Coexpression cluster:C177
From FANTOM5_SSTAR
Full id: C177_melanoma_Melanocyte_mesenchymal_retina_Mallassezderived_Gingival_squamous
Phase1 CAGE Peaks
Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont
link to source dataset
data
p.value | FDR | nGenes | nPathway | Name |
---|---|---|---|---|
9.34407833048571e-05 | 0.0295740079159873 | 3 | 121 | Lysosome (KEGG):04142 |
5.82213656356506e-05 | 0.0295740079159873 | 4 | 295 | IL-2 down reg. targets (Netpath):NetPath_14 |
Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner
link to source dataset
data
GO ID | GO name | FDR corrected p-value |
---|---|---|
GO:0009072 | aromatic amino acid family metabolic process | 0.0244980923056979 |
GO:0051066 | dihydrobiopterin metabolic process | 0.0244980923056979 |
GO:0042720 | mitochondrial inner membrane peptidase complex | 0.0244980923056979 |
GO:0004244 | mitochondrial inner membrane peptidase activity | 0.0244980923056979 |
GO:0004168 | dolichol kinase activity | 0.0244980923056979 |
GO:0004155 | 6,7-dihydropteridine reductase activity | 0.0244980923056979 |
GO:0005604 | basement membrane | 0.0244980923056979 |
GO:0015031 | protein transport | 0.0244980923056979 |
GO:0044444 | cytoplasmic part | 0.0244980923056979 |
GO:0046907 | intracellular transport | 0.0244980923056979 |
GO:0045184 | establishment of protein localization | 0.0244980923056979 |
GO:0006627 | mitochondrial protein processing | 0.0244980923056979 |
GO:0005737 | cytoplasm | 0.0244980923056979 |
GO:0008104 | protein localization | 0.0244980923056979 |
GO:0033036 | macromolecule localization | 0.0276871341969204 |
GO:0004167 | dopachrome isomerase activity | 0.0285100576328194 |
GO:0051649 | establishment of cellular localization | 0.0323570694221632 |
GO:0044420 | extracellular matrix part | 0.0323570694221632 |
GO:0051641 | cellular localization | 0.0323570694221632 |
GO:0006886 | intracellular protein transport | 0.0329806791542966 |
GO:0008333 | endosome to lysosome transport | 0.0337658358600434 |
GO:0006729 | tetrahydrobiopterin biosynthetic process | 0.0337658358600434 |
GO:0042438 | melanin biosynthetic process | 0.0337658358600434 |
GO:0033162 | melanosome membrane | 0.0337658358600434 |
GO:0006583 | melanin biosynthetic process from tyrosine | 0.0337658358600434 |
GO:0045009 | chitosome | 0.0337658358600434 |
GO:0030814 | regulation of cAMP metabolic process | 0.0337658358600434 |
GO:0016192 | vesicle-mediated transport | 0.034302368557875 |
GO:0046146 | tetrahydrobiopterin metabolic process | 0.034302368557875 |
GO:0030799 | regulation of cyclic nucleotide metabolic process | 0.034302368557875 |
GO:0006582 | melanin metabolic process | 0.034302368557875 |
GO:0006725 | aromatic compound metabolic process | 0.0353543814896279 |
GO:0005768 | endosome | 0.0364966712371678 |
GO:0043231 | intracellular membrane-bound organelle | 0.0364966712371678 |
GO:0043227 | membrane-bound organelle | 0.0364966712371678 |
GO:0051018 | protein kinase A binding | 0.0379597442071673 |
GO:0005095 | GTPase inhibitor activity | 0.0399482200961987 |
GO:0006140 | regulation of nucleotide metabolic process | 0.0399482200961987 |
GO:0006605 | protein targeting | 0.0407812542156949 |
GO:0031090 | organelle membrane | 0.0423437545104869 |
GO:0006558 | L-phenylalanine metabolic process | 0.0423437545104869 |
GO:0004065 | arylsulfatase activity | 0.0423437545104869 |
GO:0006559 | L-phenylalanine catabolic process | 0.0423437545104869 |
GO:0009003 | signal peptidase activity | 0.0448192957972126 |
GO:0007041 | lysosomal transport | 0.0471832292337848 |
GO:0006570 | tyrosine metabolic process | 0.0477529839959068 |
GO:0043408 | regulation of MAPKKK cascade | 0.0477529839959068 |
GO:0043229 | intracellular organelle | 0.0477529839959068 |
GO:0043226 | organelle | 0.0477529839959068 |
Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji
links to source dataset
cell_data
uberon_data
disease_data
