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|ontology_enrichment_uberon=UBERON:0000490!6.88e-14!138;UBERON:0002100!1.17e-11!216;UBERON:0003914!5.72e-11!118;UBERON:0005256!1.14e-10!143;UBERON:0003104!1.46e-10!238;UBERON:0009142!1.46e-10!238;UBERON:0004872!1.27e-08!84;UBERON:0002049!4.01e-08!79;UBERON:0007798!4.01e-08!79;UBERON:0000055!6.12e-08!69;UBERON:0001637!8.69e-08!42;UBERON:0003509!8.69e-08!42;UBERON:0004572!8.69e-08!42;UBERON:0001048!2.80e-07!168;UBERON:0000914!3.61e-07!83;UBERON:0002329!3.61e-07!83;UBERON:0003077!3.61e-07!83;UBERON:0003059!3.61e-07!83;UBERON:0007282!3.61e-07!83;UBERON:0009618!3.61e-07!83;UBERON:0007285!3.61e-07!83;UBERON:0003929!4.62e-07!54;UBERON:0000926!8.07e-07!448;UBERON:0004120!8.07e-07!448;UBERON:0006603!8.07e-07!448;UBERON:0001981!8.57e-07!60;UBERON:0007500!8.57e-07!60;UBERON:0004537!8.57e-07!60;UBERON:0006965!8.57e-07!60
|ontology_enrichment_uberon=UBERON:0000490!6.88e-14!138;UBERON:0002100!1.17e-11!216;UBERON:0003914!5.72e-11!118;UBERON:0005256!1.14e-10!143;UBERON:0003104!1.46e-10!238;UBERON:0009142!1.46e-10!238;UBERON:0004872!1.27e-08!84;UBERON:0002049!4.01e-08!79;UBERON:0007798!4.01e-08!79;UBERON:0000055!6.12e-08!69;UBERON:0001637!8.69e-08!42;UBERON:0003509!8.69e-08!42;UBERON:0004572!8.69e-08!42;UBERON:0001048!2.80e-07!168;UBERON:0000914!3.61e-07!83;UBERON:0002329!3.61e-07!83;UBERON:0003077!3.61e-07!83;UBERON:0003059!3.61e-07!83;UBERON:0007282!3.61e-07!83;UBERON:0009618!3.61e-07!83;UBERON:0007285!3.61e-07!83;UBERON:0003929!4.62e-07!54;UBERON:0000926!8.07e-07!448;UBERON:0004120!8.07e-07!448;UBERON:0006603!8.07e-07!448;UBERON:0001981!8.57e-07!60;UBERON:0007500!8.57e-07!60;UBERON:0004537!8.57e-07!60;UBERON:0006965!8.57e-07!60
|pathway_enrichment=2.88643650599953e-06;0.000913557154148851;2;49;N-Glycan biosynthesis (KEGG):00510!3.40211704163772e-05;0.00717846695785558;2;167;Protein processing in endoplasmic reticulum (KEGG):04141!0.000107161409738044;0.0169582930910455;2;296;Metabolism of proteins (Reactome):REACT_17015!0.000238131011744962;0.0301473860869122;2;441;AR up reg. targets (Netpath):NetPath_2!1.46039942267834e-06;0.000913557154148851;2;35;{INS,35} (Static Module):NA
|pathway_enrichment=2.88643650599953e-06;0.000913557154148851;2;49;N-Glycan biosynthesis (KEGG):00510!3.40211704163772e-05;0.00717846695785558;2;167;Protein processing in endoplasmic reticulum (KEGG):04141!0.000107161409738044;0.0169582930910455;2;296;Metabolism of proteins (Reactome):REACT_17015!0.000238131011744962;0.0301473860869122;2;441;AR up reg. targets (Netpath):NetPath_2!1.46039942267834e-06;0.000913557154148851;2;35;{INS,35} (Static Module):NA
