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Coexpression cluster:C245: Difference between revisions

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|tf_chipseq_enrich=ESR1#2099;8:4.47543320671338:0.000385994508764504:0.00377779781659226!GATA3#2625;9:4.45688449481553:0.000165950068319642:0.00204069930357178
|tf_chipseq_enrich=ESR1#2099;8:4.47543320671338:0.000385994508764504:0.00377779781659226!GATA3#2625;9:4.45688449481553:0.000165950068319642:0.00204069930357178
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0529,0.623778,0.881977,0.996136,0.412585,1,0.942886,0.516361,0.813208,0.278094,0.942271,0.995321,0.988738,0.979022,0.727962,0.994628,0.992998,0.997973,0.765801,0.968919,0.791149,0.975246,0.999436,0.9466,0.938965,0.431951,0.765211,0.509258,0.998877,0.946558,0.58869,0.839206,0.998583,0.735318,0.77183,0.879952,0.462049,0.729465,0.999999,0.998705,0.62314,0.853303,0.609794,0.689661,0.762941,0.10915,0.94228,0.469832,0.756604,0.844155,0.999998,0.993432,0.988791,0.986137,0.902439,0.980146,0.972481,1,0.662796,0.590962,0.999894,0.319725,0.68538,0.998577,0.742447,0.990404,0.998178,0.48534,0.914631,0.867135,1,1,0.985585,0.989031,0.877666,0.72148,0.35325,0.605023,0.84233,0.985342,0.763264,0.575438,0.88245,0.385843,0.990912,0.808845,0.505581,0.926349,0.570098,0.637987,0.89183,0.53378,0.968873,0.869015,0.989886,0.660143,0.992511,0.765148,0.997967,0.95172,0.981228,0.82805,0.859755,0.999298,0.862199,0.999521,0.802931,0.694748,0.745866,0.947597,0.999997,0.816063,0.745325,0.829217,0.679864,0.942563,0.949869,0.290442,0.954422,0.967371,0.98067,0.507819,0.991327,0.995058,0.947536,0.674509,0.79937,0.994783,0.889347,0.88821,0.891534,0.970455,0.839089,0.918855,0.994757,0.937741,0.854421,0.99575,0.595739,0.377227,0.377877,0.84971,0.824888,0.959717,0.650352,0.736347,0.789103,0.722803,0.81739,0.998943,0.999972,0.307091,0.994532,0.972739,0.989041,0.991911,0.999932,1,0.490228,0.999941,0.727981,0.557185,0.927885,0.997063,0.990338,0.852115,0.915803,0.859924,0.999992,0.904147,0.473097,0.99762,0.998706,0.766749,0.994999,0.713157,0.985666,0.992661,0.955043,0.998408,0.997959,0.998514,0.799797,0.569592,0.987204,0.909801,0.992611,1,1,0.509611,0.999978,0.999888,0.978118,0.984623,0.998848,0.998942,0.999999,0.986064,0.417077,0.996337,0.287444,0.999878,0.991988,0.97997,0.989869,0.910141,0.983246,0.750497,0.999997,0.994209,1,0.999993,0.0465536,0.999999,0.999961,0.999676,1,0.991251,0.999992,0.999429,0.999999,1,0.999999,0.920079,0.776501,0.60816,0.78211,0.971941,0.686657,0.99962,0.87564,0.955472,0.151266,0.183897,0.117423,0.689104,0.412096,0.838977,0.857984,0.0894994,0.860097,0.98351,0.968546,0.881019,0.567224,0.998528,0.999975,0.999298,0.978607,0.973142,0.820044,0.769496,0.999449,0.993669,0.959743,1,0.999916,0.674792,0.988718,0.767824,0.999126,0.999998,0.999561,0.922129,0.995235,0.294974,0.999452,0.964838,0.574558,0.0234758,0.397577,0.992461,0.867378,0.978497,0.998192,0.999345,0.996278,0.999761,0.968863,0.947952,0.718888,0.869799,0.984564,0.835404,0.496036,0.914891,0.98545,0.37836,0.995067,0.990471,0.880203,0.926158,0.963287,0.989983,0.802923,0.998719,0.900507,0.774312,0.940167,0.998997,0.972255,0.176785,0.996374,0.765071,0.746503,0.882172,0.999955,0.963772,0.999048,0.942803,0.96629,0.990901,0.715685,0.83512,0.990074,0.142406,0.941579,0.997556,0.705764,0.875773,0.379121,0.954818,0.882736,0.861856,0.930814,0.780