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Coexpression cluster:C748: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.42e-16!106;DOID:0050687!1.81e-13!143
|ontology_enrichment_disease=DOID:305!1.42e-16!106;DOID:0050687!1.81e-13!143
|ontology_enrichment_uberon=UBERON:0004119!9.63e-29!169;UBERON:0000925!9.63e-29!169;UBERON:0006595!9.63e-29!169;UBERON:0001007!3.23e-22!155;UBERON:0001555!3.23e-22!155;UBERON:0007026!3.23e-22!155;UBERON:0003104!7.16e-20!238;UBERON:0009142!7.16e-20!238;UBERON:0004921!1.40e-19!129;UBERON:0004185!1.40e-19!129;UBERON:0000077!4.28e-19!130;UBERON:0000481!1.00e-17!347;UBERON:0001004!2.46e-17!72;UBERON:0001041!5.24e-15!98;UBERON:0000466!1.52e-14!126;UBERON:0000464!2.03e-14!104;UBERON:0002100!3.15e-14!216;UBERON:0000475!6.89e-14!365;UBERON:0001048!8.43e-14!168;UBERON:0000468!1.25e-13!659;UBERON:0000065!9.46e-13!53;UBERON:0005911!5.87e-11!82;UBERON:0000161!9.59e-11!35;UBERON:0000072!1.14e-10!46;UBERON:0000467!2.75e-10!625;UBERON:0000480!3.94e-10!626;UBERON:0009569!7.23e-10!113;UBERON:0000915!7.34e-10!52;UBERON:0005156!7.67e-10!59;UBERON:0000990!7.67e-10!59;UBERON:0000922!8.03e-10!612;UBERON:0000064!9.81e-10!219;UBERON:0008947!1.11e-09!38;UBERON:0003258!1.11e-09!38;UBERON:0003100!2.00e-09!41;UBERON:0002050!3.05e-09!605;UBERON:0005423!3.05e-09!605;UBERON:0000923!6.03e-09!604;UBERON:0005291!6.03e-09!604;UBERON:0006598!6.03e-09!604;UBERON:0002532!6.03e-09!604;UBERON:0000063!1.03e-08!97;UBERON:0005177!1.37e-08!107;UBERON:0005153!2.04e-08!37;UBERON:0000062!2.64e-08!511;UBERON:0000477!2.72e-08!286;UBERON:0000119!3.36e-08!312;UBERON:0000483!4.16e-08!309;UBERON:0000166!5.59e-08!21;UBERON:0005178!6.25e-08!34;UBERON:0002224!6.25e-08!34;UBERON:0003133!6.50e-08!48;UBERON:0002553!7.36e-08!70;UBERON:0003134!8.21e-08!37;UBERON:0000474!8.21e-08!37;UBERON:0000478!1.21e-07!24;UBERON:0005181!1.68e-07!35;UBERON:0005157!1.97e-07!51;UBERON:0005631!2.23e-07!14;UBERON:0000158!2.23e-07!14;UBERON:0004175!5.05e-07!25;UBERON:0003102!6.10e-07!95;UBERON:0001444!6.76e-07!48;UBERON:0005795!8.60e-07!22
|ontology_enrichment_uberon=UBERON:0004119!9.63e-29!169;UBERON:0000925!9.63e-29!169;UBERON:0006595!9.63e-29!169;UBERON:0001007!3.23e-22!155;UBERON:0001555!3.23e-22!155;UBERON:0007026!3.23e-22!155;UBERON:0003104!7.16e-20!238;UBERON:0009142!7.16e-20!238;UBERON:0004921!1.40e-19!129;UBERON:0004185!1.40e-19!129;UBERON:0000077!4.28e-19!130;UBERON:0000481!1.00e-17!347;UBERON:0001004!2.46e-17!72;UBERON:0001041!5.24e-15!98;UBERON:0000466!1.52e-14!126;UBERON:0000464!2.03e-14!104;UBERON:0002100!3.15e-14!216;UBERON:0000475!6.89e-14!365;UBERON:0001048!8.43e-14!168;UBERON:0000468!1.25e-13!659;UBERON:0000065!9.46e-13!53;UBERON:0005911!5.87e-11!82;UBERON:0000161!9.59e-11!35;UBERON:0000072!1.14e-10!46;UBERON:0000467!2.75e-10!625;UBERON:0000480!3.94e-10!626;UBERON:0009569!7.23e-10!113;UBERON:0000915!7.34e-10!52;UBERON:0005156!7.67e-10!59;UBERON:0000990!7.67e-10!59;UBERON:0000922!8.03e-10!612;UBERON:0000064!9.81e-10!219;UBERON:0008947!1.11e-09!38;UBERON:0003258!1.11e-09!38;UBERON:0003100!2.00e-09!41;UBERON:0002050!3.05e-09!605;UBERON:0005423!3.05e-09!605;UBERON:0000923!6.03e-09!604;UBERON:0005291!6.03e-09!604;UBERON:0006598!6.03e-09!604;UBERON:0002532!6.03e-09!604;UBERON:0000063!1.03e-08!97;UBERON:0005177!1.37e-08!107;UBERON:0005153!2.04e-08!37;UBERON:0000062!2.64e-08!511;UBERON:0000477!2.72e-08!286;UBERON:0000119!3.36e-08!312;UBERON:0000483!4.16e-08!309;UBERON:0000166!5.59e-08!21;UBERON:0005178!6.25e-08!34;UBERON:0002224!6.25e-08!34;UBERON:0003133!6.50e-08!48;UBERON:0002553!7.36e-08!70;UBERON:0003134!8.21e-08!37;UBERON:0000474!8.21e-08!37;UBERON:0000478!1.21e-07!24;UBERON:0005181!1.68e-07!35;UBERON:0005157!1.97e-07!51;UBERON:0005631!2.23e-07!14;UBERON:0000158!2.23e-07!14;UBERON:0004175!5.05e-07!25;UBERON:0003102!6.10e-07!95;UBERON:0001444!6.76e-07!48;UBERON:0005795!8.60e-07!22
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1,0.058394,0.0141389,0.263853,0.250981,0.137663,0.544895,0.187021,0.257444,0.191052,0.144803,0.120932,0.135307,1.74267e-05,0.150458,0.560857,0.167908,0.505898,7.05998e-05,0.116017,0.075073,0.013905,0.137272,0.201882,0.321342,0.08392,0.344691,0.069039,0.305067,0.100939,0.000909035,0.0204897,0.135223,0.285057,0.187413,0.112254,0.657997,0.0624082,0.538309,0.402629,0.279295,0.629279,0.710696,0.0032855,0.50054,0.268916,0.522767,0.0183977,0.117309,0.108678,0.488883,0.426313,0.289378,0.393714,0.00886177,0.162791,0.306168,0.068487,0.097199,0.255865,0.345558,0.396241,0.403546,2.61903e-06,9.51058e-05,0.17731,0.318785,0.171564,0.208652,0.250155,0.302707,0.434718,0.119189,0.246188,0.118294,0.0639501,0.901226,0.592704,0.356157,0.372151,0.0451309,0.512553,0.00312989,0.195403,0.163718,0.839641,0.205682,0.506771,0.377047,0.237617,0.238248,0.716786,0.124403,0.388692,0.506277,0.0680932,0.000137917,0.571685,0.59446,0.343085,0.225589,0.344355,0.169548,0.308886,0.207307,0.25036,0.157465,0.348305,0.0299292,0.609431,0.457137,0.131401,0.40648,0.155356,0.0180529,0.359054,0.300739,0.500395,0.334046,0.600989,0.194141,0.00334596,0.251557,0.00176371,0.0237271,0.548455,0.228581,0.324886,0.000769577,0.501626,0.198407,0.452722,0.211264,0.540994,0.445539,0.47537,0.462646,0.239328,0.297755,0.0223235,0.435273,0.121448,0.313173,0.0248965,0.0322846,0.545801,0.417939,0.61307,0.287038,0.00180894,0.0118513,0.274764,0.0627111,0.0102617,0.354821,0.176004,0.0346749,0.306067,0.00594513,0.650129,0.426094,0.319827,0.664512,0.330545,0.355935,0.0905574,0.146815,0.29423,0.626159,0.488206,0.535384,0.267489,0.52756,0.129535,0.397904,9.56218e-05,0.200162,0.279605,0.0366776,0.0135931,0.250798,0.0137765,0.0689647,0.126073,0.00019631,0.40264,0.150341,0.0164278,0.140293,0.240109,0.177833,0.57144,0.251455,0.009615,0.626294,0.505038,0.149589,0.641527,0.553662,0.553243,0.228256,3.17976e-05,0.0335258,0.826791,0.0393321,0.156511,0.504637,0.541499,0.232897,0.0155032,0.170313,0.753773,5.10681e-05,1.33378e-05,0.611154,0.00182323,0.0674012,0.267073,0.347521,0.0164354,0.175367,0.112321,0.131755,0.481939,0.0287