|tfbs_overrepresentation=0.147255,0.0586687,0.716932,0.0477154,0.199763,0.287811,0.0430074,0.101122,0.03272,0.0257057,0.139423,0.00229455,0.188771,0.125978,0.148679,0.0619003,0.140982,0.0982016,0.0528514,0.108057,0.188635,0.132577,0.081977,0.0948982,0.0415721,0.215492,0.209392,0.0907212,0.143747,0.0933697,0.0226057,0.114046,0.0180314,0.208242,0.0665252,0.0844722,0.0308399,0.0429682,0.120351,0.0667043,0.0964797,0.0246116,0.140039,0.184019,0.00762432,0.0362416,0.0380166,0.18151,0.111283,0.121201,0.154071,0.0541794,0.0701653,0.0929951,0.198787,0.0384161,0.107455,0.212709,0.0783235,0.105572,0.0294301,0.149417,0.108602,0.0759481,0.054569,0.0504887,0.352278,0.0600088,0.0860723,0.0148026,0.378921,0.067678,0.089036,0.119383,0.00747605,0.0171177,0.0964936,0.0436945,0.0372495,0.00725252,0.0956287,0.226912,0.0425,0.114846,0.291327,0.251834,0.064341,0.209032,0.608896,0.062747,0.0857568,0.0495878,0.0953825,0.0473737,0.0853887,0.115028,0.21992,0.153631,0.0927458,0.27413,0.0574857,0.0422457,0.141874,0.0370665,0.219088,0.0409286,0.0669887,0.0649715,0.144217,0.269326,0.182599,0.0339971,0.149552,0.0176855,0.005305,0.0337525,0.0203386,0.0566549,0.139021,0.0838393,0.16671,0.214708,0.140123,0.00378931,0.102368,0.176912,0.0906875,0.0147934,0.0843604,0.134932,0.0595773,0.0748346,0.0572164,0.0227861,0.125792,0.108101,0.0648644,0.0553359,0.0330399,0.00395526,0.022776,0.127606,0.203923,0.155998,0.596561,0.0693171,0.0988228,0.00365114,0.0389418,0.120833,0.200647,0.143677,0.180712,0.0265818,0.0427088,0.117549,0.0747594,0.228385,0.0516985,0.0337251,0.227719,0.0952829,0.116642,0.147788,0.273479,0.114283,0.0400322,0.127369,0.0403542,0.312091,0.179689,0.137725,0.46397,0.0541353,0.0799324,0.090079,0.140334,0.181817,0.178449,0.0356339,0.158844,0.122474,0.0274061,0.115574,0.0737247,0.118847,0.183031,0.0401756,0.0828697,0.173562,0.107145,0.187297,0.122935,0.228812,0.112671,0.0470731,0.0782523,0.0602859,0.00234165,0.109673,0.0893019,0.060398,0.0308319,0.0606036,0.136451,0.259411,0.27358,0.15185,0.206299,0.178359,0.0458667,0.104357,0.121154,0.1129,0.312578,0.169057,0.164202,0.100942,0.062995,0.10299,0.14193,0.37245,0.15606,0.161026,0.0738599,0.126611,0.138852,0.085973,0.060453,0.059896,0.206862,0.0859236,0.0418404,0.0765029,0.0959204,0.0931946,0.0472272,0.263087,0.163502,0.214803,0.182472,0.348993,0.0983991,0.0830921,0.116283,0.136838,0.0815104,0.111647,0.372804,0.117027,0.159052,0.185164,0.185743,0.0980288,0.0980899,0.159674,0.107242,0.201859,0.0695832,0.582402,0.0619218,0.1751,0.163376,0.128096