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Coexpression cluster:C2434: Difference between revisions

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|ontology_enrichment_disease=DOID:305!3.56e-18!106;DOID:0050687!1.75e-13!143;DOID:299!8.67e-08!25
|ontology_enrichment_disease=DOID:305!3.56e-18!106;DOID:0050687!1.75e-13!143;DOID:299!8.67e-08!25
|ontology_enrichment_uberon=UBERON:0004119!2.24e-20!169;UBERON:0000925!2.24e-20!169;UBERON:0006595!2.24e-20!169;UBERON:0004921!1.45e-19!129;UBERON:0004185!1.45e-19!129;UBERON:0000466!1.52e-18!126;UBERON:0000062!6.81e-18!511;UBERON:0001007!6.97e-18!155;UBERON:0001555!6.97e-18!155;UBERON:0007026!6.97e-18!155;UBERON:0005177!8.18e-18!107;UBERON:0000481!2.25e-16!347;UBERON:0000077!1.83e-15!130;UBERON:0001041!2.12e-15!98;UBERON:0005172!1.71e-14!55;UBERON:0005173!1.71e-14!55;UBERON:0001048!5.20e-14!168;UBERON:0009569!1.14e-13!113;UBERON:0002417!7.97e-13!61;UBERON:0000916!7.97e-13!61;UBERON:0005911!1.43e-12!82;UBERON:0000464!3.62e-12!104;UBERON:0000922!4.56e-12!612;UBERON:0007023!2.24e-11!115;UBERON:0002050!4.67e-10!605;UBERON:0005423!4.67e-10!605;UBERON:0000923!8.10e-10!604;UBERON:0005291!8.10e-10!604;UBERON:0006598!8.10e-10!604;UBERON:0002532!8.10e-10!604;UBERON:0000064!9.68e-10!219;UBERON:0003104!1.38e-09!238;UBERON:0009142!1.38e-09!238;UBERON:0001008!1.62e-09!45;UBERON:0007499!2.21e-09!25;UBERON:0002553!2.59e-09!70;UBERON:0009856!2.67e-09!26;UBERON:0006554!3.00e-09!44;UBERON:0009497!3.94e-09!25;UBERON:0000015!3.94e-09!25;UBERON:0002423!3.94e-09!25;UBERON:0006235!3.94e-09!25;UBERON:0004161!3.94e-09!25;UBERON:0002365!5.46e-09!31;UBERON:0002330!5.46e-09!31;UBERON:0000058!9.27e-09!26;UBERON:0000468!1.13e-08!659;UBERON:0003929!1.75e-08!54;UBERON:0000489!2.41e-08!32;UBERON:0003103!3.68e-08!69;UBERON:0008835!3.81e-08!22;UBERON:0003894!3.81e-08!22;UBERON:0009854!4.52e-08!23;UBERON:0002530!5.02e-08!59;UBERON:0002113!8.04e-08!27;UBERON:0003918!8.04e-08!27;UBERON:0005095!8.04e-08!27;UBERON:0007687!8.04e-08!27;UBERON:0000477!1.57e-07!286;UBERON:0004111!1.59e-07!241;UBERON:0003886!1.62e-07!63;UBERON:0003887!1.69e-07!21;UBERON:0002107!2.60e-07!19;UBERON:0006925!2.60e-07!19;UBERON:0008836!2.60e-07!19;UBERON:0000475!3.02e-07!365;UBERON:0001004!4.02e-07!72;UBERON:0000080!4.04e-07!18;UBERON:0002120!4.04e-07!18;UBERON:0004875!4.04e-07!18;UBERON:0005721!4.04e-07!18;UBERON:0005754!4.04e-07!18;UBERON:0007297!4.04e-07!18;UBERON:0005409!5.89e-07!35;UBERON:0006555!7.22e-07!17;UBERON:0005103!7.22e-07!17;UBERON:0000083!7.22e-07!17;UBERON:0009201!7.22e-07!17;UBERON:0004819!7.22e-07!17;UBERON:0006553!7.22e-07!17;UBERON:0003074!7.22e-07!17;UBERON:0003060!7.22e-07!17
