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Difference between revisions of "Coexpression cluster:C227"

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|gostat_on_coexpression_clusters=GO:0005055!laminin receptor activity!0.0172190497820848!3921$GO:0004700!atypical protein kinase C activity!0.0172190497820848!5590$GO:0006349!genetic imprinting!0.0229553539426068!3481$GO:0018445!prothoracicotrophic hormone activity!0.0229553539426068!3481$GO:0005159!insulin-like growth factor receptor binding!0.0245899540279904!3481$GO:0004697!protein kinase C activity!0.0245899540279904!5590$GO:0001565!phorbol ester receptor activity!0.0245899540279904!5590$GO:0008286!insulin receptor signaling pathway!0.0389942395441504!3481$GO:0005184!neuropeptide hormone activity!0.0389942395441504!3481$GO:0005843!cytosolic small ribosomal subunit (sensu Eukaryota)!0.0389942395441504!3921$GO:0007165!signal transduction!0.0409608036317618!5590;3921;3481$GO:0007154!cell communication!0.0474708623037988!5590;3921;3481$GO:0008305!integrin complex!0.0482976234877922!3921$GO:0019992!diacylglycerol binding!0.0482976234877922!5590$GO:0040029!regulation of gene expression, epigenetic!0.0496531872163847!3481
 
|gostat_on_coexpression_clusters=GO:0005055!laminin receptor activity!0.0172190497820848!3921$GO:0004700!atypical protein kinase C activity!0.0172190497820848!5590$GO:0006349!genetic imprinting!0.0229553539426068!3481$GO:0018445!prothoracicotrophic hormone activity!0.0229553539426068!3481$GO:0005159!insulin-like growth factor receptor binding!0.0245899540279904!3481$GO:0004697!protein kinase C activity!0.0245899540279904!5590$GO:0001565!phorbol ester receptor activity!0.0245899540279904!5590$GO:0008286!insulin receptor signaling pathway!0.0389942395441504!3481$GO:0005184!neuropeptide hormone activity!0.0389942395441504!3481$GO:0005843!cytosolic small ribosomal subunit (sensu Eukaryota)!0.0389942395441504!3921$GO:0007165!signal transduction!0.0409608036317618!5590;3921;3481$GO:0007154!cell communication!0.0474708623037988!5590;3921;3481$GO:0008305!integrin complex!0.0482976234877922!3921$GO:0019992!diacylglycerol binding!0.0482976234877922!5590$GO:0040029!regulation of gene expression, epigenetic!0.0496531872163847!3481
 
|id=C227
 
|id=C227
|ontology_enrichment_celltype=
+
|ontology_enrichment_celltype=CL:0000349!1.86e-12!19;CL:0000188!1.39e-08!9
 
|ontology_enrichment_disease=
 
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!2.61e-14!347;UBERON:0004119!2.84e-13!169;UBERON:0000925!2.84e-13!169;UBERON:0006595!2.84e-13!169;UBERON:0003104!4.09e-13!238;UBERON:0009142!4.09e-13!238;UBERON:0004921!9.27e-13!129;UBERON:0004185!9.27e-13!129;UBERON:0000077!2.51e-11!130;UBERON:0001007!1.13e-10!155;UBERON:0001555!1.13e-10!155;UBERON:0007026!1.13e-10!155;UBERON:0000468!2.52e-10!659;UBERON:0000064!3.13e-10!219;UBERON:0001041!1.22e-09!98;UBERON:0005631!3.10e-09!14;UBERON:0000158!3.10e-09!14;UBERON:0004923!9.61e-09!57;UBERON:0000063!3.81e-08!97;UBERON:0002100!3.91e-08!216;UBERON:0003103!5.69e-08!69;UBERON:0000922!6.28e-08!612;UBERON:0000478!9.22e-08!24;UBERON:0001557!1.16e-07!19;UBERON:0000466!1.80e-07!126;UBERON:0001737!2.01e-07!9;UBERON:0009569!2.25e-07!113;UBERON:0002417!3.29e-07!61;UBERON:0000916!3.29e-07!61;UBERON:0005177!3.89e-07!107;UBERON:0001048!4.68e-07!168;UBERON:0000475!8.58e-07!365
+
|ontology_enrichment_uberon=UBERON:0005631!1.11e-15!14;UBERON:0000158!1.11e-15!14;UBERON:0001737!9.60e-14!9;UBERON:0001557!5.82e-13!19;UBERON:0000478!2.27e-12!24;UBERON:0003124!1.37e-11!7;UBERON:0004119!4.76e-09!160;UBERON:0000925!4.76e-09!160;UBERON:0006595!4.76e-09!160;UBERON:0004921!5.39e-09!118;UBERON:0001041!7.78e-09!87;UBERON:0000481!3.81e-08!342;UBERON:0001007!7.44e-08!145;UBERON:0001555!7.44e-08!145;UBERON:0007026!7.44e-08!145;UBERON:0003104!9.16e-08!160;UBERON:0009142!9.16e-08!160;UBERON:0001987!2.17e-07!4;UBERON:0004340!2.17e-07!4;UBERON:0000072!3.41e-07!47;UBERON:0004923!7.07e-07!66;UBERON:0000475!9.44e-07!264
 