,0.0345133,0.0810678,0.0811639,0.0920653,0.118078,0.0755168,0.278352,0.063292,0.254773,0.446759,0.0865903,0.0380459,0.130174,0.219944,0.713218,0.451377,0.635872,0.563047,0.252249,0.228731,0.335423,0.261644,0.261553,0.118991,0.0806291,0.309233,0.49143,0.330703,0.0146881,0.329568,0.53472,0.615744,0.271958,0.292154,0.405773,0.0921263,0.217139,0.230901,0.187251,0.362792,0.181715,0.423979,0.109988,0.330894,0.218329,0.427027,0.376924,0.463191,0.0217334,0.528324,0.520763,0.370782,0.101703,0.0297533,0.253571,0.276829,0.301787,0.141124,0.316882,0.223503,0.503224,0.603208,0.283727,0.314747,0.577664,0.0474194,0.448095,0.576651,0.416816,0.292835,0.137839,0.439556,0.373868,0.57762,0.608919,0.18237,0.0359955,0.248484,0.747852,0.275351,0.236471,0.185661,0.346319,0.535598,0.270984,0.0179843,0.0340542,0.513852,0.522083,0.248634,0.281576,0.135034,0.163244,0.0670502,0.0730934,0.184794,0.596648,0.421596,0.217247,0.1002,0.671377,0.546839,0.191921,0.448039,0.218623,0.312808,0.032738,0.0451077,0.0747529,0.229003,0.000764752,0.589326,0.00568155,0.294698,0.34331,0.138202,0.289204,0.327108,0.683186,0.278044,0.085507,0.428671,0.228096,0.336314,0.19763,0.15631,0.00172609,0.104858,0.48267,0.420626,0.516462,0.582303,0.335105,0.144809,0.145539,0.385517,0.376191,0.447325,0.459928,0.252232,0.152681,0.0465712,0.137098,0.259235,0.134788,0.0985856,0.546222,0.293698,0.284593,0.343734,0.306556,0.305777,0.601433,0.503082,0.522888,0.284629,0.262537,0.359455,0.226257,0.0965765,0.41707,0.363685,0.464871,0.166672,0.206222,0.171685,0.651524,0.437176,0.269226,0.339277,0.00922147,0.281425,0.141758,0.455379,0.00680512,0.159617,0.238587,0.0799758,0.232251,0.189515,0.0891382,0.0595618,0.524997,0.257493,0.347298,0.182325,0.34988,0.475069,0.0958562,0.6408,0.630264,0.316179,0.00249247,0.0556835,0.192544,0.0779981,0.0575676,0.144322,0.223391,0.0223093,0.442884,0.0214618,0.191777,0.111931,0.28934,0.0435386,0.303336,0.126478,0.134852,0.10689,0.273326,0.0627924,0.381386,0.0179103,0.303939,0.279795,0.390395,0.0464827,0.169603,0.114583,0.104559,0.0899537,0.0866966,0.15983,0.107111,0.0438639,0.00389058,0.123593,0.129156,0.0238665,0.193675,0.346372,0.0499762,0.0828956,0.0666953,0.182185,0.111277,0.219383,0.332809,0.19559,0.132201,0.188694,0.0481795,0.199971,0.0966069,0.127758,0.175785,0.184486,0.169234,0.00395801,0.0952322,0.0112557,0.222432,0.107043,0.275244,0.00481323,0.0160457,0.141119,0.211595,0.0300692,0.131551,0.0445237,0.052362,0.208866,0.153187,0.0797897,0.0974211,0.160149,0.123526,0.0906475,0.0558058,0.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}}
}}