Ontology term | p-value | n |
---|---|---|
dark melanocyte | 3.99e-50 | 1 |
melanocyte | 8.54e-21 | 10 |
melanoblast | 8.54e-21 | 10 |
pigment cell | 3.41e-15 | 14 |
neurecto-epithelial cell | 5.70e-11 | 20 |
columnar/cuboidal epithelial cell | 2.14e-08 | 27 |
ecto-epithelial cell | 7.16e-07 | 34 |
glandular epithelial cell | 7.91e-07 | 9 |
Ontology term | p-value | n |
---|---|---|
retina | 1.57e-09 | 6 |
photoreceptor array | 1.57e-09 | 6 |
posterior segment of eyeball | 1.57e-09 | 6 |
Ontology term | p-value | n |
---|---|---|
melanoma | 4.32e-26 | 2 |
Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon
link to source data
Novel motifs
data
Jaspar motifs
data
Novel motifs
JASPAR motifs
Motifs | -log10(p-value) |
---|---|
MA0003.1 | 7.44798e-12 |
MA0004.1 | 0.566052 |
MA0006.1 | 0.0350811 |
MA0007.1 | 0.0017566 |
MA0009.1 | 1.13589 |
MA0014.1 | 4.83151e-06 |
MA0017.1 | 0.210596 |
MA0019.1 | 0.16983 |
MA0024.1 | 0.061653 |
MA0025.1 | 0.170546 |
MA0027.1 | 1.4555 |
MA0028.1 | 0.00129978 |
MA0029.1 | 0.241246 |
MA0030.1 | 0.49665 |
MA0031.1 | 0.68278 |
MA0038.1 | 0.445814 |
MA0040.1 | 0.528809 |
MA0041.1 | 0.0185454 |
MA0042.1 | 0.102271 |
MA0043.1 | 0.102818 |
MA0046.1 | 0.0978884 |
MA0048.1 | 0.000141107 |
MA0050.1 | 0.103155 |
MA0051.1 | 0.249916 |
MA0052.1 | 3.81957 |
MA0055.1 | 0.00211192 |
MA0056.1 | 0 |
MA0057.1 | 0.00431148 |
MA0058.1 | 1.60942 |
MA0059.1 | 0.407669 |
MA0060.1 | 0.0147333 |
MA0061.1 | 0.000841846 |
MA0063.1 | 0 |
MA0066.1 | 0.0086217 |
MA0067.1 | 0.785233 |
MA0068.1 | 4.49145 |
MA0069.1 | 0.656129 |
MA0070.1 | 0.305732 |
MA0071.1 | 0.353067 |
MA0072.1 | 0.0895901 |
MA0073.1 | 0.000395383 |
MA0074.1 | 0.248686 |
MA0076.1 | 0.00457822 |
MA0077.1 | 0.291944 |
MA0078.1 | 0.229816 |
MA0081.1 | 0.0137996 |
MA0083.1 | 0.344888 |
MA0084.1 | 0.429854 |
MA0087.1 | 0.297857 |
MA0088.1 | 0.0924224 |
MA0089.1 | 0 |
MA0090.1 | 0.523863 |
MA0091.1 | 0.118986 |
MA0092.1 | 0.285349 |
MA0093.1 | 0.657538 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.137059 |
MA0101.1 | 0.0801412 |
MA0103.1 | 0.0299854 |
MA0105.1 | 0.00466001 |
MA0106.1 | 0.0130334 |
MA0107.1 | 0.0845823 |
MA0108.2 | 0.379063 |
MA0109.1 | 0 |
MA0111.1 | 2.02034 |
MA0113.1 | 0.60135 |
MA0114.1 | 0.130285 |
MA0115.1 | 0.236407 |
MA0116.1 | 0.148746 |
MA0117.1 | 0.120117 |
MA0119.1 | 1.1743 |
MA0122.1 | 0.414695 |
MA0124.1 | 0.603604 |
MA0125.1 | 0.939192 |
MA0130.1 | 0 |
MA0131.1 | 0.024232 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 0.75036 |
MA0136.1 | 0.463761 |
MA0139.1 | 0.010042 |
MA0140.1 | 0.347066 |
MA0141.1 | 1.0164 |
MA0142.1 | 1.355 |
MA0143.1 | 0.601856 |
MA0144.1 | 0.346269 |
MA0145.1 | 0.00349806 |
MA0146.1 | 1.34675e-07 |
MA0147.1 | 0.0524811 |
MA0148.1 | 0.919498 |
MA0149.1 | 0.00473599 |
MA0062.2 | 0.00211653 |
MA0035.2 | 1.81905 |
MA0039.2 | 1.21259e-07 |
MA0138.2 | 0.0928309 |
MA0002.2 | 0.761905 |
MA0137.2 | 0.41265 |
MA0104.2 | 0.0144344 |
MA0047.2 | 0.793015 |
MA0112.2 | 2.53958e-05 |
MA0065.2 | 0.0136198 |
MA0150.1 | 0.936581 |
MA0151.1 | 0 |
MA0152.1 | 0.361977 |
MA0153.1 | 0.151302 |
MA0154.1 | 0.000829132 |
MA0155.1 | 0.000727938 |
MA0156.1 | 0.285526 |
MA0157.1 | 0.122453 |
MA0158.1 | 0 |
MA0159.1 | 0.478699 |
MA0160.1 | 0.71837 |
MA0161.1 | 0 |
MA0162.1 | 8.81332e-07 |
MA0163.1 | 0.000305072 |
MA0164.1 | 0.637386 |
MA0080.2 | 0.341511 |
MA0018.2 | 0.0132062 |
MA0099.2 | 0.573623 |
MA0079.2 | 5.0145e-15 |
MA0102.2 | 0.459987 |
MA0258.1 | 0.00131953 |
MA0259.1 | 0.0609889 |
MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner
link to source dataset
data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
TF | #promoters | Enrichment | p-value | q-value |
---|---|---|---|---|
FOXA2#3170 | 13 | 3.3009899874706 | 0.000154412868309872 | 0.0019681139313418 |
RXRA#6256 | 11 | 2.27650297454089 | 0.00896649454498156 | 0.0340008613674871 |
Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA
link to data source
data