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Coexpression cluster:C2407: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.05e-18!106;DOID:0050687!6.31e-12!143;DOID:299!3.01e-07!25
|ontology_enrichment_disease=DOID:305!1.05e-18!106;DOID:0050687!6.31e-12!143;DOID:299!3.01e-07!25
|ontology_enrichment_uberon=UBERON:0004119!2.68e-24!169;UBERON:0000925!2.68e-24!169;UBERON:0006595!2.68e-24!169;UBERON:0001007!1.99e-18!155;UBERON:0001555!1.99e-18!155;UBERON:0007026!1.99e-18!155;UBERON:0000466!1.20e-17!126;UBERON:0000464!1.07e-16!104;UBERON:0000077!5.10e-16!130;UBERON:0003104!9.26e-16!238;UBERON:0009142!9.26e-16!238;UBERON:0004921!1.28e-15!129;UBERON:0004185!1.28e-15!129;UBERON:0000481!1.35e-15!347;UBERON:0002100!4.31e-14!216;UBERON:0005911!2.76e-13!82;UBERON:0009569!7.87e-13!113;UBERON:0005177!1.24e-12!107;UBERON:0000475!5.90e-12!365;UBERON:0001004!8.81e-12!72;UBERON:0000468!2.84e-11!659;UBERON:0000064!1.05e-10!219;UBERON:0001008!2.08e-10!45;UBERON:0000065!2.58e-10!53;UBERON:0006554!3.25e-10!44;UBERON:0003064!3.49e-10!37;UBERON:0005181!9.77e-10!35;UBERON:0005178!1.02e-09!34;UBERON:0002224!1.02e-09!34;UBERON:0000915!1.60e-09!52;UBERON:0001041!1.99e-09!98;UBERON:0005631!4.57e-09!14;UBERON:0000158!4.57e-09!14;UBERON:0001048!5.64e-09!168;UBERON:0005153!1.35e-08!37;UBERON:0002553!1.57e-08!70;UBERON:0000483!1.62e-08!309;UBERON:0000119!2.78e-08!312;UBERON:0000058!3.37e-08!26;UBERON:0003886!3.55e-08!63;UBERON:0000467!4.06e-08!625;UBERON:0008947!4.90e-08!38;UBERON:0003258!4.90e-08!38;UBERON:0005256!4.95e-08!143;UBERON:0005156!6.30e-08!59;UBERON:0000990!6.30e-08!59;UBERON:0000480!6.43e-08!626;UBERON:0000072!9.49e-08!46;UBERON:0005157!9.67e-08!51;UBERON:0000063!1.15e-07!97;UBERON:0000062!1.61e-07!511;UBERON:0004111!2.19e-07!241;UBERON:0000477!2.71e-07!286;UBERON:0007196!2.89e-07!14;UBERON:0001558!2.89e-07!14;UBERON:0000080!4.39e-07!18;UBERON:0002120!4.39e-07!18;UBERON:0004875!4.39e-07!18;UBERON:0005721!4.39e-07!18;UBERON:0005754!4.39e-07!18;UBERON:0007297!4.39e-07!18;UBERON:0004876!7.00e-07!20;UBERON:0002048!7.03e-07!22;UBERON:0000117!7.03e-07!22;UBERON:0000171!7.03e-07!22;UBERON:0000170!7.03e-07!22;UBERON:0005597!7.03e-07!22;UBERON:0000118!7.03e-07!22;UBERON:0000922!7.32e-07!612;UBERON:0000161!7.37e-07!35;UBERON:0006555!9.34e-07!17;UBERON:0005103!9.34e-07!17;UBERON:0000083!9.34e-07!17;UBERON:0009201!9.34e-07!17;UBERON:0004819!9.34e-07!17;UBERON:0006553!9.34e-07!17;UBERON:0003074!9.34e-07!17;UBERON:0003060!9.34e-07!17
|ontology_enrichment_uberon=UBERON:0004119!2.68e-24!169;UBERON:0000925!2.68e-24!169;UBERON:0006595!2.68e-24!169;UBERON:0001007!1.99e-18!155;UBERON:0001555!1.99e-18!155;UBERON:0007026!1.99e-18!155;UBERON:0000466!1.20e-17!126;UBERON:0000464!1.07e-16!104;UBERON:0000077!5.10e-16!130;UBERON:0003104!9.26e-16!238;UBERON:0009142!9.26e-16!238;UBERON:0004921!1.28e-15!129;UBERON:0004185!1.28e-15!129;UBERON:0000481!1.35e-15!347;UBERON:0002100!4.31e-14!216;UBERON:0005911!2.76e-13!82;UBERON:0009569!7.87e-13!113;UBERON:0005177!1.24e-12!107;UBERON:0000475!5.90e-12!365