Revision as of 18:54, 8 August 2012


Full id: C3113_Smooth_Fibroblast_lymphangiectasia_colon_gall_mesenchymal_Chondrocyte



Phase1 CAGE Peaks

Hg19::chr11:125462725..125462768,+p1@STT3A
Hg19::chr11:125462771..125462784,+p2@STT3A
Hg19::chr20:35807714..35807756,+p1@RPN2


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
2.88643650599953e-060.000913557154148851249N-Glycan biosynthesis (KEGG):00510
3.40211704163772e-050.007178466957855582167Protein processing in endoplasmic reticulum (KEGG):04141
0.0001071614097380440.01695829309104552296Metabolism of proteins (Reactome):REACT_17015
0.0002381310117449620.03014738608691222441AR up reg. targets (Netpath):NetPath_2
1.46039942267834e-060.000913557154148851235{INS,35} (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:0018196peptidyl-asparagine modification2.70453216891284e-06
GO:0008250oligosaccharyl transferase complex2.70453216891284e-06
GO:0018279protein amino acid N-linked glycosylation via asparagine2.70453216891284e-06
GO:0004579dolichyl-diphosphooligosaccharide-protein glycotransferase activity2.70453216891284e-06
GO:0004576oligosaccharyl transferase activity2.70453216891284e-06
GO:0006487protein amino acid N-linked glycosylation2.02987218342151e-05
GO:0018193peptidyl-amino acid modification9.16662163693145e-05
GO:0006486protein amino acid glycosylation0.000145576305078965
GO:0043413biopolymer glycosylation0.000145576305078965
GO:0009101glycoprotein biosynthetic process0.000145576305078965
GO:0009100glycoprotein metabolic process0.000172974356899452
GO:0016758transferase activity, transferring hexosyl groups0.00028975026014442
GO:0016757transferase activity, transferring glycosyl groups0.000641139106386873
GO:0005789endoplasmic reticulum membrane0.000641139106386873
GO:0042175nuclear envelope-endoplasmic reticulum network0.000641139106386873
GO:0044432endoplasmic reticulum part0.00074540353528002
GO:0005783endoplasmic reticulum0.00213141778283036
GO:0012505endomembrane system0.00259198081383691
GO:0031090organelle membrane0.00530674891805402
GO:0009059macromolecule biosynthetic process0.00540140149668042
GO:0009058biosynthetic process0.0126675766612062
GO:0006464protein modification process0.0146815119011832
GO:0043412biopolymer modification0.0152200256949047
GO:0043234protein complex0.0152991783171678
GO:0016740transferase activity0.0188610573477174
GO:0032991macromolecular complex0.0256206593985365
GO:0044446intracellular organelle part0.026913961854617
GO:0044422organelle part0.026913961854617
GO:0044444cytoplasmic part0.0321256485265397
GO:0044267cellular protein metabolic process0.0455954016299721
GO:0044260cellular macromolecule metabolic process0.0455954016299721
GO:0019538protein metabolic process0.0473822131853775



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>disease_data<br>


Cell Type
Ontology termp-valuen
animal cell3.14e-26679
eukaryotic cell3.14e-26679
non-terminally differentiated cell5.46e-21180
embryonic cell4.50e-15248
somatic cell6.90e-15591
native cell3.27e-12722
fibroblast3.94e-1275
epithelial cell7.27e-11254
mesodermal cell4.51e-10119
muscle precursor cell2.14e-0857
myoblast2.14e-0857
multi-potent skeletal muscle stem cell2.14e-0857
muscle cell7.79e-0854
smooth muscle cell1.55e-0742
smooth muscle myoblast1.55e-0742
contractile cell5.06e-0759
vascular associated smooth muscle cell5.18e-0732
Uber Anatomy
Ontology termp-valuen
unilaminar epithelium6.88e-14138
trunk1.17e-11216
epithelial tube5.72e-11118
trunk mesenchyme1.14e-10143
mesenchyme1.46e-10238
entire embryonic mesenchyme1.46e-10238
splanchnic layer of lateral plate mesoderm1.27e-0884
vasculature4.01e-0879
vascular system4.01e-0879
vessel6.12e-0869
artery8.69e-0842
arterial blood vessel8.69e-0842
arterial system8.69e-0842
primordium2.80e-07168
somite3.61e-0783
paraxial mesoderm3.61e-0783
presomitic mesoderm3.61e-0783
presumptive segmental plate3.61e-0783
trunk paraxial mesoderm3.61e-0783
presumptive paraxial mesoderm3.61e-0783
gut epithelium4.62e-0754
mesoderm8.07e-07448
mesoderm-derived structure8.07e-07448
presumptive mesoderm8.07e-07448
blood vessel8.57e-0760
epithelial tube open at both ends8.57e-0760
blood vasculature8.57e-0760
vascular cord8.57e-0760
Disease
Ontology termp-valuen
disease of cellular proliferation1.96e-10239
cancer3.34e-10235
ovarian cancer1.74e-0714


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)

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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.