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Coexpression cluster:C137: Difference between revisions

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|ontology_enrichment_disease=DOID:14566!1.51e-09!239;DOID:162!7.82e-09!235;DOID:305!1.48e-07!106
|ontology_enrichment_disease=DOID:14566!1.51e-09!239;DOID:162!7.82e-09!235;DOID:305!1.48e-07!106
|ontology_enrichment_uberon=UBERON:0000922!4.10e-07!612;UBERON:0000062!4.63e-07!511;UBERON:0001737!5.22e-07!9
|ontology_enrichment_uberon=UBERON:0000922!4.10e-07!612;UBERON:0000062!4.63e-07!511;UBERON:0001737!5.22e-07!9
|tf_chipseq_enrich=CEBPB#1051;26:1.55826946068756:0.0140609214528899:0.0493467043791247!NR3C1#2908;18:2.02642421023394:0.00334943287737872:0.0172994125058383
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.928091,0.578625,0.757684,0.999256,0.723773,0.999985,0.819825,0.524127,0.912519,0.918672,0.817369,0.999968,0.754314,0.903689,0.985754,0.999498,0.910403,0.981957,0.465566,0.920805,0.891527,0.287423,0.970962,0.710032,0.96457,0.700455,0.990674,0.396627,0.999934,0.999146,0.883322,0.93475,0.999715,0.986839,0.971936,0.963616,0.85757,0.948225,0.993831,0.993781,0.905566,0.990356,0.897276,0.773895,0.969219,0.987213,0.385946,0.784433,0.663536,0.998642,0.99552,0.998228,0.847551,0.983401,0.976163,0.959166,0.992005,1,0.488759,0.173175,0.954844,0.526769,0.927632,0.998461,0.962384,0.871397,0.997659,0.799366,0.385763,0.618729,1,1,0.694811,0.917717,0.962202,0.954547,0.883838,0.656578,0.822675,0.79823,0.676209,0.874023,0.994355,0.626417,0.996278,0.859427,0.817918,0.754016,0.870156,0.914313,0.623185,0.627377,0.997868,0.956623,0.553024,0.266127,0.833882,0.969907,0.999136,0.854955,0.962521,0.917908,0.698145,0.99859,0.603998,0.95592,0.976183,0.94327,0.031276,0.715674,0.999997,0.623161,0.0200123,0.926543,0.145283,0.9921,0.97525,0.940977,0.995165,0.988925,0.960801,0.781135,0.709282,0.995807,0.737738,0.491264,0.348574,0.983328,0.969163,0.968515,0.950149,0.970231,0.0799696,0.997568,0.721462,0.90205,0.843628,0.996775,0.216509,0.899802,0.682637,0.908593,0.985202,0.918428,0.987269,0.899653,0.976801,0.0772401,0.980247,0.898819,0.982645,0.932825,0.998558,0.765612,0.994758,0.996998,0.999999,0.999341,0.803943,0.975739,0.947528,0.860524,0.998268,0.989327,0.65423,0.944766,0.951936,0.990445,1,0.655826,0.98324,0.985197,0.999972,0.853532,0.993933,0.204946,0.768129,0.637704,0.999208,0.95683,0.61215,0.999982,0.971451,0.0575669,0.958866,0.958209,0.770259,1,1,0.999989,0.986559,0.999911,0.998145,0.999994,0.992279,0.99826,0.999852,0.992954,0.0615018,0.943347,0.884024,0.993565,0.978711,0.726648,0.195809,0.670969,0.9775,0.999943,1,0.952,0.999997,1,0.520802,0.999999,0.999967,0.998407,1,0.99869