|ontology_enrichment_uberon=UBERON:0004119!2.24e-20!169;UBERON:0000925!2.24e-20!169;UBERON:0006595!2.24e-20!169;UBERON:0004921!1.45e-19!129;UBERON:0004185!1.45e-19!129;UBERON:0000466!1.52e-18!126;UBERON:0000062!6.81e-18!511;UBERON:0001007!6.97e-18!155;UBERON:0001555!6.97e-18!155;UBERON:0007026!6.97e-18!155;UBERON:0005177!8.18e-18!107;UBERON:0000481!2.25e-16!347;UBERON:0000077!1.83e-15!130;UBERON:0001041!2.12e-15!98;UBERON:0005172!1.71e-14!55;UBERON:0005173!1.71e-14!55;UBERON:0001048!5.20e-14!168;UBERON:0009569!1.14e-13!113;UBERON:0002417!7.97e-13!61;UBERON:0000916!7.97e-13!61;UBERON:0005911!1.43e-12!82;UBERON:0000464!3.62e-12!104;UBERON:0000922!4.56e-12!612;UBERON:0007023!2.24e-11!115;UBERON:0002050!4.67e-10!605;UBERON:0005423!4.67e-10!605;UBERON:0000923!8.10e-10!604;UBERON:0005291!8.10e-10!604;UBERON:0006598!8.10e-10!604;UBERON:0002532!8.10e-10!604;UBERON:0000064!9.68e-10!219;UBERON:0003104!1.38e-09!238;UBERON:0009142!1.38e-09!238;UBERON:0001008!1.62e-09!45;UBERON:0007499!2.21e-09!25;UBERON:0002553!2.59e-09!70;UBERON:0009856!2.67e-09!26;UBERON:0006554!3.00e-09!44;UBERON:0009497!3.94e-09!25;UBERON:0000015!3.94e-09!25;UBERON:0002423!3.94e-09!25;UBERON:0006235!3.94e-09!25;UBERON:0004161!3.94e-09!25;UBERON:0002365!5.46e-09!31;UBERON:0002330!5.46e-09!31;UBERON:0000058!9.27e-09!26;UBERON:0000468!1.13e-08!659;UBERON:0003929!1.75e-08!54;UBERON:0000489!2.41e-08!32;UBERON:0003103!3.68e-08!69;UBERON:0008835!3.81e-08!22;UBERON:0003894!3.81e-08!22;UBERON:0009854!4.52e-08!23;UBERON:0002530!5.02e-08!59;UBERON:0002113!8.04e-08!27;UBERON:0003918!8.04e-08!27;UBERON:0005095!8.04e-08!27;UBERON:0007687!8.04e-08!27;UBERON:0000477!1.57e-07!286;UBERON:0004111!1.59e-07!241;UBERON:0003886!1.62e-07!63;UBERON:0003887!1.69e-07!21;UBERON:0002107!2.60e-07!19;UBERON:0006925!2.60e-07!19;UBERON:0008836!2.60e-07!19;UBERON:0000475!3.02e-07!365;UBERON:0001004!4.02e-07!72;UBERON:0000080!4.04e-07!18;UBERON:0002120!4.04e-07!18;UBERON:0004875!4.04e-07!18;UBERON:0005721!4.04e-07!18;UBERON:0005754!4.04e-07!18;UBERON:0007297!4.04e-07!18;UBERON:0005409!5.89e-07!35;UBERON:0006555!7.22e-07!17;UBERON:0005103!7.22e-07!17;UBERON:0000083!7.22e-07!17;UBERON:0009201!7.22e-07!17;UBERON:0004819!7.22e-07!17;UBERON:0006553!7.22e-07!17;UBERON:0003074!7.22e-07!17;UBERON:0003060!7.22e-07!17
