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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.valueFDRnGenesnPathwayName
6.15571812123322e-050.03896569570740632130Biological 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 IDGO nameFDR corrected p-value
GO:0004508steroid 17-alpha-monooxygenase activity0.00732956552454962
GO:0006704glucocorticoid biosynthetic process0.0122145041866808
GO:0047760butyrate-CoA ligase activity0.0122145041866808
GO:0008211glucocorticoid metabolic process0.0128244743045017
GO:0006700C21-steroid hormone biosynthetic process0.0154653297256805
GO:0008395steroid hydroxylase activity0.0154653297256805
GO:0008207C21-steroid hormone metabolic process0.0154653297256805
GO:0044255cellular lipid metabolic process0.0154653297256805
GO:0016878acid-thiol ligase activity0.0154653297256805
GO:0009636response to toxin0.0162555467239316
GO:0006629lipid metabolic process0.0162555467239316
GO:0016877ligase activity, forming carbon-sulfur bonds0.0162555467239316
GO:0005739mitochondrion0.0162555467239316
GO:0030424axon0.0170852081807174
GO:0043025cell soma0.0170852081807174
GO:0042446hormone biosynthetic process0.0196738632930984
GO:0019825oxygen binding0.0245351119003364
GO:0043005neuron projection0.0295746793628032
GO:0007548sex differentiation0.0295746793628032
GO:0003006reproductive developmental process0.0295746793628032
GO:0042445hormone metabolic process0.0295746793628032
GO:0006694steroid biosynthetic process0.0295746793628032
GO:0005792microsome0.0485203145647627
GO:0042598vesicular fraction0.0485203145647627
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0485203145647627
GO:0031980mitochondrial lumen0.0485203145647627
GO:0005759mitochondrial matrix0.0485203145647627
GO:0006631fatty acid metabolic process0.0485203145647627
GO:0043231intracellular membrane-bound organelle0.0485203145647627
GO:0043227membrane-bound organelle0.0485203145647627



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


Cell Type
Ontology termp-valuen
metabolising cell3.56e-1912
endopolyploid cell3.56e-1912
parenchymal cell3.56e-1912
polyploid cell3.56e-1912
hepatocyte3.56e-1912
Uber Anatomy
Ontology termp-valuen
endocrine gland2.50e-1935
liver1.23e-1819
digestive gland1.23e-1819
liver bud1.23e-1819
hepatic diverticulum4.17e-1622
liver primordium4.17e-1622
digestive tract diverticulum2.08e-1523
endocrine system6.16e-1545
epithelial sac3.53e-1425
epithelium of foregut-midgut junction3.53e-1425
anatomical boundary3.53e-1425
hepatobiliary system3.53e-1425
foregut-midgut junction3.53e-1425
septum transversum3.53e-1425
sac1.23e-1326
abdomen element2.04e-1254
abdominal segment element2.04e-1254
gut epithelium2.28e-1254
thyroid gland2.52e-125
pharyngeal pouch2.52e-125
thyroid diverticulum2.52e-125
pharyngeal pouch 22.52e-125
thyroid primordium2.52e-125
exocrine gland1.95e-1131
exocrine system1.95e-1131
gland2.80e-1159
abdominal segment of trunk4.00e-1160
abdomen4.00e-1160
endo-epithelium2.45e-1082
trunk region element2.80e-08101
subdivision of trunk2.17e-07112


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)
MA0003.10.026277
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.262822
MA0017.11.10421
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.11.59836
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.0586456
MA0056.10
MA0057.10.147053
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.11.24837
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.199491
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.00076337
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.660742
MA0089.10
MA0090.10.490736
MA0091.10.561458
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.11.02896
MA0103.10.381434
MA0105.10.419295
MA0106.12.8345
MA0107.10.320267
MA0108.20.868347
MA0109.10
MA0111.11.25994
MA0113.10.725375
MA0114.10.845337
MA0115.11.28169
MA0116.10.323925
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.226048
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.11.8938
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.21.50688
MA0039.20.00570825
MA0138.20.765223
MA0002.20.255126
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.20.101413
MA0065.20.109623
MA0150.11.21643
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.10.0383129
MA0163.10.273773
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.20.00575781
MA0102.21.58513
MA0258.10.289793
MA0259.10.336472
MA0442.10



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.