335,0.994586,0.922989,0.971497,0.773923,0.843639,0.60696,0.46674,0.897245,0.797379,0.978159,0.745473,0.996453,0.961327,0.74483,0.633154,0.475789,0.799555,0.822804,0.840773,0.964229,0.777992,0.974081,0.787834,0.985939,0.999981,0.973354,0.904301,0.482332,0.944865,0.946946,0.810018,0.988984,0.982738,0.891854,0.694378,0.983072,0.45528,0.834016,0.911802,0.973637,0.849428,0.982499,0.805984,0.923977,0.98621,0.966233,0.0959378,0.721395,0.986242,0.977258,0.889225,0.944258,0.702432,0.834371,0.991493,0.851837,0.513093,0.714562,0.625758,0.211003,0.678363,0.917343,0.999633,0.954334,0.679996,0.851119,0.878131,0.675619,0.936854,0.957714,0.833344,0.981346,0.698374,0.973685,0.802744,0.879314,0.828008,0.972367,0.800154,0.465496,0.697049,0.720451,0.724242,0.747523,0.79637,0.974827,0.920614,0.642371,0.985948,0.939489,0.903306,0.895045,0.659793,0.99056,0.994368,0.862305,0.915538,0.93674,0.571377,0.566998,0.818003,0.727927,0.908175,0.839583,0.968672,0.151317,0.557455,0.984077,0.96591,0.721133,0.827762,0.466401,0.984051,0.342099,0.635812,0.636998,0.577682,0.77444,0.533372,0.63673,0.993129,0.805342,0.80914,0.733025,0.955264,0.978789,0.788676,0.849417,0.342933,0.907773,0.340989,0.330256,0.715828,0.766397,0.920063,0.879895,0.562668,0.719302,0.248371,0.496593,0.27671,0.603098,0.988004,0.865266,0.99644,0.531019,0.917536,0.906573,0.584557,0.991191,0.998491,0.902585,0.972294,0.85883,0.91933,0.730735,0.622357,0.924168,0.38553,0.985374,0.99289,0.725282,0.895301,0.939369,0.0990439,0.894129,0.906672,0.744669,0.983612,0.728712,0.994872,0.963043,0.843167,0.834907,0.850823,0.503695,0.617499,0.842414,0.807404,0.917511,0.859089,0.958052,0.979443,0.741375,0.828542,0.310449,0.838961,0.473602,0.820411,0.821233,0.969662,0.793429,0.57772
|tfbs_overrepresentation_for_novel_motifs=0.00736655,0.000308442,0.0359338,0.284863,0.467831,0.833258,0.0485097,1.2478,0.0763621,0.00618559,0.0958654,0.489439,0.0762757,0.0450301,0.687629,1.08881,0.143965,0.674027,0.0937755,0.0311326,0.104213,0.00573727,0.0265699,0.671276,0.151674,0.249942,0.051861,0.0261069,0.0039451,0.0371377,0.0180937,0.493855,0.0217503,0.038416,0.00216378,0.287303,0.0131883,0.0285294,0.284247,0.0577659,0.769975,0.0154874,0.218617,0.458326,0.00121136,0.135037,0.0488472,0.0886388,1.02201,0.0715578,0.0769513,0.0525829,0.098987,0.211146,0.316712,0.174544,0.726834,0.145508,0.0727081,0.0364427,0.188785,0.185845,0.377624,0.129305,0.0553856,0.11212,0.384112,0.698465,0.479218,0.554649,0.0135735,0.790213,0.00152896,0.315234,0.000842365,0.272488,0.332559,0.120722,0.156762,0.144739,0.281703,0.128752,1.66783,0.771327,0.278052,1.07537e-07,0.0144315,0.546347,0.295448,0.789473,0.459385,0.259197,0.174303,0.0636726,0.0223393,2.1074,0.260667,0.200157,0.0896785,0.000796569,0.449097,0.170985,0.196687,0.878205,0.346431,0.021162,0.137438,0.382593,0.0114584,0.00294582,1.64719,0.194975,1.52725,0.251289,0.420206,0.752548,2.19856e-09,0.0808793,0.110994,0.783166,1.50656,0.292613,0.115524,0.468437,2.20014,0.121103,0.703793,0.177257,0.340904,0.155247,1.32612,0.0185791,0.351843,0.802387,0.470054,0.0283186,1.31898,0.110619,1.11009,1.22318,0.838185,0.405073,0.400769,0.19796,0.107461,0.0345275,0.672668,1.06901,0.597239,0.000845033,0.00893457,1.17656e-07,0.720403,0.029518,0.41434,0.581253,0.581944,1.51456,0.151741,0.00828217,0.404104,0.247272,1.4755,0.0441907,0.368944,0.0550052,0.0189713,0.406626,1.62152e-08
}}
}}

