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Coexpression cluster:C424: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000481!4.12e-20!347;UBERON:0000475!2.80e-19!365;UBERON:0000468!3.51e-17!659;UBERON:0005256!1.37e-14!143;UBERON:0000467!7.88e-14!625;UBERON:0000480!1.58e-13!626;UBERON:0003104!5.25e-13!238;UBERON:0009142!5.25e-13!238;UBERON:0000477!9.79e-13!286;UBERON:0002100!1.41e-12!216;UBERON:0000914!4.58e-12!83;UBERON:0002329!4.58e-12!83;UBERON:0003077!4.58e-12!83;UBERON:0003059!4.58e-12!83;UBERON:0007282!4.58e-12!83;UBERON:0009618!4.58e-12!83;UBERON:0007285!4.58e-12!83;UBERON:0002385!6.23e-12!63;UBERON:0001015!6.23e-12!63;UBERON:0000383!6.23e-12!63;UBERON:0007023!1.13e-11!115;UBERON:0001134!3.12e-11!61;UBERON:0002036!3.12e-11!61;UBERON:0003082!3.12e-11!61;UBERON:0004290!8.64e-11!70;UBERON:0000922!1.03e-09!612;UBERON:0000062!1.28e-09!511;UBERON:0004111!1.47e-09!241;UBERON:0000486!1.77e-09!82;UBERON:0000119!1.86e-09!312;UBERON:0002050!1.90e-09!605;UBERON:0005423!1.90e-09!605;UBERON:0000483!2.19e-09!309;UBERON:0000923!3.14e-09!604;UBERON:0005291!3.14e-09!604;UBERON:0006598!3.14e-09!604;UBERON:0002532!3.14e-09!604;UBERON:0003102!1.23e-08!95;UBERON:0007100!4.89e-08!27;UBERON:0000490!7.35e-08!138;UBERON:0000948!2.20e-07!24;UBERON:0005498!2.20e-07!24;UBERON:0004140!2.20e-07!24;UBERON:0009881!2.20e-07!24;UBERON:0004141!2.20e-07!24;UBERON:0003084!2.20e-07!24;UBERON:0007005!2.20e-07!24;UBERON:0004139!2.20e-07!24;UBERON:0004291!2.20e-07!24;UBERON:0001007!3.42e-07!155;UBERON:0001555!3.42e-07!155;UBERON:0007026!3.42e-07!155;UBERON:0003914!7.27e-07!118
|ontology_enrichment_uberon=UBERON:0000481!4.12e-20!347;UBERON:0000475!2.80e-19!365;UBERON:0000468!3.51e-17!659;UBERON:0005256!1.37e-14!143;UBERON:0000467!7.88e-14!625;UBERON:0000480!1.58e-13!626;UBERON:0003104!5.25e-13!238;UBERON:0009142!5.25e-13!238;UBERON:0000477!9.79e-13!286;UBERON:0002100!1.41e-12!216;UBERON:0000914!4.58e-12!83;UBERON:0002329!4.58e-12!83;UBERON:0003077!4.58e-12!83;UBERON:0003059!4.58e-12!83;UBERON:0007282!4.58e-12!83;UBERON:0009618!4.58e-12!83;UBERON:0007285!4.58e-12!83;UBERON:0002385!6.23e-12!63;UBERON:0001015!6.23e-12!63;UBERON:0000383!6.23e-12!63;UBERON:0007023!1.13e-11!115;UBERON:0001134!3.12e-11!61;UBERON:0002036!3.12e-11!61;UBERON:0003082!3.12e-11!61;UBERON:0004290!8.64e-11!70;UBERON:0000922!1.03e-09!612;UBERON:0000062!1.28e-09!511;UBERON:0004111!1.47e-09!241;UBERON:0000486!1.77e-09!82;UBERON:0000119!1.86e-09!312;UBERON:0002050!1.90e-09!605;UBERON:0005423!1.90e-09!605;UBERON:0000483!2.19e-09!309;UBERON:0000923!3.14e-09!604;UBERON:0005291!3.14e-09!604;UBERON:0006598!3.14e-09!604;UBERON:0002532!3.14e-09!604;UBERON:0003102!1.23e-08!95;UBERON:0007100!4.89e-08!27;UBERON:0000490!7.35e-08!138;UBERON:0000948!2.20e-07!24;UBERON:0005498!2.20e-07!24;UBERON:0004140!2.20e-07!24;UBERON:0009881!2.20e-07!24;UBERON:0004141!2.20e-07!24;UBERON:0003084!2.20e-07!24;UBERON:0007005!2.20e-07!24;UBERON:0004139!2.20e-07!24;UBERON:0004291!2.20e-07!24;UBERON:0001007!3.42e-07!155;UBERON:0001555!3.42e-07!155;UBERON:0007026!3.42e-07!155;UBERON:0003914!7.27e-07!118
