Coexpression cluster:C58
From FANTOM5_SSTAR
Full id: C58_Melanocyte_melanoma_retina_Retinal_eye_migratory_H9
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
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 8.03848239734226e-07 | 0.000508835935751765 | 4 | 41 | Tyrosine metabolism (KEGG):00350 |
| 2.9998725986943e-05 | 0.00949459677486745 | 4 | 101 | Melanogenesis (KEGG):04916 |
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:0045009 | chitosome | 1.01550561555299e-15 |
| GO:0033162 | melanosome membrane | 1.01550561555299e-15 |
| GO:0048770 | pigment granule | 2.0127813577785e-13 |
| GO:0042470 | melanosome | 2.0127813577785e-13 |
| GO:0046148 | pigment biosynthetic process | 9.16657857646154e-10 |
| GO:0048069 | eye pigmentation | 1.09223589456247e-09 |
| GO:0048066 | pigmentation during development | 1.09223589456247e-09 |
| GO:0042440 | pigment metabolic process | 1.28656442500503e-09 |
| GO:0042438 | melanin biosynthetic process | 2.24898991768669e-09 |
| GO:0006583 | melanin biosynthetic process from tyrosine | 2.24898991768669e-09 |
| GO:0019748 | secondary metabolic process | 4.05189448198049e-09 |
| GO:0006582 | melanin metabolic process | 4.36891639684899e-09 |
| GO:0031410 | cytoplasmic vesicle | 6.77732025937624e-09 |
| GO:0031982 | vesicle | 7.37543217418518e-09 |
| GO:0016023 | cytoplasmic membrane-bound vesicle | 2.31196890711952e-08 |
| GO:0031988 | membrane-bound vesicle | 2.45751310409556e-08 |
| GO:0006570 | tyrosine metabolic process | 1.19370324868788e-07 |
| GO:0030659 | cytoplasmic vesicle membrane | 1.65130678029567e-07 |
| GO:0044433 | cytoplasmic vesicle part | 1.75340061229367e-07 |
| GO:0012506 | vesicle membrane | 2.26077734734176e-07 |
| GO:0042441 | eye pigment metabolic process | 2.26077734734176e-07 |
| GO:0006726 | eye pigment biosynthetic process | 2.26077734734176e-07 |
| GO:0005737 | cytoplasm | 1.87106705033339e-06 |
| GO:0016020 | membrane | 3.04899380799492e-06 |
| GO:0009072 | aromatic amino acid family metabolic process | 1.02917455232679e-05 |
| GO:0044444 | cytoplasmic part | 7.61692228091255e-05 |
| GO:0006725 | aromatic compound metabolic process | 8.94339243027082e-05 |
| GO:0012505 | endomembrane system | 0.000123166212943886 |
| GO:0016021 | integral to membrane | 0.000156493734980448 |
| GO:0031224 | intrinsic to membrane | 0.000169024544737753 |
| GO:0009308 | amine metabolic process | 0.000324428666777075 |
| GO:0031090 | organelle membrane | 0.000350535978297858 |
| GO:0006807 | nitrogen compound metabolic process | 0.000458947234800906 |
| GO:0044425 | membrane part | 0.000637281098808289 |
| GO:0006519 | amino acid and derivative metabolic process | 0.00126165692039151 |
| GO:0044424 | intracellular part | 0.00133592842829585 |
| GO:0032501 | multicellular organismal process | 0.00358674910664708 |
| GO:0032502 | developmental process | 0.00358674910664708 |
| GO:0005624 | membrane fraction | 0.00374764391159449 |
| GO:0045807 | positive regulation of endocytosis | 0.00379983817690436 |
| GO:0006520 | amino acid metabolic process | 0.00536881457738956 |
| GO:0044464 | cell part | 0.00536881457738956 |
| GO:0005507 | copper ion binding | 0.00679192261221231 |
| GO:0043231 | intracellular membrane-bound organelle | 0.00728675590190563 |
| GO:0043227 | membrane-bound organelle | 0.00728675590190563 |
| GO:0030100 | regulation of endocytosis | 0.0119569322366124 |
| GO:0000267 | cell fraction | 0.0128265022808157 |
| GO:0051050 | positive regulation of transport | 0.0128265022808157 |
| GO:0042803 | protein homodimerization activity | 0.0128265022808157 |
| GO:0042802 | identical protein binding | 0.0128265022808157 |
| GO:0006369 | transcription termination from RNA polymerase II promoter | 0.0128265022808157 |
