO:0000339RNA cap binding0.0265895153713653
GO:0008589regulation of smoothened signaling pathway0.0265895153713653
GO:0001754eye photoreceptor cell differentiation0.0265895153713653
GO:0030901midbrain development0.0273468007267111
GO:0046530photoreceptor cell differentiation0.0310704218977338
GO:0007224smoothened signaling pathway0.0360475526660574
GO:0048663neuron fate commitment0.0360475526660574
GO:0001708cell fate specification0.0360475526660574
GO:0008543fibroblast growth factor receptor signaling pathway0.0360475526660574
GO:0003676nucleic acid binding0.0360475526660574
GO:0030426growth cone0.0360475526660574
GO:0030427site of polarized growth0.0360475526660574
GO:0048592eye morphogenesis0.0454975813188519
GO:0042472inner ear morphogenesis0.0454975813188519
GO:0009953dorsal/ventral pattern formation0.0454975813188519
GO:0042471ear morphogenesis0.0480699371691776



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>

Cell Type
Ontology termp-valuen
embryonic stem cell1.67e-225
neuron3.42e-096
neuroblast3.42e-096
electrically signaling cell3.42e-096
pigment cell1.79e-0814
neural cell1.03e-0725
neuronal stem cell4.15e-078
neurectodermal cell5.15e-0759


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.

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