,0.999996,0.507318,0.999999,1,1,0.874982,0.406955,0.150785,0.418612,0.552571,0.89488,0.711297,0.137654,0.0435691,0.0430243,0.932825,0.464406,0.604311,0.999616,0.955636,0.0286131,0.669634,0.924292,0.972483,0.997538,0.876478,0.9564,0.999957,0.723752,0.887935,0.88457,0.459286,0.999475,0.875853,0.997956,0.995827,0.902033,1,0.999919,0.555657,0.750565,0.286673,0.775566,0.999987,0.999164,0.793884,0.9998,0.960863,1,0.420794,0.641005,0.740659,0.986418,0.949713,0.853328,0.997009,0.920599,0.933172,0.998352,0.544526,0.999506,0.998474,0.978688,0.097781,0.676812,0.987094,0.766092,0.694827,0.218571,0.056344,0.982091,0.740434,0.450638,0.666269,0.362882,0.438812,0.952194,0.868794,0.809716,0.627373,0.650313,0.113645,0.886254,0.543479,0.952159,0.183157,0.957792,0.835266,0.932496,0.824721,0.999145,0.409122,0.960172,0.272965,0.804354,0.551559,0.560513,0.90245,0.995341,0.918493,0.595679,0.994446,0.119434,0.974041,0.502894,0.787866,0.990874,0.86306,0.939451,0.325452,0.930083,0.696464,0.468854,0.796178,0.78138,0.712592,0.771614,0.814803,0.421631,0.87257,0.892398,0.342221,0.673171,0.144694,0.34236,0.244355,0.287404,0.986815,0.988419,0.535596,0.755223,0.888334,0.963207,0.869357,0.735412,0.924079,0.868336,0.956924,0.387361,0.75921,0.518844,0.894102,0.980019,0.651569,0.769846,0.437809,0.697411,0.516645,0.999862,0.379305,0.756778,0.288386,0.890917,0.606279,0.965672,0.813945,0.103835,0.963608,0.899882,0.917258,0.973182,0.9529,0.60132,0.962843,0.824536,0.0871529,0.686455,0.6118,0.81594,0.868693,0.793477,0.865251,0.977142,0.095546,0.993841,0.75539,0.998551,0.878462,0.963219,0.962883,0.698564,0.914281,0.150295,0.87364,0.883408,0.178248,0.437483,0.135356,0.980525,0.886241,0.889513,0.964152,0.99094,0.19877,0.788889,0.833848,0.943886,0.906188,0.911864,0.503653,0.909426,0.688626,0.800421,0.735473,0.96913,0.899664,0.96527,0.672836,0.763288,0.998029,0.844964,0.560766,0.967174,0.972387,0.828685,0.780793,0.992503,0.996375,0.21051,0.893005,0.989719,0.735559,0.913063,0.702384,0.588834,0.697445,0.841689,0.913592,0.726511,0.691092,0.723117,0.981814,0.94872,0.902292,0.976687,0.942693,0.339119,0.92662,0.946391,0.366201,0.952285,0.86583,0.411293,0.994054,0.59399,0.592799,0.919599,0.80981,0.883096,0.0536543,0.0453274,0.929418,0.990614,0.516363,0.285869,0.94892,0.0782813,0.988824,0.912144,0.422757,0.86288,0.315764,0.293067,0.293067,0.983481,0.997726,0.194499,0.981893,0.754178,0.929637,0.793383,0.649043,0.788084,0.790254,0.622269,0.826979,0.918727,0.231325,0.0362915,0.543564,0.872687,0.632784,0.31384,0.877627,0.889144,0.822823,0.759416,0.859546,0.838814,0.361338,0.938843,0.962005,0.739019,0.991097,0.965917,0.0545866,0.233519,0.841441,0.828804,0.974709,0.694153
}}
}}