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766,8.38788e-06,0.178782,0.019419,0.0866228,0.0408454,0.282657,0.105411,0.0997542,0.209692,0.248936,0.0725263,0.102587,0.0742013,0.0552936,0.0457886,0.0514927,0.324236,0.220368,0.258624,0.064656,0.0277507,0.460406,0.0438521,0.000317433,0.281453,0.0522771,0.0787278,0.515487,0.159873,0.142462,0.143935,0.332403,0.0379537,0.0230803,0.187953,0.051459,0.114868,0.0726892,0.18732,0.32305,0.278397,0.245002,0.170848,0.0303627,0.302909,0.363016,0.100188,0.223102,0.107653,0.235857,0.419621,0.191914,0.184022,0.216557,0.182956,0.116818,0.00167639,0.0757944,0.0625685,0.124464,0.544477,0.173134,0.101893,0.142875,0.167635,0.171311,0.458838,0.0465855,0.0685131,0.130287,0.0661526,0.0815772,0.0993937,0.122878,0.187329,0.0451012,0.0976639,0.351199,0.00252788,0.171375,0.278645,0.365775,0.155708,0.248017,0.22995,0.652972,0.0760151,0.0629459,0.486024,0.0803251,0.226641,0.379174,0.0939463,0.00500232,0.0779623,0.0471607,0.014226,0.000147351,0.0464703,0.0130885,0.265324,0.279778,0.141699,0.0887743,0.142302,0.0653269,0.125712,0.264432,0.0994829,0.0604041,0.144185,0.0925862,0.289561,0.199201,0.049937,0.172796,0.0595495,0.071232,0.149346,0.121978,0.22302,0.137423,0.284016,0.0754883,0.299492,0.100006,0.362866,0.197817,0.0345492,0.279874,0.133127,0.410303,0.223717,0.426452,0.196838,0.0826805,0.0332683,0.193021,0.0153391,0.202165,0.0946865,0.120618,0.079499,0.18762,0.195618,0.127688,0.201169,0.220353,0.24948,2.08837e-06,0.291976,0.00720587,0.364334,0.15547,0.110256,0.415419,0.14794,0.147307,0.240761,0.225961,0.124417,0.335582,0.317428,0.0178393,0.130771,0.327768,0.135777,0.147842,0.0339286,0.217363,0.119015,0.690952,0.21618,0.243266,0.107021,0.238657,0.20272,0.392453,6.31811e-05,0.0780061,0.315336,0.230477,0.279823,0.295555,0.00567943,0.0420826,0.0478217,0.158752,0.170854,0.0575231,0.174063,0.514243,0.459091,0.00137171,0.502211,0.296013,0.00447273,0.537932,0.0247432,0.170061,0.548059,0.25423,7.35929e-05,0.45013,0.153911,0.472542,0.00670713,0.747471,0.0410736,0.818701,0.483077,0.0131065,0.0147688,0.184287,0.627201,0.0237007,0.293249,0.290703,0.622694,0.722684,0.478691,0.360199,0.608176,0.657141,0.519564,0.365494,0.212703,0.56318,0.364079,0.680099,0.579886,0.421038,0.569409,0.328518,0.545608,0.310552,0.865054,0.483764,0.261345,0.19941,0.209437,0.11765,0.748403,0.598945,0.169076,0.464001,0.871271,0.214786,0.0565519,0.278028,0.315519,0.261575,0.257956