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Coexpression cluster:C2229: Difference between revisions

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|ontology_enrichment_disease=DOID:305!4.35e-19!106;DOID:0050687!1.12e-11!143;DOID:1749!2.05e-07!14
|ontology_enrichment_disease=DOID:305!4.35e-19!106;DOID:0050687!1.12e-11!143;DOID:1749!2.05e-07!14
|ontology_enrichment_uberon=UBERON:0004119!3.76e-25!169;UBERON:0000925!3.76e-25!169;UBERON:0006595!3.76e-25!169;UBERON:0000077!3.19e-20!130;UBERON:0001007!1.42e-18!155;UBERON:0001555!1.42e-18!155;UBERON:0007026!1.42e-18!155;UBERON:0000466!4.46e-18!126;UBERON:0004921!6.32e-18!129;UBERON:0004185!6.32e-18!129;UBERON:0000464!1.03e-17!104;UBERON:0005177!6.88e-17!107;UBERON:0000481!2.53e-16!347;UBERON:0001041!8.84e-16!98;UBERON:0001004!1.02e-15!72;UBERON:0000065!4.93e-14!53;UBERON:0008947!1.42e-13!38;UBERON:0003258!1.42e-13!38;UBERON:0003104!1.67e-13!238;UBERON:0009142!1.67e-13!238;UBERON:0005911!3.05e-12!82;UBERON:0005178!4.14e-12!34;UBERON:0002224!4.14e-12!34;UBERON:0001008!9.62e-12!45;UBERON:0006554!1.59e-11!44;UBERON:0001048!1.62e-11!168;UBERON:0005181!1.93e-11!35;UBERON:0000063!9.39e-11!97;UBERON:0005153!1.19e-10!37;UBERON:0009569!1.45e-10!113;UBERON:0000922!2.09e-10!612;UBERON:0000072!5.95e-10!46;UBERON:0000062!6.84e-10!511;UBERON:0005157!1.00e-08!51;UBERON:0000058!1.87e-08!26;UBERON:0002050!1.95e-08!605;UBERON:0005423!1.95e-08!605;UBERON:0007196!2.29e-08!14;UBERON:0001558!2.29e-08!14;UBERON:0000064!3.27e-08!219;UBERON:0000475!3.74e-08!365;UBERON:0000923!3.95e-08!604;UBERON:0005291!3.95e-08!604;UBERON:0006598!3.95e-08!604;UBERON:0002532!3.95e-08!604;UBERON:0000468!4.13e-08!659;UBERON:0002553!7.00e-08!70;UBERON:0002048!7.25e-08!22;UBERON:0000117!7.25e-08!22;UBERON:0000171!7.25e-08!22;UBERON:0000170!7.25e-08!22;UBERON:0005597!7.25e-08!22;UBERON:0000118!7.25e-08!22;UBERON:0002100!8.21e-08!216;UBERON:0003064!1.58e-07!37;UBERON:0000489!2.46e-07!32;UBERON:0002113!2.94e-07!27;UBERON:0003918!2.94e-07!27;UBERON:0005095!2.94e-07!27;UBERON:0007687!2.94e-07!27;UBERON:0000915!5.12e-07!52;UBERON:0003101!6.14e-07!22;UBERON:0000079!6.14e-07!22;UBERON:0000080!6.60e-07!18;UBERON:0002120!6.60e-07!18;UBERON:0004875!6.60e-07!18;UBERON:0005721!6.60e-07!18;UBERON:0005754!6.60e-07!18;UBERON:0007297!6.60e-07!18
|ontology_enrichment_uberon=UBERON:0004119!3.76e-25!169;UBERON:0000925!3.76e-25!169;UBERON:0006595!3.76e-25!169;UBERON:0000077!3.19e-20!130;UBERON:0001007!1.42e-18!155;UBERON:0001555!1.42e-18!155;UBERON:0007026!1.42e-18!155;UBERON:0000466!4.46e-18!126;UBERON:0004921!6.32e-18!129;UBERON:0004185!6.32e-18!129;UBERON:0000464!1.03e-17!104;UBERON:0005177!6.88e-17!107;UBERON:0000481!2.53e-16!347;UBERON:0001041!8.84e-16!98;UBERON:0001004!1.02e-15!72;UBERON:0000065!4.93e-14!53;UBERON:0008947!1.42e-13!38;UBERON:0003258!1.42e-13!38;UBERON:0003104!1.67e-13!238;UBERON:0009142!1.67e-13!238;UBERON:0005911!3.05e-12!82;UBERON:0005178!4.14e-12!34;UBERON:0002224!4.14e-12!34;UBERON:0001008!9.62e-12!45;UBERON:0006554!1.59e-11!44;UBERON:0001048!1.62e-11!168;UBERON:0005181!1.93e-11!35;UBERON:0000063!9.39e-11!97;UBERON:0005153!1.19e-10!37;UBERON:0009569!1.45e-10!113;UBERON:0000922!2.09e-10!612;UBERON:0000072!5.95e-10!46;UBERON:0000062!6.84e-10!511;UBERON:0005157!1.00e-08!51;UBERON:0000058!1.87e-08!26;UBERON:0002050!1.95e-08!605;UBERON:0005423!1.95e-08!605;UBERON:0007196!2.29e-08!14;UBERON:0001558!2.29e-08!14;UBERON:0000064!3.27e-08!219;UBERON:0000475!3.74e-08!365;UBERON:0000923!3.95e-08!604;UBERON:0005291!3.95e-08!604;UBERON:0006598!3.95e-08!604;UBERON:0002532!3.95e-08!604;UBERON:0000468!4.13e-08!659;UBERON:0002553!7.00e-08!70;UBERON:0002048!7.25e-08!22;UBERON:0000117!7.25e-08!22;UBERON:0000171!7.25e-08!22;UBERON:0000170!7.25e-08!22;UBERON:0005597!7.25e-08!22;UBERON:0000118!7.25e-08!22;UBERON:0002100!8.21e-08!216;UBERON:0003064!1.58e-07!37;UBERON:0000489!2.46e-07!32;UBERON:0002113!2.94e-07!27;UBERON:0003918!2.94e-07!27;UBERON:0005095!2.94e-07!27;UBERON:0007687!2.94e-07!27;UBERON:0000915!5.12e-07!52;UBERON:0003101!6.14e-07!22;UBERON:0000079!6.14e-07!22;UBERON:0000080!6.60e-07!18;UBERON:0002120!6.60e-07!18;UBERON:0004875!6.60e-07!18;UBERON:0005721!6.60e-07!18;UBERON:0005754!6.60e-07!18;UBERON:0007297!6.60e-07!18