;UBERON:0001004!8.81e-12!72;UBERON:0000468!2.84e-11!659;UBERON:0000064!1.05e-10!219;UBERON:0001008!2.08e-10!45;UBERON:0000065!2.58e-10!53;UBERON:0006554!3.25e-10!44;UBERON:0003064!3.49e-10!37;UBERON:0005181!9.77e-10!35;UBERON:0005178!1.02e-09!34;UBERON:0002224!1.02e-09!34;UBERON:0000915!1.60e-09!52;UBERON:0001041!1.99e-09!98;UBERON:0005631!4.57e-09!14;UBERON:0000158!4.57e-09!14;UBERON:0001048!5.64e-09!168;UBERON:0005153!1.35e-08!37;UBERON:0002553!1.57e-08!70;UBERON:0000483!1.62e-08!309;UBERON:0000119!2.78e-08!312;UBERON:0000058!3.37e-08!26;UBERON:0003886!3.55e-08!63;UBERON:0000467!4.06e-08!625;UBERON:0008947!4.90e-08!38;UBERON:0003258!4.90e-08!38;UBERON:0005256!4.95e-08!143;UBERON:0005156!6.30e-08!59;UBERON:0000990!6.30e-08!59;UBERON:0000480!6.43e-08!626;UBERON:0000072!9.49e-08!46;UBERON:0005157!9.67e-08!51;UBERON:0000063!1.15e-07!97;UBERON:0000062!1.61e-07!511;UBERON:0004111!2.19e-07!241;UBERON:0000477!2.71e-07!286;UBERON:0007196!2.89e-07!14;UBERON:0001558!2.89e-07!14;UBERON:0000080!4.39e-07!18;UBERON:0002120!4.39e-07!18;UBERON:0004875!4.39e-07!18;UBERON:0005721!4.39e-07!18;UBERON:0005754!4.39e-07!18;UBERON:0007297!4.39e-07!18;UBERON:0004876!7.00e-07!20;UBERON:0002048!7.03e-07!22;UBERON:0000117!7.03e-07!22;UBERON:0000171!7.03e-07!22;UBERON:0000170!7.03e-07!22;UBERON:0005597!7.03e-07!22;UBERON:0000118!7.03e-07!22;UBERON:0000922!7.32e-07!612;UBERON:0000161!7.37e-07!35;UBERON:0006555!9.34e-07!17;UBERON:0005103!9.34e-07!17;UBERON:0000083!9.34e-07!17;UBERON:0009201!9.34e-07!17;UBERON:0004819!9.34e-07!17;UBERON:0006553!9.34e-07!17;UBERON:0003074!9.34e-07!17;UBERON:0003060!9.34e-07!17
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07,0.621787,0.178782,0.019419,0.0866228,0.271849,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.226143,0.460406,0.0438521,0.435508,0.281453,0.0522771,0.0787278,0.164404,0.159873,0.142462,0.143935,0.332403,0.0379537,0.287316,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.487259,0.051371,0.363016,0.100188,0.223102,0.107653,0.0303023,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.389792,0.000107259,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.0721023,0.548036,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.107849,0.415079,0.000365702,0.0769795,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.286748,0.00128218,0.0471607,0.163865,0.226359,0.626334,0.307186,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.0501465,0.100006,0.362866,0.197817,0.251078,0.279874,0.133127,0.410303,0.223717,0.426452,0.0207859,0.0826805,0.246601,0.193021,0.608002,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,0.178639,0.000449988,0.0578865,0.364334,0.15547,0.110256,0.415419,0.000606841,0.147307,0.240761,0.225961,0.124417,0.000841317,0.317428,0.182843,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.0896967,0.61565,0.0780061,0.315336,0.230477,0.043419,0.0487563,0.502112,0.140541,0.0478217,0.507599,0.170854,0.0575231,0.174063,0.0368787,0.459091,0.189333,0.000773574,0.296013,0.282366,0.537932,0.459994,0.170