,0.264245,0.379063,0.326516,0.522925,0.113006,0.475063,0.202522,0.183837,0.507324,0.126097,0.3955,0.442469,0.000111592,0.294954,0.156999,0.35974,0.667777,0.0912179,0.234254,0.357409,0.146291,0.721266,0.50338,0.620526,0.404625,0.759068,0.424691,0.715362,0.479581,0.62689,0.884725,0.642173,0.284496,0.512545,0.162017,0.00164085,0.829402,0.110875,0.263302,0.552023,0.180735,0.775168,0.216102,0.254659,0.109605,0.397869,0.582542,0.226491,0.417131,0.463987,0.0782409,0.503881,0.0237654,0.639483,0.483658,3.35458e-06,0.301581,0.0376831,0.346776,0.000485493,0.0458396,0.438176,0.349112,0.741477,0.0134085,0.307816,0.461541,0.386339,0.382854,0.598787,0.478745,0.0158475,0.319747,0.475047,0.557967,0.608127,0.282281,0.612712,0.2536,0.246827,0.564333,0.70712,0.387134,0.559969,0.358813,0.668972,0.574252,0.148933,0.00937114,0.457747,0.0694762,0.476541,0.0118751,0.022473,0.42505,0.254628,0.355111,0.479347,0.416962,0.632833,0.0828233,0.738545,0.264038,0.22798,0.102495,0.350933,0.263896,0.0446972,0.24452,0.329284,0.242783,0.0947248,0.336551,0.210656,0.246234,0.211271,0.281295,0.267248,0.118257,0.125087,0.0250035,0.321224,0.0265924,0.325254,0.266651,0.546295,0.231754,0.249415,0.283107,0.285648,0.10809,0.391071,0.279553,0.25563,0.240967,0.160955,0.036192,0.0432189,0.00782177,0.16188,0.23235,0.290415,0.00106183,0.112422,0.170886,0.267687,0.315656,0.284866,0.0887542,0.000306974,0.338547,0.147872,0.189388,0.293546,0.210125,0.292967,0.0258076,0.0509944,0.0871471,0.0689852,0.0602698,0.0662546,0.259328,0.00289389,0.201057,0.15696,0.129351,0.141936,0.0786166,0.276997,0.205513,0.282389,0.251421,0.162089,0.330223,0.387837,0.000167787,0.207281,0.327401,0.195748,0.27845,0.161712,0.237871,0.239139,0.095257,0.0612213,0.332769,0.262022,0.274403,0.266687,0.184534,0.248707,0.31749,0.15156,0.287598,0.00673322,0.223773,0.25788,0.181895,0.253768,0.30702,0.202977,0.170837,0.0604859,0.0452813,0.222656,0.228479,0.127111,0.259989,0.390754,0.355805,0.279739,0.108118,0.259901,0.139723,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.332746,0.271338,0.242121,0.298673,0.244395,0.106889,0.128632,0.0845989,3.27633e-05,0.0842401,0.13698,0.0874421,0.100355,0.167854,0.142846,0.0583767,0.088258,0.117657,0.0486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.0233701,0.0387226,0.256405,0.000106808,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.00325002,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.0585101,0.264707,0.450113
}}
}}