Revision as of 14:31, 5 September 2012


Full id: C137_large_ductal_melanoma_cervical_Endothelial_Smooth_chronic



Phase1 CAGE Peaks

Hg19::chr11:17555398..17555410,-p9@USH1C
Hg19::chr11:17555415..17555420,-p11@USH1C
Hg19::chr11:17555421..17555441,-p6@USH1C
Hg19::chr12:131856235..131856282,-p@chr12:131856235..131856282
-
Hg19::chr12:40426483..40426524,-p@chr12:40426483..40426524
-
Hg19::chr12:70944095..70944107,+p@chr12:70944095..70944107
+
Hg19::chr13:46786138..46786153,+p2@LRRC63
Hg19::chr14:88452908..88452916,-p@chr14:88452908..88452916
-
Hg19::chr14:88452922..88452929,-p@chr14:88452922..88452929
-
Hg19::chr14:88452944..88452960,-p@chr14:88452944..88452960
-
Hg19::chr15:22550789..22550806,+p@chr15:22550789..22550806
+
Hg19::chr15:22550810..22550816,+p@chr15:22550810..22550816
+
Hg19::chr15:91143571..91143582,+p@chr15:91143571..91143582
+
Hg19::chr16:3332452..3332454,+p@chr16:3332452..3332454
+
Hg19::chr16:57832004..57832027,-p4@KIFC3
Hg19::chr16:57832028..57832042,-p10@KIFC3
Hg19::chr16:65159735..65159744,-p@chr16:65159735..65159744
-
Hg19::chr16:65159769..65159787,-p@chr16:65159769..65159787
-
Hg19::chr16:65432589..65432593,+p@chr16:65432589..65432593
+
Hg19::chr16:82662683..82662690,-p@chr16:82662683..82662690
-
Hg19::chr17:53809214..53809228,-p5@TMEM100
Hg19::chr17:53809233..53809251,-p3@TMEM100
Hg19::chr17:66511224..66511241,+p29@PRKAR1A
Hg19::chr17:9716257..9716264,-p@chr17:9716257..9716264
-
Hg19::chr17:9739681..9739708,+p5@GLP2R
Hg19::chr17:9739716..9739725,+p13@GLP2R
Hg19::chr17:9739727..9739738,+p11@GLP2R
Hg19::chr18:5478350..5478363,-p10@EPB41L3
Hg19::chr18:5478399..5478403,-p24@EPB41L3
Hg19::chr18:5540365..5540373,-p22@EPB41L3
Hg19::chr18:61368086..61368120,+p@chr18:61368086..61368120
+
Hg19::chr18:61370192..61370197,+p1@SERPINB11
Hg19::chr18:67562993..67563000,-p@chr18:67562993..67563000
-
Hg19::chr18:67563022..67563032,-p@chr18:67563022..67563032
-
Hg19::chr19:46665277..46665280,-p@chr19:46665277..46665280
-
Hg19::chr19:46684088..46684108,-p@chr19:46684088..46684108
-
Hg19::chr19:46684114..46684142,-p@chr19:46684114..46684142
-
Hg19::chr1:154699181..154699196,+p@chr1:154699181..154699196
+
Hg19::chr1:15653306..15653329,+p8@FHAD1
Hg19::chr1:15653374..15653410,+p5@FHAD1
Hg19::chr1:15653436..15653448,+p12@FHAD1
Hg19::chr1:156783663..156783673,-p11@SH2D2A
Hg19::chr1:156785210..156785223,-p10@SH2D2A
Hg19::chr1:156785242..156785247,-p19@SH2D2A
Hg19::chr1:156785292..156785301,-p13@SH2D2A
Hg19::chr1:156786243..156786257,-p6@SH2D2A
Hg19::chr1:188856517..188856523,-p1@ENST00000414765
Hg19::chr1:188856567..188856573,-p2@ENST00000414765
Hg19::chr1:188856590..188856595,-p4@ENST00000414765
Hg19::chr1:188856977..188857009,-p3@ENST00000414765
Hg19::chr1:188857554..188857562,-p@chr1:188857554..188857562
-
Hg19::chr1:188861179..188861222,-p@chr1:188861179..188861222
-
Hg19::chr1:188874798..188874820,+p1@ENST00000445072
Hg19::chr1:234565260..234565271,-p@chr1:234565260..234565271
-
Hg19::chr1:246469346..246469359,-p7@SMYD3
Hg19::chr1:246469406..246469412,-p18@SMYD3
Hg19::chr1:246887738..246887749,+p7@SCCPDH
Hg19::chr1:246887780..246887791,+p6@SCCPDH
Hg19::chr1:54665916..54665927,+p2@MRPL37
Hg19::chr1:68927028..68927036,-p@chr1:68927028..68927036
-
Hg19::chr21:11130568..11130575,+p@chr21:11130568..11130575
+
Hg19::chr2:115929667..115929677,+p@chr2:115929667..115929677
+
Hg19::chr2:228190043..228190054,+p5@MFF
Hg19::chr2:228190066..228190086,+p4@MFF
Hg19::chr3:16739396..16739405,-p5@ENST00000426218
Hg19::chr3:189838995..189839000,-p31@LEPREL1
Hg19::chr3:189839367..189839371,-p16@LEPREL1