893,0.712022,2.20673e-07,0.0112341,0.777522,0.408502,0.299227,0.885729,0.640351,0.315208,0.0377429,0.00444362,0.249306,0.476008,0.25263,0.000166266,2.51555e-06,0.375451,0.0954407,0.207815,0.0110989,0.00203358,0.0332524,0.0497677,0.565648,0.00988628,0.569953,0.7303,0.66279,0.603444,0.210203,0.528874,0.463307,0.428013,0.857261,0.309722,0.402709,0.477215,0.481099,0.61753,0.374787,0.706587,0.805341,0.162692,0.520009,0.12404,0.0565082,0.144125,0.573259,0.0193191,0.417126,0.0189094,0.196274,0.266177,0.26833,0.753361,0.00818442,0.536766,0.601724,0.861382,0.316277,0.897492,0.218103,0.392105,0.205775,0.0253063,0.422014,0.0246269,0.488066,0.554368,0.0413089,0.752172,0.00086774,0.506508,0.773368,0.030571,0.0212653,0.574038,6.2129e-05,0.0655992,0.274127,0.492562,0.627335,0.052466,0.689958,0.515389,0.0692357,0.470391,0.330458,0.00502904,0.737831,0.268558,0.817749,0.0474923,0.734805,0.459127,0.534679,0.925812,0.0915746,0.830046,0.0774547,0.475591,0.231952,0.483731,0.192775,0.541372,0.197592,0.000767435,0.739832,0.19207,0.705416,0.0127981,0.0894909,0.120279,0.689775,0.00763928,0.692595,0.105527,0.425923,0.224938,0.449528,0.194139,0.00291319,0.833847,0.187056,0.000584725,0.375731,0.503571,0.206772,0.509116,0.257235,0.695354,0.569392,0.118164,0.180861,0.300376,0.534569,0.0312682,0.105355,0.478226,0.183091,0.139529,0.230569,0.574762,0.292558,0.307527,0.486305,0.655454,0.520027,0.66105,0.573809,0.886204,0.0372567,0.545693,0.599595,0.603486,0.199458,0.744402,0.594113,0.555962,0.531493,0.382823,0.557694,0.114406,0.301747,0.0858791,0.165298,0.610721,0.0335958,0.27961,0.402705,0.575463,0.647625,0.602291,0.225542,0.211908,0.679099,0.355997,0.438647,0.615425,0.477261,0.0162611,0.148085,0.134057,0.0266445,0.178456,0.157134,0.109358,0.562004,0.212024,0.127623,0.374709,0.0565109,0.343584,0.201618,0.22457,0.468824,0.598491,0.189894,0.385114,0.100033,0.0482035,0.166426,0.472069,0.664008,0.0230232,0.592401,0.384353,0.526219,0.173921,0.240646,0.665997,0.0266902,0.566369,0.220971,0.573867,0.429354,0.186324,0.650216,0.363633,0.0683243,0.0870111,0.154625,0.559644,0.424261,0.192998,0.635262,0.129832,0.402607,0.663459,0.603153,0.49975,0.16045,0.311923,0.201306,0.744036,0.7016,0.594401,0.269963,0.562934,0.338919,0.182919,0.183452,0.0231923,0.257575,0.141393,0.183331,0.0552794,0.671299,0.216743,0.533448,0.255283,0.537287,0.267192,0.315214,0.215792,0.379171,0.214946,0.333105,0.222472,0.252354,0.396678,0.345496,0.152456,0.224382,0.291235,0.128266,0.412357,0.567591,0.368106,0.710254,0.0737773,0.429017,0.308191,0.295133,0.0501453,0.0707124,0.372922,0.290717,0.161813,0.705698,0.310473,0.404324,0.473851,0.208157,0.557233,0.71055,0.260286,0.422565,0.363221,0.594194,0.238174,0.361802,0.548539,0.183016,0.70279,0.344927,0.651673,0.482941,0.605877,0.302498,0.766699,0.608655,0.574325,0.30896,0.280668,0.75272,0.498751,0.133309,0.11203,0.236983,0.685564,0.323272,0.602683,0.159121,0.466029,0.589709,0.656486,0.570694,0.8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}}
}}