Revision as of 13:54, 26 November 2012


Full id: C245_prostate_penis_salivary_esophagus_kidney_Neutrophils_Pancreatic



Phase1 CAGE Peaks

Hg19::chr11:82843480..82843485,+p@chr11:82843480..82843485
+
Hg19::chr12:102010953..102010982,+p5@MYBPC1
Hg19::chr14:38033393..38033405,+p1@ENST00000554829
Hg19::chr14:74454889..74454892,-p10@ENTPD5
Hg19::chr15:45803320..45803343,+p1@HMGN2P46
Hg19::chr18:56620389..56620397,+p37@ZNF532
Hg19::chr18:56620411..56620421,+p36@ZNF532
Hg19::chr18:56720530..56720541,-p@chr18:56720530..56720541
-
Hg19::chr18:56720695..56720715,-p@chr18:56720695..56720715
-
Hg19::chr19:20432113..20432119,-p@chr19:20432113..20432119
-
Hg19::chr19:36157417..36157420,+p1@UPK1A
Hg19::chr19:51357959..51357992,+p2@KLK3
Hg19::chr19:51358166..51358186,+p1@KLK3
Hg19::chr19:51358195..51358202,+p6@KLK3
Hg19::chr19:51376683..51376701,+p1@KLK2
Hg19::chr19:51379148..51379157,+p9@KLK2
Hg19::chr19:51412603..51412620,-p2@KLK4
Hg19::chr1:58999660..58999680,-p@chr1:58999660..58999680
-
Hg19::chr20:56338330..56338340,-p@chr20:56338330..56338340
-
Hg19::chr20:56338376..56338381,-p@chr20:56338376..56338381
-
Hg19::chr21:42884017..42884035,-p@chr21:42884017..42884035
-
Hg19::chr2:13677795..13677800,+p2@ENST00000434509
Hg19::chr3:107201385..107201388,-p@chr3:107201385..107201388
-
Hg19::chr3:107201513..107201523,-p@chr3:107201513..107201523
-
Hg19::chr3:131978701..131978713,-p@chr3:131978701..131978713
-
Hg19::chr3:131978783..131978794,-p@chr3:131978783..131978794
-
Hg19::chr3:131978834..131978840,-p@chr3:131978834..131978840
-
Hg19::chr3:131978851..131978858,-p@chr3:131978851..131978858
-
Hg19::chr3:131978870..131978881,-p@chr3:131978870..131978881
-
Hg19::chr3:131986361..131986385,-p@chr3:131986361..131986385
-
Hg19::chr3:132036207..132036218,+p3@ACPP
Hg19::chr3:132036243..132036268,+p1@ACPP
Hg19::chr3:44916098..44916104,+p1@TGM4
Hg19::chr4:143522258..143522278,-p@chr4:143522258..143522278
-
Hg19::chr4:80584855..80584865,+p2@ENST00000506460
Hg19::chr4:80584874..80584882,+p3@ENST00000506460
Hg19::chr4:80584903..80584914,+p1@ENST00000506460
Hg19::chr4:95561522..95561531,+p@chr4:95561522..95561531
+
Hg19::chr4:95572086..95572087,+p@chr4:95572086..95572087
+
Hg19::chr5:29485545..29485554,-p@chr5:29485545..29485554
-
Hg19::chr5:59672718..59672753,-p@chr5:59672718..59672753
-
Hg19::chr6:10691162..10691202,+p@chr6:10691162..10691202
+
Hg19::chr6:110964453..110964459,-p16@CDK19
Hg19::chr6:44698851..44698873,+p1@uc003oxm.2
Hg19::chr6:92061457..92061461,-p@chr6:92061457..92061461
-
Hg19::chr7:38313235..38313268,-p1@TRGJP
Hg19::chr7:83218322..83218330,-p@chr7:83218322..83218330
-
Hg19::chr7:89874193..89874199,+p7@C7orf63
Hg19::chr8:1877489..1877493,+p@chr8:1877489..1877493
+
Hg19::chr9:120228535..120228539,-p1@ENST00000436524
Hg19::chr9:5339875..5339881,-p1@RLN1
Hg19::chr9:79379348..79379360,+p1@PCA3
Hg19::chr9:90560553..90560557,+p@chr9:90560553..90560557
+
Hg19::chr9:90562275..90562281,+p@chr9:90562275..90562281
+
Hg19::chrX:24154688..24154714,+p@chrX:24154688..24154714
+


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:0004252serine-type endopeptidase activity0.00752394627533929
GO:0008236serine-type peptidase activity0.00752394627533929
GO:0017171serine hydrolase activity0.00752394627533929
GO:0018184protein amino acid polyamination0.0108177322500883
GO:0004175endopeptidase activity0.0308914333603252
GO:0017110nucleoside-diphosphatase activity0.0308914333603252
GO:0004293tissue kallikrein activity0.0308914333603252



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><br>uberon_data<br><br>


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
ESR1#209984.475433206713380.0003859945087645040.00377779781659226
GATA3#262594.456884494815530.0001659500683196420.00204069930357178



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

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