Hg19::chr3:189840026..189840048,-p10@LEPREL1
Hg19::chr3:189840061..189840073,-p14@LEPREL1
Hg19::chr3:189840106..189840120,-p18@LEPREL1
Hg19::chr3:63804973..63804980,+p3@C3orf49
Hg19::chr3:63805017..63805035,+p2@C3orf49
Hg19::chr3:63805044..63805054,+p1@C3orf49
Hg19::chr4:103265976..103265993,-p11@SLC39A8
Hg19::chr4:103266043..103266060,-p12@SLC39A8
Hg19::chr4:103266068..103266091,-p10@SLC39A8
Hg19::chr4:103266101..103266106,-p20@SLC39A8
Hg19::chr4:159131359..159131372,+p11@TMEM144
Hg19::chr4:159131486..159131501,+p8@TMEM144
Hg19::chr4:40194268..40194278,+p27@RHOH
Hg19::chr4:74586784..74586789,-p@chr4:74586784..74586789
-
Hg19::chr5:119697827..119697855,+p@chr5:119697827..119697855
+
Hg19::chr5:119697859..119697884,+p@chr5:119697859..119697884
+
Hg19::chr5:136896379..136896398,-p@chr5:136896379..136896398
-
Hg19::chr5:5558678..5558683,+p@chr5:5558678..5558683
+
Hg19::chr5:57878034..57878045,+p9@RAB3C
Hg19::chr5:59744572..59744583,-p57@PDE4D
Hg19::chr5:59783574..59783584,+p6@PART1
Hg19::chr6:1312753..1312800,+p4@FOXQ1
Hg19::chr6:138060034..138060045,-p1@ENST00000411615
p1@ENST00000419220
Hg19::chr6:138060103..138060111,-p3@ENST00000411615
p3@ENST00000419220
Hg19::chr6:138060178..138060193,-p2@ENST00000411615
p2@ENST00000419220
Hg19::chr6:145434485..145434492,+p@chr6:145434485..145434492
+
Hg19::chr6:162477886..162477932,-p@chr6:162477886..162477932
-
Hg19::chr6:166575975..166575983,-p@chr6:166575975..166575983
-
Hg19::chr6:166579326..166579334,-p@chr6:166579326..166579334
-
Hg19::chr6:166581324..166581327,-p7@T
Hg19::chr6:166581333..166581349,-p2@T
Hg19::chr6:166581938..166581955,-p3@T
Hg19::chr6:166582133..166582149,-p1@T
Hg19::chr6:22113567..22113578,+p@chr6:22113567..22113578
+
Hg19::chr6:22113587..22113603,+p@chr6:22113587..22113603
+
Hg19::chr6:22113608..22113630,+p@chr6:22113608..22113630
+
Hg19::chr6:22113639..22113643,+p@chr6:22113639..22113643
+
Hg19::chr6:33644021..33644058,+p@chr6:33644021..33644058
+
Hg19::chr6:36952360..36952367,-p@chr6:36952360..36952367
-
Hg19::chr7:151169194..151169198,-p17@RHEB
Hg19::chr7:158225991..158225999,+p@chr7:158225991..158225999
+
Hg19::chr7:158226043..158226065,+p@chr7:158226043..158226065
+
Hg19::chr7:158237237..158237241,+p@chr7:158237237..158237241
+
Hg19::chr7:158242968..158242975,+p@chr7:158242968..158242975
+
Hg19::chr7:31938679..31938703,-p@chr7:31938679..31938703
-
Hg19::chr7:32083456..32083492,-p@chr7:32083456..32083492
-
Hg19::chr7:68735026..68735050,+p@chr7:68735026..68735050
+
Hg19::chr7:68735078..68735090,+p@chr7:68735078..68735090
+
Hg19::chr7:68735132..68735135,+p@chr7:68735132..68735135
+
Hg19::chr7:68735137..68735150,+p@chr7:68735137..68735150
+
Hg19::chr7:68735214..68735224,+p@chr7:68735214..68735224
+
Hg19::chr8:129431377..129431384,-p@chr8:129431377..129431384
-
Hg19::chr8:52307771..52307797,+p@chr8:52307771..52307797
+
Hg19::chr9:138393091..138393107,+p@chr9:138393091..138393107
+
Hg19::chr9:138393119..138393159,+p@chr9:138393119..138393159
+
Hg19::chr9:138393171..138393178,+p@chr9:138393171..138393178
+
Hg19::chr9:138393188..138393204,+p@chr9:138393188..138393204
+
Hg19::chr9:138393225..138393257,+p@chr9:138393225..138393257
+
Hg19::chr9:138393587..138393606,-p8@C9orf116
Hg19::chr9:138393704..138393727,+p@chr9:138393704..138393727
+
Hg19::chr9:138394283..138394314,+p9@MRPS2
Hg19::chr9:33306373..33306392,+p@chr9:33306373..33306392
+
Hg19::chr9:79009244..79009257,-p4@RFK
Hg19::chrX:110341059..110341099,+p@chrX:110341059..110341099
+
Hg19::chrX:142113711..142113717,+p1@SPANXN4
Hg19::chrX:23803131..23803142,+p7@SAT1