Revision as of 11:38, 5 September 2012


Full id: C2434_Renal_pancreas_Hepatocyte_Alveolar_gastric_kidney_nonsmall



Phase1 CAGE Peaks

Hg19::chr17:72428185..72428199,+p4@GPRC5C
Hg19::chr17:72428218..72428264,+p1@GPRC5C
Hg19::chr17:72428266..72428277,+p6@GPRC5C
Hg19::chr17:72428301..72428329,+p@chr17:72428301..72428329
+


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>

Cell Type
Ontology termp-valuen
epithelial cell3.58e-19254
endodermal cell2.58e-1359
endo-epithelial cell6.58e-0943
kidney cell1.40e-0718
kidney epithelial cell1.40e-0718
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.24e-20169
endoderm2.24e-20169
presumptive endoderm2.24e-20169
subdivision of digestive tract1.45e-19129
endodermal part of digestive tract1.45e-19129
immaterial anatomical entity1.52e-18126
organ6.81e-18511
digestive system6.97e-18155
digestive tract6.97e-18155
primitive gut6.97e-18155
trunk region element8.18e-18107
multi-tissue structure2.25e-16347
mixed endoderm/mesoderm-derived structure1.83e-15130
foregut2.12e-1598
abdomen element1.71e-1455
abdominal segment element1.71e-1455
primordium5.20e-14168
subdivision of trunk1.14e-13113
abdominal segment of trunk7.97e-1361
abdomen7.97e-1361
endo-epithelium1.43e-1282
anatomical space3.62e-12104
embryo4.56e-12612
adult organism2.24e-11115
embryonic structure4.67e-10605
developing anatomical structure4.67e-10605
germ layer8.10e-10604
embryonic tissue8.10e-10604
presumptive structure8.10e-10604
epiblast (generic)8.10e-10604
organ part9.68e-10219
mesenchyme1.38e-09238
entire embryonic mesenchyme1.38e-09238
renal system1.62e-0945
epithelial sac2.21e-0925
anatomical cavity2.59e-0970
sac2.67e-0926
urinary system structure3.00e-0944
epithelium of foregut-midgut junction3.94e-0925
anatomical boundary3.94e-0925
hepatobiliary system3.94e-0925
foregut-midgut junction3.94e-0925
septum transversum3.94e-0925
exocrine gland5.46e-0931
exocrine system5.46e-0931
duct9.27e-0926
multi-cellular organism1.13e-08659
gut epithelium1.75e-0854
cavitated compound organ2.41e-0832
compound organ3.68e-0869
hepatic diverticulum3.81e-0822
liver primordium3.81e-0822
digestive tract diverticulum4.52e-0823
gland5.02e-0859
kidney8.04e-0827
kidney mesenchyme8.04e-0827
kidney rudiment8.04e-0827
kidney field8.04e-0827
anatomical cluster1.57e-07286
anatomical conduit1.59e-07241
body cavity precursor1.62e-0763
intraembryonic coelom1.69e-0721
liver2.60e-0719
digestive gland2.60e-0719
liver bud2.60e-0719
organism subdivision3.02e-07365
respiratory system4.02e-0772
mesonephros4.04e-0718
pronephros4.04e-0718
nephrogenic cord4.04e-0718
pronephric mesoderm4.04e-0718
rostral part of nephrogenic cord4.04e-0718
presumptive pronephric mesoderm4.04e-0718
gastrointestinal system5.89e-0735
excretory tube7.22e-0717
mesonephric epithelium7.22e-0717
mesonephric tubule7.22e-0717
nephric duct7.22e-0717
kidney epithelium7.22e-0717
renal duct7.22e-0717
mesonephric duct7.22e-0717
pronephric duct7.22e-0717
Disease
Ontology termp-valuen
carcinoma3.56e-18106
cell type cancer1.75e-13143
adenocarcinoma8.67e-0825


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
E2F1#186944.907389214879320.001724022357361790.0106484813401448
EGR1#195844.988179094810140.001615011500076050.0101413050779487
FOXA1#3169411.08141974938556.62943068949433e-050.00107045626434771
FOXA2#3170424.63046375266522.71504128667089e-069.42673527056585e-05
HDAC2#3066413.41562023662633.0859005065161e-050.000626532587480628
HEY1#2346244.040111043105710.00375304636917980.0185985485053746
HNF4A#3172423.13229036295373.48990320893214e-060.000115561826644789
MXI1#460149.96157162875930.0001015224754950450.00142320883466134
MYC#460945.22228187160940.001344309395272740.00887473634215483
NANOG#79923429.24477848101271.36586687657858e-065.3287176213295e-05
NRF1#4899412.21027944771094.49717228915276e-050.000793646800788823
SIN3A#2594245.408884726815140.001168172384885160.00796050865881644
SMARCB1#6598418.25271578115749.00423392720929e-060.00024137402133568
SP1#666745.69838137814090.0009482606065333980.00683946059984403
TAF1#687243.343046285745290.008005664898701650.0322098634854573
TBP#690843.706770687096390.005296377814784350.0244118629506272
TCF7L2#6934410.77017656313737.42969445082454e-050.00115417203443353
USF2#739239.74414803880220.001718341848410070.0107186229651854



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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