|pathway_enrichment=1.2723518646306e-05;0.00805398730311171;3;312;Diabetes pathways (Reactome):REACT_15380
 
|pathway_enrichment=1.2723518646306e-05;0.00805398730311171;3;312;Diabetes pathways (Reactome):REACT_15380
 
|tf_chipseq_enrich=EGR1#1958;23:1.82108125683545:0.00180305873952337:0.0109089127387951
 
|tf_chipseq_enrich=EGR1#1958;23:1.82108125683545:0.00180305873952337:0.0109089127387951
 
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8185,0.703082,0.59175,0.522028,0.565099,0.737384,0.980173,0.507819,0.651021,0.00304557,0.99994,0.506519,0.884692,0.00010885,0.570729,0.725141,0.258264,0.29556,0.911133,0.913507,0.610899,0.456328,0.993615,0.962338,0.564855,0.853656,0.695352,0.961873,0.57732,0.994136,0.645131,0.947701,0.999973,0.996597,0.565581,0.810378,0.0497197,0.833696,0.985546,0.99981,0.8481,0.959362,0.97859,0.958517,0.858651,0.999582,0.999181,0.63855,0.876741,0.0788943,0.949927,0.00183017,0.697649,0.944417,0.94816,0.056082,0.70368,0.673011,0.889039,0.659713,0.738229,0.00158134,0.611292,0.00649727,0.516576,0.801824,0.965919,2.87691e-08,0.987408,0.994168,0.993724,0.930455,0.465886,0.983682,0.999143,0.712113,0.640836,1.45266e-05,0.147245,0.982542,0.339144,0.788566,0.899995,0.434811,0.532739,0.940317,0.982441,0.998124,0.0022915,0.992219,0.888885,0.0966985,0.768736,0.910872,0.654943,0.87948,0.992069,0.808023,0.62518,0.0389102,0.783511,0.995413,0.969766,0.553727,0.949603,0.619774,0.687724,0.921727,0.871114,0.758118,0.902542,0.967533,0.709517,0.996325,0.809773,0.972514,0.968932,0.0427945,0.994322,0.657475,0.997726,0.981472,0.00867812,0.858993,0.743138,0.460245,0.965874,0.996681,0.971481,0.79127,0.867931,0.728742,0.962094,0.967564,0.8837,0.970915,0.0190866,0.989112,0.954927,0.995652,0.567465,0.993525,0.131396,0.54894,0.997989,0.717097,0.918719,0.98694,0.377824,0.876638,0.998402,0.997557,0.958427,0.890007,0.291831,0.899571,0.91952,0.419376,0.978934,0.86409,0.956131,0.978427,0.987602,0.831829,0.986357,0.971792,0.953076,0.128163,0.72173,0.997437,0.234901,0.88896,0.00456943,0.999983,0.233995,0.537818,0.00545093,0.341768,0.606664,0.950805,0.0128656,1.0242e-05,0.799929,0.419165,0.475903,0.000230824,0.77128,0.999347,0.385859,0.194677,0.184634,0.90448,0.00392448,0.413459,0.675568,0.111954,0.00513029,0.905103,0.0165607,0.999969,0.542081,5.42514e-05,0.0009561,0.157074,0.000162947,0.244376,0.995528,0.000601934,0.939132,0.0179064,0.999119,0.996697,0.947546,0.214724,0.999227,0.0384352,0.0145767,0.182899,2.1586e-06,0.961916,0.858325,0.991011,0.871525,0.999946,0.835559,0.235977,0.0203722,0.368457,0.0335892,0.975311,0.896551,6.24511e-08,0.0600183,0.503132,0.00284131,0.178073,0.00687796,0.000468262,0.369298,0.0349959,0.111043,0.0221766,0.992038,0.079551,0.947381,0.00101001,0.79508