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118999,0.0737069,0.357807,0.621787,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.0339332,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.0277507,0.460406,0.0438521,0.435508,0.0439557,0.0522771,0.0787278,0.164404,0.159873,0.142462,0.143935,0.332403,0.0379537,0.6545,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.0757944,0.0625685,0.124464,0.0454742,0.173134,0.101893,0.142875,0.167635,0.171311,0.20386,0.0465855,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,2.73495e-09,0.0451012,0.0976639,0.351199,0.833813,0.415079,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.0278785,0.00147405,0.0939463,0.286748,0.00128218,0.0471607,0.163865,0.226359,0.960445,0.709625,0.265324,0.043404,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,1.08812e-10,0.0826805,0.246601,0.193021,0.240896,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.0475113,0.320355,0.364334,0.15547,0.110256,0.000238291,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.182843,0.130771,0.327768,0.00966571,0.147842,0.0339286,0.217363,0.119015,0.00709584,0.21618,0.000201473,0.107021,0.000185372,0.20272,0.392453,0.61565,0.0780061,0.315336,0.230477,0.279823,0.295555,0.502112,0.724669,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.514243,0.1267,0.00137171,0.502211,0.000478378,0.649813,0.537932,0.459994,0.523209,0.0465928,0.25423,0.490559,0.00332016,0.00559995,0.0272171,0.685908,0.00294638,0.0074346,0.818701,0.483077,0.590496,0.603763,0.184287,7.66752e-05,0.000629457,0.293249,0.0470729,0.0757071,0.00208746,0.478691,0.360199,0.0153629,0.657141,0.00893555,0.365494,0.212703,0.56318,0.0110532,0.315494,0.000282658,0.104625,0.0108102,0.328518,0.545608,0.310552,0.594773,0.483764,0.00961647,0.784052,0.209437,0.0118712,0.748403,0.0651244,0.169076,0.464001,0.60737,0.579004,0.150592,0.113944,0.586133,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.0205071,4.1712e-07,0.202522,6.0346e-05,0.507324,0.126097,0.3955,0.442469,0.212239,0.294954,0.156999,0.35974,0.667777,0.39549,0.234254,0.073225,0.017253,0.721266,0.50338,0.0746831,0.404625,0.416164,0.424691,0.00931622,0.00452282,0.62689,0.00176979,0.00068395,0.284496,0.512545,0.512178,0.563206,0.260945,0.684899,0.263302,0.552023,0.180735,0.189249,0.216102,0.0355932,6.89796e-06,0.397869,0.0585759,0.226491,0.417131,0.463987,0.0782409,0.503881,0.124057,0.0202528,0.0295677,0.00339209,0.000519892,0.261657,0.346776,0.000485493,0.00866064,0.438176,0.349112,0.391754,0.385425,0.307816,0.461541,0.386339,0.382854,0.598787,6.09746e-05,0.000445343,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.12664,0.387134,0.559969,0.358813,0.303004,0.0113028,0.493455,0.346636,0.457747,0.348802,0.137708,0.579645,0.447581,0.42505,0.254628,0.131374,0.0286377,0.416962,0.632833,0.0828233,0.387805,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.000690216,0.0265924,0.325254,0.266651,0.0460393,0.231754,0.249415,0.283107,0.285648,0.0191181,0.391071,0.279553,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,0.00106183,0.112422,0.170886,0.267687,0.315656,0.284866,2.88674e-06,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.341188,0.259328,0.437467,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.0136966,0.233244,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.328852,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.313858,0.223773,0.25788,0.181895,0.253768,0.000563201,0.202977,4.4199e-05,0.327002,0.28543,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.000372103,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.0154764,0.332746,0.271338,0.00288876,0.00571761,0.244395,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.0120454,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.00844265,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,1.27729e-11,0.151361,0.279606,0.00499935,0.150674,0.251128,0.246177,0.35674,0.0104945,0.000664446,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.00218951,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}}
}}