|pathway_enrichment=5.39695550498319e-08;1.13875761155145e-05;3;69;Complement and coagulation cascades (KEGG):04610!2.26219774485948e-05;0.00286394234499211;2;56;Staphylococcus aureus infection (KEGG):05150!0.000138328844145387;0.0145936930573384;2;138;Systemic lupus erythematosus (KEGG):05322!2.79572408770279e-06;0.000442423336878966;2;20;Complement Activation, Classical Pathway (Wikipathways):WP545!2.27747619344567e-08;7.20821215225554e-06;3;52;Complement and Coagulation Cascades (Wikipathways):WP558!1.78259609854325e-08;7.20821215225554e-06;3;48;{FCGR2B,50} (Static Module):NA
|pathway_enrichment=5.39695550498319e-08;1.13875761155145e-05;3;69;Complement and coagulation cascades (KEGG):04610!2.26219774485948e-05;0.00286394234499211;2;56;Staphylococcus aureus infection (KEGG):05150!0.000138328844145387;0.0145936930573384;2;138;Systemic lupus erythematosus (KEGG):05322!2.79572408770279e-06;0.000442423336878966;2;20;Complement Activation, Classical Pathway (Wikipathways):WP545!2.27747619344567e-08;7.20821215225554e-06;3;52;Complement and Coagulation Cascades (Wikipathways):WP558!1.78259609854325e-08;7.20821215225554e-06;3;48;{FCGR2B,50} (Static Module):NA
|tfbs_overrepresentation=0.0405792,0.0852961,0.554088,0.000714643,0.53202,0.510116,0.296492,0.426309,0.233667,0.188065,0.699171,0.0181632,0.498523,0.00087002,0.140071,0.40022,0.12394,0.0101504,0.352343,0.599414,0.0890893,0.107319,0.495538,0.0470872,0.288007,0.856524,2.78347e-05,0.177201,0.0374823,0.543499,0.547446,0.252737,0.135468,0.557086,0.423472,0.157906,0.999077,0.296262,0.273753,0.424356,0.00953389,0.180742,0.122022,0.803466,0.0860923,0.000250525,0.266601,0.47583,0.0702613,0.276597,0.737777,0.359572,0.441213,0.541988,0.262166,0.269034,0.000362771,0.852402,0.139469,0.00226259,0.212565,0.726011,0.234738,0.132512,0.36168,0.339305,0.457822,0.390477,0.513263,0.429474,0.528635,0.109111,0.171948,0.638343,0.0582666,0.129012,0.555931,0.300523,0.261909,0.0565686,0.552519,0.00528506,0.293503,0.255395,0.298043,0.409535,0.412591,0.289801,0.623245,0.404537,0.00625771,0.334273,0.551544,0.321764,0.510342,0.255999,0.703574,0.385316,0.54098,0.255987,0.377265,0.0480257,0.705957,0.260786,0.317462,0.284174,0.425758,0.117253,0.71232,0.014476,0.0806159,0.241724,0.726359,0.133029,0.210643,0.240187,0.151586,0.37286,0.336463,0.155981,0.0606013,0.131098,0.701125,0.00626454,0.214361,0.789346,0.532582,0.112397,0.157566,0.00126349,0.388235,0.129285,0.37584,0.168395,0.0946996,0.59957,0.415214,0.0112316,0.235692,0.0312075,0.168326,0.0251634,0.275942,0.742517,0.999298,0.437122,0.202908,0.0346176,0.272225,0.64308,0.267135,0.352088,0.0233836,0.193888,0.294734,0.632275,0.129068,0.874337,0.0682842,0.240014,0.611892,0.19159,0.62924,0.0410639,0.922378,0.253525,0.278804,0.297284,0.0437195,0.0331467,0.212662,0.332109,0.733358,0.359333,0.0301891,0.175195,0.701711,0.218025,0.209557,0.251942,0.000581696,0.280859,0.199333,0.0179357,0.458098,0.636578,0.480616,0.279665,0.499449,0.197464,0.229952,0.493951,0.64985,0.874893,0.0164257,0.32005,0.478929,0.391912,0.429004,0.0149577,0.526854,0.0897164,0.221618,0.393556,0.00708062,0.430937,0.254679,0.04487,0.282368,0.46585,0.