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:0005737cytoplasm0.0191544599457173
GO:0030046parallel actin filament bundle formation0.0435505411641322
GO:0048513organ development0.0435505411641322
GO:0047131saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity0.0435505411641322
GO:0009231riboflavin biosynthetic process0.0435505411641322
GO:0042727riboflavin and derivative biosynthetic process0.0435505411641322
GO:0006771riboflavin metabolic process0.0435505411641322
GO:0004753saccharopine dehydrogenase activity0.0435505411641322
GO:0042726riboflavin and derivative metabolic process0.0435505411641322
GO:0004145diamine N-acetyltransferase activity0.0435505411641322
GO:0001917photoreceptor inner segment0.0435505411641322
GO:0008531riboflavin kinase activity0.0435505411641322
GO:0048598embryonic morphogenesis0.0460967290243841
GO:0044424intracellular part0.0460967290243841
GO:0009887organ morphogenesis0.0460967290243841
GO:0019797procollagen-proline 3-dioxygenase activity0.0460967290243841
GO:0031544peptidyl-proline 3-dioxygenase activity0.0460967290243841



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
embryo4.10e-07612
organ4.63e-07511
larynx5.22e-079
Disease
Ontology termp-valuen
disease of cellular proliferation1.51e-09239
cancer7.82e-09235
carcinoma1.48e-07106


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
CEBPB#1051261.558269460687560.01406092145288990.0493467043791247
NR3C1#2908182.026424210233940.003349432877378720.0172994125058383



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

"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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