061,0.00885937,0.25423,0.490559,0.45013,0.500698,0.135135,0.0302459,0.0510811,0.529642,0.509113,0.14198,0.224887,0.603763,0.541914,0.627201,0.14959,0.757308,0.290703,0.622694,0.366999,0.478691,0.010661,0.0690757,0.0937029,0.099511,0.365494,0.212703,0.201391,0.364079,0.107716,0.579886,0.421038,0.0537414,0.328518,0.187186,0.310552,0.0529131,0.0295909,0.0342735,0.19941,0.209437,0.55323,0.161672,0.0651244,0.169076,0.12974,0.0572812,0.214786,0.605327,0.0112416,0.0500888,0.261575,0.257956,0.264245,0.0831707,0.0602936,0.522925,0.113006,0.0277366,0.202522,0.183837,0.507324,0.126097,0.3955,0.116739,0.0243103,0.294954,0.156999,0.0742603,0.667777,0.0912179,0.234254,0.357409,0.146291,0.137737,0.15578,0.000504793,0.404625,0.0034658,0.424691,0.132999,0.000577191,0.259048,0.36666,0.642173,0.00487493,0.512545,0.512178,0.0102074,0.103692,0.110875,0.263302,0.192292,0.180735,0.439629,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.102502,0.463987,0.0782409,0.0342559,0.0237654,0.00397922,0.142363,0.122467,0.301581,0.00371213,0.000976975,0.131322,0.00866064,0.0208637,0.349112,0.391754,0.385425,0.307816,0.461541,0.0866806,0.00154176,0.598787,0.139139,0.611661,0.319747,0.475047,0.557967,0.0690544,0.282281,0.0710918,0.2536,0.246827,0.564333,0.347466,0.387134,0.198743,0.358813,0.100705,0.574252,0.148933,0.346636,0.457747,0.348802,0.137708,0.215342,0.022473,0.42505,0.254628,0.355111,0.0286377,0.416962,0.00368966,0.378333,0.387805,0.0384092,0.22798,0.102495,0.0703938,0.263896,0.0446972,0.24452,0.0613938,0.242783,0.0947248,0.336551,0.0239343,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.215123,0.00727088,0.0265924,0.000730194,0.0392149,0.187728,0.231754,0.249415,0.283107,0.0453548,2.5902e-05,0.0890097,0.0433305,0.25563,0.240967,0.160955,0.256687,0.0432189,0.122439,0.16188,0.23235,0.290415,9.11204e-05,0.112422,0.170886,0.267687,0.315656,0.00489571,0.0887542,0.267811,0.338547,0.147872,0.189388,0.293546,0.210125,0.0478543,0.218414,0.0509944,0.0871471,0.0689852,0.0602698,0.00888732,0.0369803,0.0207461,0.0217216,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,2.32417e-07,0.0874139,0.233244,0.207281,0.00774558,0.195748,0.27845,0.0138433,0.0308468,0.239139,0.095257,0.0612213,0.332769,0.262022,0.04166,0.266687,0.184534,0.0338675,0.31749,0.15156,0.0460134,0.313858,0.00224298,0.25788,0.181895,0.253768,4.07902e-05,0.0221551,0.170837,0.327002,0.28543,0.00220735,0.028353,0.127111,0.259989,0.390754,6.90049e-06,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.00817441,0.0406836,0.242121,0.0498554,0.0326468,0.106889,0.128632,0.0845989,0.159153,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.0201006,0.184359,0.0634867,0.0600054,0.0364266,0.0472356,0.376537,0.322827,0.229571,0.00114556,0.335984,0.171704,0.208256,0.0387226,0.256405,0.362898,0.0510917,0.0163014,0.151361,0.279606,0.0457079,0.150674,0.251128,0.246177,0.0729297,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.00185587,0.222091,0.205977,0.067531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}}
}}

