Difference between revisions of "Coexpression cluster:C1294"
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Latest revision as of 02:41, 17 September 2013
Full id: C1294_Hepatocyte_kidney_liver_seminal_salivary_ductus_thyroid
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Hg19::chr10:104597286..104597295,- | p5@CYP17A1 |
| Hg19::chr10:104597311..104597320,- | p4@CYP17A1 |
| Hg19::chr10:104597342..104597349,- | p6@CYP17A1 |
| Hg19::chr16:20548438..20548449,- | p2@ACSM2B |
| Hg19::chr16:20548514..20548523,- | p3@ACSM2B |
| Hg19::chr18:42277095..42277130,+ | p8@SETBP1 |
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 |
|---|---|---|---|---|
| 6.15571812123322e-05 | 0.0389656957074063 | 2 | 130 | Biological oxidations (Reactome):REACT_13433 |
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:0004508 | steroid 17-alpha-monooxygenase activity | 0.00732956552454962 |
| GO:0006704 | glucocorticoid biosynthetic process | 0.0122145041866808 |
| GO:0047760 | butyrate-CoA ligase activity | 0.0122145041866808 |
| GO:0008211 | glucocorticoid metabolic process | 0.0128244743045017 |
| GO:0006700 | C21-steroid hormone biosynthetic process | 0.0154653297256805 |
| GO:0008395 | steroid hydroxylase activity | 0.0154653297256805 |
| GO:0008207 | C21-steroid hormone metabolic process | 0.0154653297256805 |
| GO:0044255 | cellular lipid metabolic process | 0.0154653297256805 |
| GO:0016878 | acid-thiol ligase activity | 0.0154653297256805 |
| GO:0009636 | response to toxin | 0.0162555467239316 |
| GO:0006629 | lipid metabolic process | 0.0162555467239316 |
| GO:0016877 | ligase activity, forming carbon-sulfur bonds | 0.0162555467239316 |
| GO:0005739 | mitochondrion | 0.0162555467239316 |
| GO:0030424 | axon | 0.0170852081807174 |
| GO:0043025 | cell soma | 0.0170852081807174 |
| GO:0042446 | hormone biosynthetic process | 0.0196738632930984 |
| GO:0019825 | oxygen binding | 0.0245351119003364 |
| GO:0043005 | neuron projection | 0.0295746793628032 |
| GO:0007548 | sex differentiation | 0.0295746793628032 |
| GO:0003006 | reproductive developmental process | 0.0295746793628032 |
| GO:0042445 | hormone metabolic process | 0.0295746793628032 |
| GO:0006694 | steroid biosynthetic process | 0.0295746793628032 |
| GO:0005792 | microsome | 0.0485203145647627 |
| GO:0042598 | vesicular fraction | 0.0485203145647627 |
| GO:0016705 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | 0.0485203145647627 |
| GO:0031980 | mitochondrial lumen | 0.0485203145647627 |
| GO:0005759 | mitochondrial matrix | 0.0485203145647627 |
| GO:0006631 | fatty acid metabolic process | 0.0485203145647627 |
| GO:0043231 | intracellular membrane-bound organelle | 0.0485203145647627 |
| GO:0043227 | membrane-bound organelle | 0.0485203145647627 |
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 |
|---|---|---|
| metabolising cell | 3.56e-19 | 12 |
| endopolyploid cell | 3.56e-19 | 12 |
| parenchymal cell | 3.56e-19 | 12 |
| polyploid cell | 3.56e-19 | 12 |
| hepatocyte | 3.56e-19 | 12 |
| Ontology term | p-value | n |
|---|---|---|
| endocrine gland | 2.50e-19 | 35 |
| liver | 1.23e-18 | 19 |
| digestive gland | 1.23e-18 | 19 |
| liver bud | 1.23e-18 | 19 |
| hepatic diverticulum | 4.17e-16 | 22 |
| liver primordium | 4.17e-16 | 22 |
| digestive tract diverticulum | 2.08e-15 | 23 |
| endocrine system | 6.16e-15 | 45 |
| epithelial sac | 3.53e-14 | 25 |
| epithelium of foregut-midgut junction | 3.53e-14 | 25 |
| anatomical boundary | 3.53e-14 | 25 |
| hepatobiliary system | 3.53e-14 | 25 |
| foregut-midgut junction | 3.53e-14 | 25 |
| septum transversum | 3.53e-14 | 25 |
| sac | 1.23e-13 | 26 |
| abdomen element | 2.04e-12 | 54 |
