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Difference between revisions of "Coexpression cluster:C1294"

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|gostat_on_coexpression_clusters=GO:0004508!steroid 17-alpha-monooxygenase activity!0.00732956552454962!1586$GO:0006704!glucocorticoid biosynthetic process!0.0122145041866808!1586$GO:0047760!butyrate-CoA ligase activity!0.0122145041866808!348158$GO:0008211!glucocorticoid metabolic process!0.0128244743045017!1586$GO:0006700!C21-steroid hormone biosynthetic process!0.0154653297256805!1586$GO:0008395!steroid hydroxylase activity!0.0154653297256805!1586$GO:0008207!C21-steroid hormone metabolic process!0.0154653297256805!1586$GO:0044255!cellular lipid metabolic process!0.0154653297256805!1586;348158$GO:0016878!acid-thiol ligase activity!0.0154653297256805!348158$GO:0009636!response to toxin!0.0162555467239316!1586$GO:0006629!lipid metabolic process!0.0162555467239316!1586;348158$GO:0016877!ligase activity, forming carbon-sulfur bonds!0.0162555467239316!348158$GO:0005739!mitochondrion!0.0162555467239316!1586;348158$GO:0030424!axon!0.0170852081807174!1586$GO:0043025!cell soma!0.0170852081807174!1586$GO:0042446!hormone biosynthetic process!0.0196738632930984!1586$GO:0019825!oxygen binding!0.0245351119003364!1586$GO:0043005!neuron projection!0.0295746793628032!1586$GO:0007548!sex differentiation!0.0295746793628032!1586$GO:0003006!reproductive developmental process!0.0295746793628032!1586$GO:0042445!hormone metabolic process!0.0295746793628032!1586$GO:0006694!steroid biosynthetic process!0.0295746793628032!1586$GO:0005792!microsome!0.0485203145647627!1586$GO:0042598!vesicular fraction!0.0485203145647627!1586$GO:0016705!oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen!0.0485203145647627!1586$GO:0031980!mitochondrial lumen!0.0485203145647627!348158$GO:0005759!mitochondrial matrix!0.0485203145647627!348158$GO:0006631!fatty acid metabolic process!0.0485203145647627!348158$GO:0043231!intracellular membrane-bound organelle!0.0485203145647627!26040;1586;348158$GO:0043227!membrane-bound organelle!0.0485203145647627!26040;1586;348158
 
|gostat_on_coexpression_clusters=GO:0004508!steroid 17-alpha-monooxygenase activity!0.00732956552454962!1586$GO:0006704!glucocorticoid biosynthetic process!0.0122145041866808!1586$GO:0047760!butyrate-CoA ligase activity!0.0122145041866808!348158$GO:0008211!glucocorticoid metabolic process!0.0128244743045017!1586$GO:0006700!C21-steroid hormone biosynthetic process!0.0154653297256805!1586$GO:0008395!steroid hydroxylase activity!0.0154653297256805!1586$GO:0008207!C21-steroid hormone metabolic process!0.0154653297256805!1586$GO:0044255!cellular lipid metabolic process!0.0154653297256805!1586;348158$GO:0016878!acid-thiol ligase activity!0.0154653297256805!348158$GO:0009636!response to toxin!0.0162555467239316!1586$GO:0006629!lipid metabolic process!0.0162555467239316!1586;348158$GO:0016877!ligase activity, forming carbon-sulfur bonds!0.0162555467239316!348158$GO:0005739!mitochondrion!0.0162555467239316!1586;348158$GO:0030424!axon!0.0170852081807174!1586$GO:0043025!cell soma!0.0170852081807174!1586$GO:0042446!hormone biosynthetic process!0.0196738632930984!1586$GO:0019825!oxygen binding!0.0245351119003364!1586$GO:0043005!neuron projection!0.0295746793628032!1586$GO:0007548!sex differentiation!0.0295746793628032!1586$GO:0003006!reproductive developmental process!0.0295746793628032!1586$GO:0042445!hormone metabolic process!0.0295746793628032!1586$GO:0006694!steroid biosynthetic process!0.0295746793628032!1586$GO:0005792!microsome!0.0485203145647627!1586$GO:0042598!vesicular fraction!0.0485203145647627!1586$GO:0016705!oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen!0.0485203145647627!1586$GO:0031980!mitochondrial lumen!0.0485203145647627!348158$GO:0005759!mitochondrial matrix!0.0485203145647627!348158$GO:0006631!fatty acid metabolic process!0.0485203145647627!348158$GO:0043231!intracellular membrane-bound organelle!0.0485203145647627!26040;1586;348158$GO:0043227!membrane-bound organelle!0.0485203145647627!26040;1586;348158
 
