Coexpression cluster:C2298
From FANTOM5_SSTAR
Full id: C2298_pagetoid_liposarcoma_mesothelioma_mucinous_epidermoid_large_bile
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Hg19::chr14:52021357..52021368,+ | p13@FRMD6 |
| Hg19::chr14:52021378..52021407,+ | p3@FRMD6 |
| Hg19::chr14:52021408..52021419,+ | p8@FRMD6 |
| Hg19::chr14:52021434..52021439,+ | p22@FRMD6 |
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
No results for this coexpression
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
No GOStat results
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
| Ontology term | p-value | n |
|---|---|---|
| fibroblast | 2.14e-20 | 76 |
| skin fibroblast | 7.02e-15 | 23 |
| animal cell | 7.05e-11 | 679 |
| eukaryotic cell | 7.05e-11 | 679 |
| muscle precursor cell | 2.43e-08 | 58 |
| myoblast | 2.43e-08 | 58 |
| multi-potent skeletal muscle stem cell | 2.43e-08 | 58 |
| vascular associated smooth muscle cell | 4.95e-08 | 32 |
| smooth muscle cell | 6.63e-08 | 43 |
| smooth muscle myoblast | 6.63e-08 | 43 |
| non-terminally differentiated cell | 8.51e-08 | 106 |
| somatic cell | 3.49e-07 | 588 |
| muscle cell | 5.87e-07 | 55 |
| native cell | 7.37e-07 | 722 |
| Ontology term | p-value | n |
|---|---|---|
| surface structure | 7.26e-11 | 99 |
| skin of body | 7.76e-09 | 41 |
| multilaminar epithelium | 9.35e-09 | 83 |
| integument | 1.77e-08 | 46 |
| integumental system | 1.77e-08 | 46 |
| organism subdivision | 3.43e-08 | 264 |
| somite | 3.51e-08 | 71 |
| presomitic mesoderm | 3.51e-08 | 71 |
| presumptive segmental plate | 3.51e-08 | 71 |
| dermomyotome | 3.51e-08 | 71 |
| trunk paraxial mesoderm | 3.51e-08 | 71 |
| paraxial mesoderm | 6.31e-08 | 72 |
| presumptive paraxial mesoderm | 6.31e-08 | 72 |
| epithelial vesicle | 8.22e-08 | 78 |
| dense mesenchyme tissue | 1.11e-07 | 73 |
| skeletal muscle tissue | 3.15e-07 | 62 |
| striated muscle tissue | 3.15e-07 | 62 |
| myotome | 3.15e-07 | 62 |
| trunk mesenchyme | 6.54e-07 | 122 |
| muscle tissue | 9.80e-07 | 64 |
| musculature | 9.80e-07 | 64 |
| musculature of body | 9.80e-07 | 64 |
| unilaminar epithelium | 9.99e-07 | 148 |
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 | 0.0214529 |
| MA0004.1 | 0.71247 |
| MA0006.1 | 0.532262 |
| MA0007.1 | 0.6918 |
| MA0009.1 | 1.20602 |
| MA0014.1 | 0.0695829 |
| MA0017.1 | 0.577281 |
| MA0019.1 | 0.873355 |
| MA0024.1 | 1.09684 |
| MA0025.1 | 1.34373 |
| MA0027.1 | 2.83281 |
| MA0028.1 | 0.550763 |
| MA0029.1 | 1.11704 |
| MA0030.1 | 1.10506 |
| MA0031.1 | 1.03735 |
| MA0038.1 | 0.824639 |
| MA0040.1 | 1.12314 |
| MA0041.1 | 0.732902 |
| MA0042.1 | 0.697662 |
| MA0043.1 | 1.20635 |
| MA0046.1 | 1.19471 |
| MA0048.1 | 0.25531 |
| MA0050.1 | 0.69864 |
| MA0051.1 | 0.820063 |
| MA0052.1 | 1.12718 |
| MA0055.1 | 0.125954 |
| MA0056.1 | 0 |
| MA0057.1 | 0.248209 |