| abdominal segment element | 2.04e-12 | 54 |
| gut epithelium | 2.28e-12 | 54 |
| thyroid gland | 2.52e-12 | 5 |
| pharyngeal pouch | 2.52e-12 | 5 |
| thyroid diverticulum | 2.52e-12 | 5 |
| pharyngeal pouch 2 | 2.52e-12 | 5 |
| thyroid primordium | 2.52e-12 | 5 |
| exocrine gland | 1.95e-11 | 31 |
| exocrine system | 1.95e-11 | 31 |
| gland | 2.80e-11 | 59 |
| abdominal segment of trunk | 4.00e-11 | 60 |
| abdomen | 4.00e-11 | 60 |
| endo-epithelium | 2.45e-10 | 82 |
| trunk region element | 2.80e-08 | 101 |
| subdivision of trunk | 2.17e-07 | 112 |
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 | 0.026277 |
| MA0004.1 | 0.558729 |
| MA0006.1 | 0.391183 |
| MA0007.1 | 0.539222 |
| MA0009.1 | 1.03681 |
| MA0014.1 | 0.262822 |
| MA0017.1 | 1.10421 |
| MA0019.1 | 0.7124 |
| MA0024.1 | 0.929647 |
| MA0025.1 | 1.17262 |
| MA0027.1 | 2.65688 |
| MA0028.1 | 0.408079 |
| MA0029.1 | 0.949428 |
| MA0030.1 | 0.937696 |
| MA0031.1 | 0.871496 |
| MA0038.1 | 1.59836 |
| MA0040.1 | 0.955415 |
| MA0041.1 | 0.578072 |
| MA0042.1 | 0.544748 |
| MA0043.1 | 1.03713 |
| MA0046.1 | 1.02569 |
| MA0048.1 | 0.152639 |
| MA0050.1 | 0.545671 |
| MA0051.1 | 0.661179 |
| MA0052.1 | 0.959373 |
| MA0055.1 | 0.0586456 |
| MA0056.1 | 0 |
| MA0057.1 | 0.147053 |
| MA0058.1 | 0.458909 |
| MA0059.1 | 0.457555 |
| MA0060.1 | 0.267412 |
| MA0061.1 | 1.24837 |
| MA0063.1 | 0 |
| MA0066.1 | 0.66601 |
| MA0067.1 | 1.35893 |
| MA0068.1 | 0.199491 |
| MA0069.1 | 1.02175 |
| MA0070.1 | 1.01032 |
| MA0071.1 | 0.625297 |
| MA0072.1 | 1.00572 |
| MA0073.1 | 0.00076337 |
| MA0074.1 | 0.660398 |
| MA0076.1 | 0.475586 |
| MA0077.1 | 0.997832 |
| MA0078.1 | 0.763954 |
| MA0081.1 | 0.457725 |
| MA0083.1 | 1.04447 |
| MA0084.1 | 1.5477 |
| MA0087.1 | 1.00322 |
| MA0088.1 | 0.660742 |
| MA0089.1 | 0 |
| MA0090.1 | 0.490736 |
| MA0091.1 | 0.561458 |
| MA0092.1 | 0.522012 |
| MA0093.1 | 0.394379 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.679972 |
| MA0101.1 | 1.02896 |
| MA0103.1 | 0.381434 |
| MA0105.1 | 0.419295 |
| MA0106.1 | 2.8345 |
| MA0107.1 | 0.320267 |
| MA0108.2 | 0.868347 |
| MA0109.1 | 0 |
| MA0111.1 | 1.25994 |
| MA0113.1 | 0.725375 |
| MA0114.1 | 0.845337 |
| MA0115.1 | 1.28169 |
| MA0116.1 | 0.323925 |
| MA0117.1 | 1.07516 |
| MA0119.1 | 0.440684 |
| MA0122.1 | 1.10154 |
| MA0124.1 | 1.23968 |
| MA0125.1 | 1.15445 |
| MA0130.1 | 0 |
| MA0131.1 | 0.782708 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.06778 |
| MA0136.1 | 0.672893 |
| MA0139.1 | 0.226048 |
| MA0140.1 | 0.622527 |
| MA0141.1 | 0.455728 |
| MA0142.1 | 0.838805 |
| MA0143.1 | 0.725558 |
| MA0144.1 | 0.299851 |
| MA0145.1 | 0.107156 |
| MA0146.1 | 1.8938 |
| MA0147.1 | 0.327615 |
| MA0148.1 | 0.584698 |
| MA0149.1 | 0.612449 |
| MA0062.2 | 0.23336 |
| MA0035.2 | 1.50688 |
| MA0039.2 | 0.00570825 |
| MA0138.2 | 0.765223 |
| MA0002.2 | 0.255126 |
| MA0137.2 | 0.414885 |
| MA0104.2 | 0.26661 |
| MA0047.2 | 0.695777 |
| MA0112.2 | 0.101413 |
| MA0065.2 | 0.109623 |
| MA0150.1 | 1.21643 |
| MA0151.1 | 0 |
| MA0152.1 | 0.629368 |
| MA0153.1 | 1.13732 |
| MA0154.1 | 0.413181 |
| MA0155.1 | 0.0961854 |
| MA0156.1 | 0.417278 |
| MA0157.1 | 0.810597 |
| MA0158.1 | 0 |
| MA0159.1 | 0.328286 |
| MA0160.1 | 0.600559 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0383129 |
| MA0163.1 | 0.273773 |
| MA0164.1 | 0.738243 |
| MA0080.2 | 0.394469 |
| MA0018.2 | 0.709805 |
| MA0099.2 | 0.629739 |
| MA0079.2 | 0.00575781 |
| MA0102.2 | 1.58513 |
| MA0258.1 | 0.289793 |
| MA0259.1 | 0.336472 |
| 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
No analysis results for this cluster
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.