|id=C1294
 
|id=C1294
|ontology_enrichment_celltype=CL:0000223!3.57e-09!59
+
|ontology_enrichment_celltype=CL:0000181!3.56e-19!12;CL:0000417!3.56e-19!12;CL:0000668!3.56e-19!12;CL:0000412!3.56e-19!12;CL:0000182!3.56e-19!12
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!6.08e-28!115;UBERON:0002530!4.41e-13!59;UBERON:0002365!3.74e-10!31;UBERON:0002330!3.74e-10!31;UBERON:0003408!2.16e-07!10;UBERON:0001044!2.52e-07!6;UBERON:0003293!2.52e-07!6;UBERON:0003294!2.52e-07!6;UBERON:0010047!2.52e-07!6;UBERON:0000167!2.52e-07!6;UBERON:0003135!4.35e-07!11;UBERON:0003101!6.93e-07!22;UBERON:0000079!6.93e-07!22
+
|ontology_enrichment_uberon=UBERON:0002368!2.50e-19!35;UBERON:0002107!1.23e-18!19;UBERON:0006925!1.23e-18!19;UBERON:0008836!1.23e-18!19;UBERON:0008835!4.17e-16!22;UBERON:0003894!4.17e-16!22;UBERON:0009854!2.08e-15!23;UBERON:0000949!6.16e-15!45;UBERON:0007499!3.53e-14!25;UBERON:0009497!3.53e-14!25;UBERON:0000015!3.53e-14!25;UBERON:0002423!3.53e-14!25;UBERON:0006235!3.53e-14!25;UBERON:0004161!3.53e-14!25;UBERON:0009856!1.23e-13!26;UBERON:0005172!2.04e-12!54;UBERON:0005173!2.04e-12!54;UBERON:0003929!2.28e-12!54;UBERON:0002046!2.52e-12!5;UBERON:0004117!2.52e-12!5;UBERON:0007689!2.52e-12!5;UBERON:0007123!2.52e-12!5;UBERON:0003091!2.52e-12!5;UBERON:0002365!1.95e-11!31;UBERON:0002330!1.95e-11!31;UBERON:0002530!2.80e-11!59;UBERON:0002417!4.00e-11!60;UBERON:0000916!4.00e-11!60;UBERON:0005911!2.45e-10!82;UBERON:0005177!2.80e-08!101;UBERON:0009569!2.17e-07!112
 
|pathway_enrichment=6.15571812123322e-05;0.0389656957074063;2;130;Biological oxidations (Reactome):REACT_13433
 
|pathway_enrichment=6.15571812123322e-05;0.0389656957074063;2;130;Biological oxidations (Reactome):REACT_13433
 