,0.0541641,0.971682,0.959217,0.100797,0.880313,8.30968e-05,0.026226,0.0869499,0.798811,0.932112,0.999109,8.58073e-09,0.999639,0.60529,0.166011,0.00103609,1.49718e-08,0.985137,0.023183,0.999716,3.60105e-07,0.999835,0.145342,0.0594185,0.945535,0.102801,0.358155,0.771175,0.987821,0.457145,0.071661,0.14292,3.31498e-08,0.0565583,0.388261,0.956705,0.0371174,0.978393,0.990237,0.839334,0.00813818,7.57007e-06,0.982488,0.999797,0.999413,0.850358,0.0573968,0.999929,0.00120556,0.167271,0.833288,8.25873e-11,0.0100927,7.77051e-06,3.00141e-14,9.3501e-07,0.685495,0.964605,5.19622e-06,0.00244686,0.996956,0.0011762,0.00579536,0.9995,0.139801,0.00455163,0.119148,0.85479,0.973461,0.893561,0.406818,0.271234,6.51794e-14,0.315409,0.98849,0.0265714,0.561273,0.999552,0.159468,0.012809,0.114202,0.999849,0.999978,0.505247,0.845429,0.998836,0.688694,0.799934,0.0154388,0.974109,0.00811681,0.000314494,0.803915,0.925511,0.0112213,0.99944,0.293742,0.213206,0.581087,0.817892,0.150529,0.991978,0.513345,0.987921,0.998147,0.44501,0.00548453,0.998439,0.718893,0.458783,0.175375,0.994496,0.955971,0.862235,0.878117,0.33509,0.163532,0.00706906,0.0248883,0.992438,0.475059,0.984274,0.989097,0.600904,1.16344e-05,0.00889366,0.520625,0.994282,0.00837734,0.270416,0.936959,0.946949,0.501347,0.33877,0.938046,0.984465,0.971178,0.25301,0.847155,0.565861,0.992604,0.0195099,0.994911,0.768655,0.368171,0.777415,0.0433905,0.963373,0.309739,0.000487118,0.102295,0.979375,0.561486,0.000721069,0.675611,0.624336,0.00327019,0.991157,0.0434775,0.0281249,0.932063,0.887144,0.910271,0.724618,0.993954,0.973309,0.893157,0.0431446,0.938288,0.00557869,0.000434368,0.244085,0.164029,0.593067,1.31365e-10,0.994143,0.937849,0.0694568,0.0713649,0.793332,0.295465,7.40363e-08,0.99165,0.961287,0.0608681,0.959761,0.988934,0.556912,0.730408,1.46916e-13,0.0398975,0.0505185,0.990881,0.957661,0.0455902,0.03406,0.0710825,0.947691,0.985849,0.773743,0.905973,0.983184,0.630857,0.99128,0.519456,0.162091,0.964874,0.000110717,0.991264,0.000182769,0.000201835,0.686747,0.967962,0.818369,0.582341,0.686481,0.560425,0.193472,0.732946,0.0759917,0.486067,0.98789,0.831438,0.885665,0.751469,0.934793,0.40333,0.901751,0.763353,0.810931,0.329037,0.911757,0.612237,0.000138392,0.860753,1.8054e-06,0.952395,0.0251918,0.994698,0.99917,0.288204,0.959625,0.99836,0.000258039,0.688547,0.995574,0.329993,0.943986,0.983555,0.551079,0.118268,0.0806337,0.974724,0.95422,5.45846e-09,0.999175,0.996537,0.315924,0.924597,0.994289,0.995113,0.474559,0.832482,0.820825,0.99904,0.999081,0.560732,0.977125,0.969404,0.872959,0.454194,0.99536,0.955755,0.354837,0.848436,0.686912,0.980852,0.973553,0.990063,0.787558,0.345794,0.654219,0.897488,0.982813,0.15497,2.55039e-05,0.997801,0.992116,0.907494
 