| MA0058.1 | 0.605914 |
| MA0059.1 | 0.604454 |
| MA0060.1 | 0.393285 |
| MA0061.1 | 0.360128 |
| MA0063.1 | 0 |
| MA0066.1 | 0.825101 |
| MA0067.1 | 1.53181 |
| MA0068.1 | 0.313194 |
| MA0069.1 | 1.19071 |
| MA0070.1 | 1.17908 |
| MA0071.1 | 0.782546 |
| MA0072.1 | 1.1744 |
| MA0073.1 | 0.00636811 |
| MA0074.1 | 0.819248 |
| MA0076.1 | 0.623864 |
| MA0077.1 | 1.16637 |
| MA0078.1 | 0.926725 |
| MA0081.1 | 0.604638 |
| MA0083.1 | 1.21381 |
| MA0084.1 | 1.72172 |
| MA0087.1 | 1.17185 |
| MA0088.1 | 0.182167 |
| MA0089.1 | 0 |
| MA0090.1 | 1.54523 |
| MA0091.1 | 0.715356 |
| MA0092.1 | 0.673508 |
| MA0093.1 | 0.535768 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.83965 |
| MA0101.1 | 0.539569 |
| MA0103.1 | 0.521546 |
| MA0105.1 | 0.232357 |
| MA0106.1 | 0.869173 |
| MA0107.1 | 0.453492 |
| MA0108.2 | 1.03412 |
| MA0109.1 | 0 |
| MA0111.1 | 0.655276 |
| MA0113.1 | 0.886811 |
| MA0114.1 | 0.447443 |
| MA0115.1 | 1.45393 |
| MA0116.1 | 0.457606 |
| MA0117.1 | 1.24497 |
| MA0119.1 | 0.586221 |
| MA0122.1 | 1.27173 |
| MA0124.1 | 1.41151 |
| MA0125.1 | 1.32534 |
| MA0130.1 | 0 |
| MA0131.1 | 0.94608 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.23748 |
| MA0136.1 | 0.832277 |
| MA0139.1 | 0.344952 |
| MA0140.1 | 0.779643 |
| MA0141.1 | 0.602484 |
| MA0142.1 | 1.00381 |
| MA0143.1 | 0.887001 |
| MA0144.1 | 0.430413 |
| MA0145.1 | 0.195821 |
| MA0146.1 | 0.061409 |
| MA0147.1 | 0.46175 |
| MA0148.1 | 0.739888 |
| MA0149.1 | 0.769072 |
| MA0062.2 | 0.353589 |
| MA0035.2 | 0.778873 |
| MA0039.2 | 0.0247757 |
| MA0138.2 | 0.928035 |
| MA0002.2 | 0.98779 |
| MA0137.2 | 0.558189 |
| MA0104.2 | 0.392359 |
| MA0047.2 | 0.856092 |
| MA0112.2 | 0.187982 |
| MA0065.2 | 0.199162 |
| MA0150.1 | 0.633493 |
| MA0151.1 | 0 |
| MA0152.1 | 0.78681 |
| MA0153.1 | 1.30799 |
| MA0154.1 | 0.229241 |
| MA0155.1 | 0.180766 |
| MA0156.1 | 0.560797 |
| MA0157.1 | 0.97481 |
| MA0158.1 | 0 |
| MA0159.1 | 0.462502 |
| MA0160.1 | 2.98688 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0928415 |
| MA0163.1 | 0.0725493 |
| MA0164.1 | 0.90014 |
| MA0080.2 | 1.32578 |
| MA0018.2 | 0.870662 |
| MA0099.2 | 0.7872 |
| MA0079.2 | 0.000248021 |
| MA0102.2 | 1.75932 |
| MA0258.1 | 0.418966 |
| MA0259.1 | 0.471671 |
| 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 |
|---|---|---|---|---|
| EP300#2033 | 4 | 6.7739417262232 | 0.000474845982144264 | 0.00433689895314078 |
| FOS#2353 | 4 | 8.9979553088944 | 0.000152514771116863 | 0.00194605866593452 |
| JUN#3725 | 4 | 12.5128291923363 | 4.07770316866756e-05 | 0.000741935960335316 |
| JUND#3727 | 4 | 6.99466394187103 | 0.00041768421781858 | 0.00391128145115706 |
| PRDM1#639 | 4 | 131.830955777461 | 3.29673728703385e-09 | 2.72395526519405e-07 |
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
This analysis result is provided for C0 - C305 clusters.