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0.444489,0.31161,0.361651,0.0953991,0.319245,0.603631,0.0650516,0.575882,0.390908,0.0773818,0.115736,0.662745,0.229952,0.205891,0.207936,0.454529,0.0563868,0.796918,0.268235,0.0761868,0.167255,0.107028,0.267379,0.117065,0.0135983,0.343977,0.00300062,0.0191097,0.417985,0.491614,0.146453,0.0559261,0.157053,0.332022,0.557852,0.273582,0.262915,0.306556,0.26147,0.170005,0.523331,0.147801,0.092369,0.18076,0.692556,0.248113,0.148878,0.206465,0.240599,0.245625,0.410665,0.696152,0.100989,0.188919,0.0975693,0.119835,0.145322,0.178533,0.267392,0.0668831,0.142859,0.477403,0.932252,0.358495,0.387334,0.494914,0.224219,0.347904,0.324262,0.795569,0.111827,0.0929171,0.63152,0.118035,0.319902,0.510835,0.137556,0.397628,0.49748,0.0699003,0.235435,0.31953,0.712551,0.99594,0.370285,0.0878758,0.204831,0.130161,0.205669,0.0963721,0.182511,0.369139,0.145449,0.0892237,0.208284,0.135613,0.401189,0.283386,0.0739625,0.247651,0.0879809,0.104922,0.215434,0.177269,0.31512,0.198881,0.394164,0.111068,0.4137,0.146194,0.491435,0.281527,0.35188,0.3889,0.192889,0.547162,0.316041,0.565635,0.280212,0.121421,0.346061,0.275075,0.754571,0.287361,0.138613,0.0163617,0.116846,0.267784,0.278571,0.185281,0.286026,0.31159,0.349805,0.255609,0.404239,0.439697,0.493192,0.223892,0.160738,0.553042,0.213489,0.212611,0.0651145,0.319005,0.180695,0.45842,0.436073,0.261316,0.189596,0.448839,0.196587,0.213353,0.0504588,0.307626,0.173101,0.00940712,0.306056,0.0664739,0.156156,0.33569,0.288104,0.526446,0.761719,0.114697,0.433479,0.324956,0.388835,0.408751,0.648685,0.855529,0.070868,0.654476,0.245,0.0850317,0.249379,0.661446,0.0664865,0.334542,0.281293,0.409327,0.792771,0.00670704,0.236406,0.305003,0.696176,0.355968,0.000630777,0.592254,0.647186,0.249357,0.252602,0.873099,0.312447,0.922804,0.260486,0.737948,0.750579,0.689958,0.0631664,0.984603,0.91547,0.402631,0.768239,0.302735,0.255824,0.145412,0.754734,0.218104,0.2667,0.494578,0.301433,0.00890326,0.492887,0.819065,0.727698,0.559471,0.717449,0.449761,0.6937,0.427531,0.577777,0.629087,0.743042,0.899649,0.297082,0.526245,0.8738,0.746016,0.622334,0.607585,0.593416,0.72684,0.953275,0.296598,0.794297,0.36546,0.360788,0.368898,0.510705,0.447298,0.670481,0.0562917,0.619669,0.287839,0.262665,0.654187,0.183051,0.530004,0.583703,0.300816,0.407994,0.225997,0.487688,0.0862754,0.529993,0.00794549,0.00477506,0.9516,0.852842,0.650025,0.766238,0.540605,0.881739,0.563634,0.848142,0.624569,0.435062,0.628517,0.455987,0.394773,0.659669,0.659285,0.711322,0.929537,0.516717,0.0114272,0.700165,0.258457,0.893393,0.305952,0.356524,0.159817,0.177234,0.145279,0.319704,0.555004,0.240491,0.773067,0.650555,0.597394,0.198803,0.628973,0.594475,0.416321,0.365565,0.47205,0.24311,0.331346,0.214684,0.474879,0.148175,0.518205,0.424119,0.60488,0.519279,0.515179,9.1927e-05,0.0176263,0.757999,0.114691,0.619652,0.706112,0.754688,0.39196,0.758981,0.355152,0.346355,0.712437,0.115549,0.520214,0.708106,0.486574,0.231819,0.722202,0.639482,4.91889e-06,0.600697,0.474504,0.621275,0.727464,0.223923,0.564042,9.62472e-05,0.28925,0.0764807,0.55481,0.777518,0.509842,0.00468286,0.368631,0.321667,0.149733,0.477082,0.368449,0.066291,0.343349,0.450702,0.341084,0.138667,0.459605,0.298707,5.61952e-06,0.299527,0.390707,0.372757,0.172033,0.181635,0.304651,0.440771,0.613566,0.445744,0.371991,0.694395,0.326635,0.349721,0.39301,0.396235,0.566617,0.171264,0.388491,0.357781,0.338712,0.231439,0.359148,0.0641227,0.177916,0.232711,0.327419,0.402268,0.0287247,0.163801,0.245045,0.373321,0.111784,0.395243,0.130132,0.0805354,0.462042,0.213394,0.270174,0.406219,0.298,0.40549,0.30902,0.0755079,0.12783,0.101672,0.0890286,0.0257591,0.362561,0.578088,0.285875,0.225945,0.18761,0.20516,0.115576,0.086142,0.291842,0.392097,0.352327,0.0295382,0.451856,0.521039,0.328594,0.294205,0.448388,0.278746,0.387086,0.232479,0.334662,0.336321,0.139427,0.450171,0.454978,0.366035,0.381922,0.372037,0.263608,0.3488,0.43615,0.218495,0.398705,0.431643,0.316114,0.0746849,0.0371914,0.35537,0.423126,0.288449,0.244977,0.447896,0.395958,0.314638,0.322324,0.184473,0.363414,0.524458,0.482957,0.388728,0.157712,0.3633,0.202084,0.104337,0.104656,0.279419,0.149946,0.0797883,0.104584,0.537494,0.454949,0.378002,0.340219,0.412672,0.0670912,0.155969,0.186603,0.124175,0.228962,0.12366,0.198264,0.128253,0.14669,0.240899,0.206424,0.0862744,0.129421,0.171188,0.0721407,0.251724,0.00126752,0.0342995,0.491191,0.573638,0.263371,0.457065,0.446399,0.360168,0.403229,0.507716,0.116904,0.323763,0.486842,0.458912,0.246162,0.295506,0.369944,0.358783,0.491474,0.417013,0.0455047,0.21822,0.388558,0.397562,0.21727,0.0708324,0.345508,0.484083,0.144065,0.0207403,0.302171,0.398223,0.178399,0.547908,0.400541,0.372405,0.182559,0.164471,0.533328,0.313891,0.292462,0.132855,0.137165,0.467981,0.191837,0.395568,0.320916,0.289812,0.384881,0.116282,0.369492,0.592234
 
}}
 
}}

Revision as of 02:05, 19 October 2012


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)

{{{tfbs_overrepresentation_jaspar}}}



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.