Coexpression cluster:C171
From FANTOM5_SSTAR
Full id: C171_merkel_neuroblastoma_pineal_retinoblastoma_carcinoid_small_eye
Phase1 CAGE Peaks
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:0007275 | multicellular organismal development | 0.000641210868674468 |
| GO:0032502 | developmental process | 0.000641210868674468 |
| GO:0048856 | anatomical structure development | 0.00144825555041831 |
| GO:0043565 | sequence-specific DNA binding | 0.00197243719679013 |
| GO:0003700 | transcription factor activity | 0.00197243719679013 |
| GO:0048731 | system development | 0.00241078521397418 |
| GO:0044424 | intracellular part | 0.00438791712875587 |
| GO:0032501 | multicellular organismal process | 0.00438791712875587 |
| GO:0019222 | regulation of metabolic process | 0.00699071498393437 |
| GO:0050794 | regulation of cellular process | 0.00955040933301972 |
| GO:0006355 | regulation of transcription, DNA-dependent | 0.0103851039816391 |
| GO:0006351 | transcription, DNA-dependent | 0.0103851039816391 |
| GO:0032774 | RNA biosynthetic process | 0.0103851039816391 |
| GO:0003677 | DNA binding | 0.010758642121758 |
| GO:0050789 | regulation of biological process | 0.0112451306537117 |
| GO:0045449 | regulation of transcription | 0.0118718949045196 |
| GO:0065008 | regulation of biological quality | 0.0118718949045196 |
| GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0118718949045196 |
| GO:0006350 | transcription | 0.0128681907351291 |
| GO:0010468 | regulation of gene expression | 0.0128681907351291 |
| GO:0005622 | intracellular | 0.0128681907351291 |
| GO:0009653 | anatomical structure morphogenesis | 0.0131530478983111 |
| GO:0031323 | regulation of cellular metabolic process | 0.0131530478983111 |
| GO:0065007 | biological regulation | 0.0141190093803605 |
| GO:0048513 | organ development | 0.0161555509443677 |
| GO:0016070 | RNA metabolic process | 0.0161555509443677 |
| GO:0048496 | maintenance of organ identity | 0.0172228248639993 |
| GO:0002347 | response to tumor cell | 0.0249005894688049 |
| GO:0005634 | nucleus | 0.0284863001369077 |
| GO:0043603 | amide metabolic process | 0.0290378655176246 |
| GO:0019627 | urea metabolic process | 0.0290378655176246 |
| GO:0000050 | urea cycle | 0.0290378655176246 |
| GO:0004055 | argininosuccinate synthase activity | 0.0316706804307545 |
| GO:0044464 | cell part | 0.0447072753794081 |
| GO:0045494 | photoreceptor cell maintenance | 0.0497023599078022 |
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>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| neural cell | 1.03e-07 | 25 |
| Ontology term | p-value | n |
|---|---|---|
| cell type cancer | 3.89e-09 | 143 |
| germ cell and embryonal cancer | 8.55e-08 | 22 |
| germ cell cancer | 8.55e-08 | 22 |
| carcinoma | 3.78e-07 | 106 |
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
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| SUZ12#23512 | 9 | 4.46576265544125 | 0.000199548401979449 | 0.00239575072471912 |
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
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