Revision as of 12:27, 5 September 2012


Full id: C2229_Amniotic_Placental_lung_thyroid_kidney_Small_testicular



Phase1 CAGE Peaks

Hg19::chr12:6485300..6485325,-p5@SCNN1A
Hg19::chr12:6485336..6485354,-p4@SCNN1A
Hg19::chr12:6485371..6485382,-p11@SCNN1A
Hg19::chr12:6485398..6485410,-p12@SCNN1A


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

No results for this coexpression

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

No GOStat results

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>

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.76e-25169
endoderm3.76e-25169
presumptive endoderm3.76e-25169
mixed endoderm/mesoderm-derived structure3.19e-20130
digestive system1.42e-18155
digestive tract1.42e-18155
primitive gut1.42e-18155
immaterial anatomical entity4.46e-18126
subdivision of digestive tract6.32e-18129
endodermal part of digestive tract6.32e-18129
anatomical space1.03e-17104
trunk region element6.88e-17107
multi-tissue structure2.53e-16347
foregut8.84e-1698
respiratory system1.02e-1572
respiratory tract4.93e-1453
respiratory primordium1.42e-1338
endoderm of foregut1.42e-1338
mesenchyme1.67e-13238
entire embryonic mesenchyme1.67e-13238
endo-epithelium3.05e-1282
thoracic cavity element4.14e-1234
thoracic cavity4.14e-1234
renal system9.62e-1245
urinary system structure1.59e-1144
primordium1.62e-11168
thoracic segment organ1.93e-1135
organ segment9.39e-1197
epithelial bud1.19e-1037
subdivision of trunk1.45e-10113
embryo2.09e-10612
segment of respiratory tract5.95e-1046
organ6.84e-10511
epithelial fold1.00e-0851
duct1.87e-0826
embryonic structure1.95e-08605
developing anatomical structure1.95e-08605
tracheobronchial tree2.29e-0814
lower respiratory tract2.29e-0814
organ part3.27e-08219
organism subdivision3.74e-08365
germ layer3.95e-08604
embryonic tissue3.95e-08604
presumptive structure3.95e-08604
epiblast (generic)3.95e-08604
multi-cellular organism4.13e-08659
anatomical cavity7.00e-0870
lung7.25e-0822
respiratory tube7.25e-0822
respiration organ7.25e-0822
pair of lungs7.25e-0822
lung primordium7.25e-0822
lung bud7.25e-0822
trunk8.21e-08216
intermediate mesoderm1.58e-0737
cavitated compound organ2.46e-0732
kidney2.94e-0727
kidney mesenchyme2.94e-0727
kidney rudiment2.94e-0727
kidney field2.94e-0727
thoracic segment of trunk5.12e-0752
male organism6.14e-0722
male reproductive system6.14e-0722
mesonephros6.60e-0718
pronephros6.60e-0718
nephrogenic cord6.60e-0718
pronephric mesoderm6.60e-0718
rostral part of nephrogenic cord6.60e-0718
presumptive pronephric mesoderm6.60e-0718
Disease
Ontology termp-valuen
carcinoma4.35e-19106
cell type cancer1.12e-11143
squamous cell carcinoma2.05e-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)

{{{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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066445.360256373075030.001211145381643620.00816122411210261
ESR1#2099430.76860329615451.11467714392546e-064.59415020656791e-05
HDAC2#3066413.41562023662633.0859005065161e-050.00062580264660201
NANOG#79923429.24477848101271.36586687657858e-065.32275263891756e-05
NR3C1#2908414.9730233311731.98868032687801e-050.000441999967352229
RAD21#5885410.35503389545638.6948481184721e-050.00129135557827803
TAF1#687243.343046285745290.008005664898701650.0321479404935213
TBP#690843.706770687096390.005296377814784350.0243656242885324
TFAP2A#7020416.5186343730451.34240829060362e-050.00032619771861878
TFAP2C#7022410.80922860986027.32289634782688e-050.00114421898813688



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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