Coexpression cluster:C535
From FANTOM5_SSTAR
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 ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0042706 | eye photoreceptor cell fate commitment | 0.0171023195572825 |
| GO:0046552 | photoreceptor cell fate commitment | 0.0171023195572825 |
| GO:0040036 | regulation of fibroblast growth factor receptor signaling pathway | 0.0265895153713653 |
| GO:0003723 | RNA binding | 0.0265895153713653 |
| GO:0008190 | eukaryotic initiation factor 4E binding | 0.0265895153713653 |
| GO:0031369 | translation initiation factor binding | 0.0265895153713653 |
| GO:0000339 | RNA cap binding | 0.0265895153713653 |
| GO:0008589 | regulation of smoothened signaling pathway | 0.0265895153713653 |
| GO:0001754 | eye photoreceptor cell differentiation | 0.0265895153713653 |
| GO:0030901 | midbrain development | 0.0273468007267111 |
| GO:0046530 | photoreceptor cell differentiation | 0.0310704218977338 |
| GO:0007224 | smoothened signaling pathway | 0.0360475526660574 |
| GO:0048663 | neuron fate commitment | 0.0360475526660574 |
| GO:0001708 | cell fate specification | 0.0360475526660574 |
| GO:0008543 | fibroblast growth factor receptor signaling pathway | 0.0360475526660574 |
| GO:0003676 | nucleic acid binding | 0.0360475526660574 |
| GO:0030426 | growth cone | 0.0360475526660574 |
| GO:0030427 | site of polarized growth | 0.0360475526660574 |
| GO:0048592 | eye morphogenesis | 0.0454975813188519 |
| GO:0042472 | inner ear morphogenesis | 0.0454975813188519 |
| GO:0009953 | dorsal/ventral pattern formation | 0.0454975813188519 |
| GO:0042471 | ear morphogenesis | 0.0480699371691776 |
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>
| Ontology term | p-value | n |
|---|---|---|
| non-terminally differentiated cell | 6.19e-24 | 180 |
| embryonic cell | 1.51e-17 | 248 |
| ectodermal cell | 2.00e-13 | 71 |
| neurectodermal cell | 7.64e-13 | 59 |
| electrically responsive cell | 8.77e-11 | 60 |
| electrically active cell | 8.77e-11 | 60 |
| neural cell | 1.46e-10 | 25 |
| contractile cell | 2.98e-09 | 59 |
| migratory neural crest cell | 8.97e-09 | 41 |
| muscle precursor cell | 3.28e-08 | 57 |
| myoblast | 3.28e-08 | 57 |
| multi-potent skeletal muscle stem cell | 3.28e-08 | 57 |
| muscle cell | 4.13e-08 | 54 |
| fibroblast | 7.45e-08 | 75 |
| mesodermal cell | 1.42e-07 | 119 |
| smooth muscle cell | 3.32e-07 | 42 |
| smooth muscle myoblast | 3.32e-07 | 42 |
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.