Revision as of 11:45, 5 September 2012


Full id: C748_amniotic_keratoacanthoma_salivary_Keratinocyte_maxillary_Corneal_esophagus



Phase1 CAGE Peaks

Hg19::chr12:52881239..52881250,-p@chr12:52881239..52881250
-
Hg19::chr18:24129045..24129064,-p5@KCTD1
Hg19::chr18:24129073..24129122,-p2@KCTD1
Hg19::chr18:28622699..28622725,-p1@DSC3
Hg19::chr18:28622729..28622751,-p2@DSC3
Hg19::chr18:28622774..28622792,-p3@DSC3
Hg19::chr6:138412531..138412579,-p@chr6:138412531..138412579
-
Hg19::chr6:138412884..138412951,-p@chr6:138412884..138412951
-
Hg19::chr6:138417550..138417583,-p@chr6:138417550..138417583
-
Hg19::chr6:138428549..138428563,-p1@PERP
Hg19::chr6:138428580..138428599,-p2@PERP


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

GO IDGO nameFDR corrected p-value
GO:0044459plasma membrane part0.0156189599557952
GO:0030054cell junction0.0156189599557952
GO:0005886plasma membrane0.0309965043918817
GO:0022610biological adhesion0.0309965043918817
GO:0007155cell adhesion0.0309965043918817



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
epithelial cell1.98e-45254
endo-epithelial cell4.33e-1743
endodermal cell1.44e-1659
embryonic cell4.12e-16248
squamous epithelial cell5.96e-1162
epithelial cell of alimentary canal1.90e-0921
ecto-epithelial cell2.23e-0733
respiratory epithelial cell2.32e-0713
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure9.63e-29169
endoderm9.63e-29169
presumptive endoderm9.63e-29169
digestive system3.23e-22155
digestive tract3.23e-22155
primitive gut3.23e-22155
mesenchyme7.16e-20238
entire embryonic mesenchyme7.16e-20238
subdivision of digestive tract1.40e-19129
endodermal part of digestive tract1.40e-19129
mixed endoderm/mesoderm-derived structure4.28e-19130
multi-tissue structure1.00e-17347
respiratory system2.46e-1772
foregut5.24e-1598
immaterial anatomical entity1.52e-14126
anatomical space2.03e-14104
trunk3.15e-14216
organism subdivision6.89e-14365
primordium8.43e-14168
multi-cellular organism1.25e-13659
respiratory tract9.46e-1353
endo-epithelium5.87e-1182
orifice9.59e-1135
segment of respiratory tract1.14e-1046
anatomical system2.75e-10625
anatomical group3.94e-10626
subdivision of trunk7.23e-10113
thoracic segment of trunk7.34e-1052
reproductive structure7.67e-1059
reproductive system7.67e-1059
embryo8.03e-10612
organ part9.81e-10219
respiratory primordium1.11e-0938
endoderm of foregut1.11e-0938
female organism2.00e-0941
embryonic structure3.05e-09605
developing anatomical structure3.05e-09605
germ layer6.03e-09604
embryonic tissue6.03e-09604
presumptive structure6.03e-09604
epiblast (generic)6.03e-09604
organ segment1.03e-0897
trunk region element1.37e-08107
epithelial bud2.04e-0837
organ2.64e-08511
anatomical cluster2.72e-08286
cell layer3.36e-08312
epithelium4.16e-08309
oral opening5.59e-0821
thoracic cavity element6.25e-0834
thoracic cavity6.25e-0834
reproductive organ6.50e-0848
anatomical cavity7.36e-0870
female reproductive organ8.21e-0837
female reproductive system8.21e-0837
extraembryonic structure1.21e-0724
thoracic segment organ1.68e-0735
epithelial fold1.97e-0751
extraembryonic membrane2.23e-0714
membranous layer2.23e-0714
internal genitalia5.05e-0725
surface structure6.10e-0795
subdivision of head6.76e-0748
embryonic uterus8.60e-0722
Disease
Ontology termp-valuen
carcinoma1.42e-16106
cell type cancer1.81e-13143


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
TFAP2C#702243.930628585403720.01418989706912680.0497792704310414
ZNF263#1012753.737200744095760.006510908182094970.027877695130773



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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