313133,0.585924,0.0865016,0.616485,0.184477,0.00420107,0.00360508,0.209742,0.405797,0.216381,0.706111,0.511563,0.156302,0.0144359,0.458731,0.661421,0.697572,0.512839,0.0898584,0.389891,0.238528,0.0446487,0.2896,0.00413764,0.553673,0.184974,0.32093,0.700653,0.760271,0.305619,0.00625033,0.856957,0.201547,0.153717,0.628032,0.329124,0.0317767,0.612133,0.512499,0.0795101,0.163081,0.00674106,0.0849697,0.561932,0.000218386,0.751353,0.0138333,0.270386,0.00292391,0.000937917,0.0936734,0.0707562,0.0568226,0.665997,0.244959,0.491527,0.491952,0.538218,0.266159,0.466429,0.0497568,0.407302,0.904872,0.949661,0.164388,0.266779,0.102765,0.00100883,0.666309,0.248329,0.117934,0.0381237,0.523442,0.845263,0.000156799,0.276393,0.911579,0.106647,9.33195e-06,0.0110555,1.13374e-06,0.221566,0.766479,0.105255,0.0478192,0.0120897,0.00465006,0.0022356,0.00127951,0.00030783,0.0262872,8.14125e-06,0.493809,6.03519e-06,0.0794156,4.0986e-06,0.606297,1.54901e-06,0.0500369,0.16327,4.28357e-05,0.0665961,0.838233,0.00896012,0.141066,8.32073e-06,0.263004,0.0200244,0.20876,0.0485151,0.0275446,3.68689e-05,0.0360235,0.329737,0.00197153,0.0732323,0.930717,0.0124254,0.00208105,0.0227888,0.0237888,0.0899839,0.0720625,4.33008e-08,0.0388966,0.0203627,0.0858791,0.000107376,0.0798708,0.0803039,0.644395,0.983661,0.769953,0.258903,0.00676181,0.806607,0.441881,0.415536,0.0439508,0.10255,0.000240915,0.225,0.243257,0.00250131,0.000100765,0.145666,1.87624e-05,0.107391,0.455137,0.00667183,0.0346195,0.972494,0.0967606,0.421747,0.0384014,3.30129e-06,0.00101682,0.0237651,0.0503011,0.0335654,0.000863964,0.00637797,0.462892,0.000315587,0.7333,0.10723,0.200453,0.000160302,0.00251543,0.15396,0.141733,0.101946,0.810454,0.733836,0.343431,0.0848115,0.342578,0.0191471,0.00940932,0.0492921,0.659972,0.00548894,0.431756,0.00188714,0.0161977,0.999997,0.961803,0.35588,0.358324,0.900482,0.088597,0.852052,0.0635218,0.410658,0.148782,0.31718,0.116126,0.000863415,0.685964,0.000224621,9.09211e-07,0.303993,4.97743e-06,0.000753973,0.172898,0.00319467,0.00024076,0.0124032,0.0183497,0.0063416,0.100478,0.0702938,0.152402,0.91988,0.432943,0.0314951,0.0319001,0.103985,0.28216,0.84539,0.229341,0.00775664,0.000285395,0.0202605,0.11664,0.273578,0.0357943,0.0594166,0.698561,0.405118,0.0239996,0.718824,0.35424,0.0903645,0.526173,0.388154,0.0408092,0.0569914,6.65769e-07,2.41043e-06,0.0246688,0.00261598,0.126631,0.00466639,0.805047,0.03559,0.439302,0.367675,0.510144,0.477779,0.377697,0.0379794,9.20916e-06,0.275221,0.192659,0.498599,0.817926,0.0712768,0.293082,0.299611,0.0283372,0.661007,0.000203756,0.595202,0.470018,0.0959591,0.896152,0.134615,0.0740372,0.269612,0.75591,0.316673,0.437751,0.62227,0.0601693,0.0010903,0.515916,0.751723,0.596001,0.301514,0.0307041,0.284609,0.669233,0.848855,0.0965297,0.256141,0.336446,0.499562,0.424311,0.0241792,0.243562,0.318279,0.833619,0.519431,0.678371,0.812294,0.32634,0.106287,0.984504,0.664961,0.787028,0.804364,0.773102,0.519913,0.550947,0.0865772,0.14517,0.0638044,0.00504817,0.0378634,0.197824,0.703882,0.0442393,0.216704,0.67644,0.305361,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}}
}}