Revision as of 11:34, 5 September 2012


Full id: C2407_Alveolar_Tracheal_Small_Bronchial_MCF7_Amniotic_Renal



Phase1 CAGE Peaks

Hg19::chr17:39680005..39680049,-p@chr17:39680005..39680049
-
Hg19::chr17:39680672..39680701,-p4@KRT19
Hg19::chr17:39680781..39680798,-p2@KRT19
Hg19::chr17:39684550..39684567,-p1@KRT19


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 structure2.68e-24169
endoderm2.68e-24169
presumptive endoderm2.68e-24169
digestive system1.99e-18155
digestive tract1.99e-18155
primitive gut1.99e-18155
immaterial anatomical entity1.20e-17126
anatomical space1.07e-16104
mixed endoderm/mesoderm-derived structure5.10e-16130
mesenchyme9.26e-16238
entire embryonic mesenchyme9.26e-16238
subdivision of digestive tract1.28e-15129
endodermal part of digestive tract1.28e-15129
multi-tissue structure1.35e-15347
trunk4.31e-14216
endo-epithelium2.76e-1382
subdivision of trunk7.87e-13113
trunk region element1.24e-12107
organism subdivision5.90e-12365
respiratory system8.81e-1272
multi-cellular organism2.84e-11659
organ part1.05e-10219
renal system2.08e-1045
respiratory tract2.58e-1053
urinary system structure3.25e-1044
intermediate mesoderm3.49e-1037
thoracic segment organ9.77e-1035
thoracic cavity element1.02e-0934
thoracic cavity1.02e-0934
thoracic segment of trunk1.60e-0952
foregut1.99e-0998
extraembryonic membrane4.57e-0914
membranous layer4.57e-0914
primordium5.64e-09168
epithelial bud1.35e-0837
anatomical cavity1.57e-0870
epithelium1.62e-08309
cell layer2.78e-08312
duct3.37e-0826
body cavity precursor3.55e-0863
anatomical system4.06e-08625
respiratory primordium4.90e-0838
endoderm of foregut4.90e-0838
trunk mesenchyme4.95e-08143
reproductive structure6.30e-0859
reproductive system6.30e-0859
anatomical group6.43e-08626
segment of respiratory tract9.49e-0846
epithelial fold9.67e-0851
organ segment1.15e-0797
organ1.61e-07511
anatomical conduit2.19e-07241
anatomical cluster2.71e-07286
tracheobronchial tree2.89e-0714
lower respiratory tract2.89e-0714
mesonephros4.39e-0718
pronephros4.39e-0718
nephrogenic cord4.39e-0718
pronephric mesoderm4.39e-0718
rostral part of nephrogenic cord4.39e-0718
presumptive pronephric mesoderm4.39e-0718
urogenital ridge7.00e-0720
lung7.03e-0722
respiratory tube7.03e-0722
respiration organ7.03e-0722
pair of lungs7.03e-0722
lung primordium7.03e-0722
lung bud7.03e-0722
embryo7.32e-07612
orifice7.37e-0735
excretory tube9.34e-0717
mesonephric epithelium9.34e-0717
mesonephric tubule9.34e-0717
nephric duct9.34e-0717
kidney epithelium9.34e-0717
renal duct9.34e-0717
mesonephric duct9.34e-0717
pronephric duct9.34e-0717
Disease
Ontology termp-valuen
carcinoma1.05e-18106
cell type cancer6.31e-12143
adenocarcinoma3.01e-0725


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
GATA3#2625427.2365163572061.81561517799785e-066.76734595199561e-05



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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