| GO:0048075 | positive regulation of eye pigmentation | 0.0128265022808157 |
| GO:0035173 | histone kinase activity | 0.0128265022808157 |
| GO:0005395 | eye pigment precursor transporter activity | 0.0128265022808157 |
| GO:0015173 | aromatic amino acid transmembrane transporter activity | 0.0128265022808157 |
| GO:0005302 | L-tyrosine transmembrane transporter activity | 0.0128265022808157 |
| GO:0016603 | glutaminyl-peptide cyclotransferase activity | 0.0128265022808157 |
| GO:0004503 | monophenol monooxygenase activity | 0.0128265022808157 |
| GO:0048073 | regulation of eye pigmentation | 0.0128265022808157 |
| GO:0003860 | 3-hydroxyisobutyryl-CoA hydrolase activity | 0.0128265022808157 |
| GO:0048087 | positive regulation of pigmentation | 0.0128265022808157 |
| GO:0016206 | catechol O-methyltransferase activity | 0.0128265022808157 |
| GO:0043229 | intracellular organelle | 0.0184456068227657 |
| GO:0005622 | intracellular | 0.0184456068227657 |
| GO:0043226 | organelle | 0.0184456068227657 |
| GO:0005764 | lysosome | 0.0210082571779636 |
| GO:0000323 | lytic vacuole | 0.0210082571779636 |
| GO:0015746 | citrate transport | 0.0211930623408738 |
| GO:0016716 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen | 0.0211930623408738 |
| GO:0006842 | tricarboxylic acid transport | 0.0211930623408738 |
| GO:0004119 | cGMP-inhibited cyclic-nucleotide phosphodiesterase activity | 0.0211930623408738 |
| GO:0015137 | citrate transmembrane transporter activity | 0.0211930623408738 |
| GO:0048070 | regulation of pigmentation during development | 0.0211930623408738 |
| GO:0015105 | arsenite transmembrane transporter activity | 0.0211930623408738 |
| GO:0015142 | tricarboxylic acid transmembrane transporter activity | 0.0211930623408738 |
| GO:0007601 | visual perception | 0.0241687437842909 |
| GO:0050953 | sensory perception of light stimulus | 0.0241687437842909 |
| GO:0003008 | system process | 0.0258990309458589 |
| GO:0005773 | vacuole | 0.0258990309458589 |
| GO:0006810 | transport | 0.0258990309458589 |
| GO:0019752 | carboxylic acid metabolic process | 0.0258990309458589 |
| GO:0006082 | organic acid metabolic process | 0.0258990309458589 |
| GO:0003836 | beta-galactoside alpha-2,3-sialyltransferase activity | 0.0258990309458589 |
| GO:0042827 | platelet dense granule | 0.0258990309458589 |
| GO:0004167 | dopachrome isomerase activity | 0.0258990309458589 |
| GO:0006883 | cellular sodium ion homeostasis | 0.0258990309458589 |
| GO:0050858 | negative regulation of antigen receptor-mediated signaling pathway | 0.0258990309458589 |
| GO:0042420 | dopamine catabolic process | 0.0258990309458589 |
| GO:0042424 | catecholamine catabolic process | 0.0258990309458589 |
| GO:0017080 | sodium channel regulator activity | 0.0258990309458589 |
| GO:0050860 | negative regulation of T cell receptor signaling pathway | 0.0258990309458589 |
| GO:0055078 | sodium ion homeostasis | 0.0258990309458589 |
| GO:0051234 | establishment of localization | 0.0302620967249725 |
| GO:0008109 | N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity | 0.0334203989349797 |
| GO:0043034 | costamere | 0.0334203989349797 |
| GO:0007089 | traversing start control point of mitotic cell cycle | 0.041314188255513 |
| GO:0009310 | amine catabolic process | 0.0420576545969071 |
| GO:0044270 | nitrogen compound catabolic process | 0.0433574730002079 |
| GO:0050811 | GABA receptor binding | 0.0475638460819058 |
| GO:0050856 | regulation of T cell receptor signaling pathway | 0.0475638460819058 |
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 |
|---|---|---|
| pigment cell | 1.21e-09 | 14 |
| melanocyte | 3.66e-08 | 10 |
| melanoblast | 3.66e-08 | 10 |
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