Revision as of 19:51, 8 August 2012


Full id: C424_Hepatocyte_liver_Synoviocyte_tenocyte_Fibroblast_Adipocyte_Cardiac



Phase1 CAGE Peaks

Hg19::chr11:57367575..57367593,+p7@SERPING1
Hg19::chr12:7167997..7168040,+p1@C1S
Hg19::chr12:7168041..7168058,+p2@C1S
Hg19::chr12:7169832..7169844,+p8@C1S
Hg19::chr12:7169889..7169902,+p6@C1S
Hg19::chr12:7169907..7169929,+p5@C1S
Hg19::chr12:7170214..7170228,+p9@C1S
Hg19::chr12:7170229..7170249,+p10@C1S
Hg19::chr12:7171627..7171662,+p4@C1S
Hg19::chr12:7175756..7175804,+p@chr12:7175756..7175804
+
Hg19::chr12:7177634..7177646,+p@chr12:7177634..7177646
+
Hg19::chr12:7177786..7177801,+p@chr12:7177786..7177801
+
Hg19::chr12:7177864..7177876,+p@chr12:7177864..7177876
+
Hg19::chr12:7187896..7187912,-p@chr12:7187896..7187912
-
Hg19::chr12:7241517..7241547,-p@chr12:7241517..7241547
-
Hg19::chr12:7241961..7241984,-p@chr12:7241961..7241984
-
Hg19::chr12:7242235..7242247,-p@chr12:7242235..7242247
-
Hg19::chr12:7242281..7242299,-p@chr12:7242281..7242299
-
Hg19::chr12:7242779..7242821,-p9@C1R
Hg19::chr12:7244160..7244201,-p6@C1R
Hg19::chr12:7244222..7244240,-p8@C1R
Hg19::chr12:7244261..7244276,-p12@C1R
Hg19::chr12:7245018..7245073,-p1@C1R
Hg19::chr12:7261772..7261874,-p1@C1RL


Enriched pathways on this co-expression cluster<b>Summary:</b><br>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.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

p.valueFDRnGenesnPathwayName
5.39695550498319e-081.13875761155145e-05369Complement and coagulation cascades (KEGG):04610
2.26219774485948e-050.00286394234499211256Staphylococcus aureus infection (KEGG):05150
0.0001383288441453870.01459369305733842138Systemic lupus erythematosus (KEGG):05322
2.79572408770279e-060.000442423336878966220Complement Activation, Classical Pathway (Wikipathways):WP545
2.27747619344567e-087.20821215225554e-06352Complement and Coagulation Cascades (Wikipathways):WP558
1.78259609854325e-087.20821215225554e-06348{FCGR2B,50} (Static Module):NA



Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0006508proteolysis0.0132525917284209
GO:0004252serine-type endopeptidase activity0.0132525917284209
GO:0008236serine-type peptidase activity0.0132525917284209
GO:0017171serine hydrolase activity0.0132525917284209
GO:0004175endopeptidase activity0.033273032044513
GO:0006958complement activation, classical pathway0.033273032044513
GO:0002455humoral immune response mediated by circulating immunoglobulin0.033273032044513
GO:0006956complement activation0.033273032044513
GO:0002541activation of plasma proteins during acute inflammatory response0.033273032044513
GO:0016064immunoglobulin mediated immune response0.033273032044513
GO:0019724B cell mediated immunity0.033273032044513
GO:0008233peptidase activity0.033273032044513
GO:0002253activation of immune response0.033273032044513
GO:0002449lymphocyte mediated immunity0.033273032044513
GO:0006959humoral immune response0.033273032044513
GO:0002460adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains0.033273032044513
GO:0002250adaptive immune response0.033273032044513
GO:0002443leukocyte mediated immunity0.033273032044513
GO:0002526acute inflammatory response0.033273032044513
GO:0050778positive regulation of immune response0.033273032044513
GO:0002684positive regulation of immune system process0.033273032044513
GO:0050776regulation of immune response0.033273032044513
GO:0007596blood coagulation0.033273032044513
GO:0002682regulation of immune system process0.033273032044513
GO:0050817coagulation0.033273032044513
GO:0007599hemostasis0.033273032044513
GO:0051240positive regulation of multicellular organismal process0.033273032044513
GO:0002252immune effector process0.033605128731863
GO:0045087innate immune response0.0336202558677497
GO:0050878regulation of body fluid levels0.0355140395553653
GO:0042060wound healing0.0355140395553653
GO:0044267cellular protein metabolic process0.0355140395553653
GO:0044260cellular macromolecule metabolic process0.0357225886968076
GO:0019538protein metabolic process0.0379340249739084
GO:0008015blood circulation0.0379340249739084
GO:0003013circulatory system process0.0379340249739084
GO:0004867serine-type endopeptidase inhibitor activity0.0387405217571341



Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
multi-tissue structure4.12e-20347
organism subdivision2.80e-19365
multi-cellular organism3.51e-17659
trunk mesenchyme1.37e-14143
anatomical system7.88e-14625
anatomical group1.58e-13626
mesenchyme5.25e-13238
entire embryonic mesenchyme5.25e-13238
anatomical cluster9.79e-13286
trunk1.41e-12216
somite4.58e-1283
paraxial mesoderm4.58e-1283
presomitic mesoderm4.58e-1283
presumptive segmental plate4.58e-1283
trunk paraxial mesoderm4.58e-1283
presumptive paraxial mesoderm4.58e-1283
muscle tissue6.23e-1263
musculature6.23e-1263
musculature of body6.23e-1263
adult organism1.13e-11115
skeletal muscle tissue3.12e-1161
striated muscle tissue3.12e-1161
myotome3.12e-1161
dermomyotome8.64e-1170
embryo1.03e-09612
organ1.28e-09511
anatomical conduit1.47e-09241
multilaminar epithelium1.77e-0982
cell layer1.86e-09312
embryonic structure1.90e-09605
developing anatomical structure1.90e-09605
epithelium2.19e-09309
germ layer3.14e-09604
embryonic tissue3.14e-09604
presumptive structure3.14e-09604
epiblast (generic)3.14e-09604
surface structure1.23e-0895
primary circulatory organ4.89e-0827
unilaminar epithelium7.35e-08138
heart2.20e-0724
primitive heart tube2.20e-0724
primary heart field2.20e-0724
anterior lateral plate mesoderm2.20e-0724
heart tube2.20e-0724
heart primordium2.20e-0724
cardiac mesoderm2.20e-0724
cardiogenic plate2.20e-0724
heart rudiment2.20e-0724
digestive system3.42e-07155
digestive tract3.42e-07155
primitive gut3.42e-07155
epithelial tube7.27e-07118


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>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. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> 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. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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