}}
 
}}

Revision as of 04:49, 19 October 2012


Full id: C227_chorionic_amniotic_Mesenchymal_Placental_gastric_diaphragm_tongue



Phase1 CAGE Peaks

Hg19::chr11:2016471..2016492,+p3@RPSA
Hg19::chr11:2016512..2016519,-p10@BC106079
Hg19::chr11:2016522..2016560,-p1@BC106079
Hg19::chr11:2016652..2016663,-p9@BC106079
Hg19::chr11:2016663..2016681,+p5@RPSA
Hg19::chr11:2016672..2016677,-p11@BC106079
Hg19::chr11:2016689..2016722,-p3@BC106079
Hg19::chr11:2016732..2016739,-p8@BC106079
Hg19::chr11:2016740..2016751,-p7@BC106079
Hg19::chr11:2016752..2016772,-p5@BC106079
Hg19::chr11:2016780..2016789,-p2@AF116709
Hg19::chr11:2016791..2016794,-p1@AF116709
Hg19::chr11:2016803..2016860,-p4@H19
Hg19::chr11:2016865..2016913,-p9@H19
Hg19::chr11:2016915..2016943,-p24@H19
Hg19::chr11:2016937..2016981,+p@chr11:2016937..2016981
+
Hg19::chr11:2016952..2016959,-p35@H19
Hg19::chr11:2016960..2016996,-p20@H19
Hg19::chr11:2017005..2017026,-p27@H19
Hg19::chr11:2017110..2017135,+p@chr11:2017110..2017135
+
Hg19::chr11:2017138..2017174,-p18@H19
Hg19::chr11:2017178..2017212,-p16@H19
Hg19::chr11:2017214..2017227,-p10@H19
Hg19::chr11:2017228..2017236,-p34@H19
Hg19::chr11:2017331..2017342,-p30@H19
Hg19::chr11:2017349..2017365,-p7@H19
Hg19::chr11:2017366..2017393,-p3@H19
Hg19::chr11:2017367..2017398,+p@chr11:2017367..2017398
+
Hg19::chr11:2017395..2017407,-p17@H19
Hg19::chr11:2017416..2017437,-p13@H19
Hg19::chr11:2017525..2017553,+p@chr11:2017525..2017553
+
Hg19::chr11:2017623..2017638,-p14@H19
Hg19::chr11:2017656..2017665,-p36@H19
Hg19::chr11:2017849..2017895,+p@chr11:2017849..2017895
+
Hg19::chr11:2017862..2017869,-p28@H19
Hg19::chr11:2017907..2017914,-p32@H19
Hg19::chr11:2017929..2017975,+p@chr11:2017929..2017975
+
Hg19::chr11:2018007..2018012,-p1@MIR675
Hg19::chr11:2018058..2018067,+p14@AF118081
Hg19::chr11:2018115..2018182,+p4@AF118081
Hg19::chr11:2018178..2018183,-p31@H19
Hg19::chr11:2018235..2018266,+p7@AF118081
Hg19::chr11:2018305..2018318,-p8@H19
Hg19::chr11:2018321..2018332,-p22@H19
Hg19::chr11:2018359..2018371,-p11@H19
Hg19::chr11:2018389..2018396,-p26@H19
Hg19::chr11:2018395..2018415,+p9@AF118081
Hg19::chr11:2018399..2018408,-p23@H19
Hg19::chr11:2018440..2018456,-p5@H19
Hg19::chr11:2018455..2018516,+p2@AF118081
Hg19::chr11:2018467..2018477,-p19@H19
Hg19::chr11:2018544..2018555,-p21@H19
Hg19::chr11:2018636..2018661,+p6@AF118081
Hg19::chr11:2018694..2018745,+p3@AF118081
Hg19::chr11:2018773..2018785,-p12@H19
Hg19::chr11:2018875..2018886,-p25@H19
Hg19::chr11:2018901..2018914,-p6@H19
Hg19::chr11:2018956..2018969,-p15@H19
Hg19::chr11:2018977..2019048,-p1@H19
Hg19::chr11:2150461..2150472,+p5@BC104421
Hg19::chr11:2160324..2160330,+p17@BC017277
Hg19::chr11:2160680..2160696,-p59@IGF2
Hg19::chr1:2066627..2066640,+p19@PRKCZ


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


p.valueFDRnGenesnPathwayName
1.2723518646306e-050.008053987303111713312Diabetes pathways (Reactome):REACT_15380



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:0005055laminin receptor activity0.0172190497820848
GO:0004700atypical protein kinase C activity0.0172190497820848
GO:0006349genetic imprinting0.0229553539426068
GO:0018445prothoracicotrophic hormone activity0.0229553539426068
GO:0005159insulin-like growth factor receptor binding0.0245899540279904
GO:0004697protein kinase C activity0.0245899540279904
GO:0001565phorbol ester receptor activity0.0245899540279904
GO:0008286insulin receptor signaling pathway0.0389942395441504
GO:0005184neuropeptide hormone activity0.0389942395441504
GO:0005843cytosolic small ribosomal subunit (sensu Eukaryota)0.0389942395441504
GO:0007165signal transduction0.0409608036317618
GO:0007154cell communication0.0474708623037988
GO:0008305integrin complex0.0482976234877922
GO:0019992diacylglycerol binding0.0482976234877922
GO:0040029regulation of gene expression, epigenetic0.0496531872163847



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><br>


Cell Type
Ontology termp-valuen
extraembryonic cell1.86e-1219
cell of skeletal muscle1.39e-089
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane1.11e-1514
membranous layer1.11e-1514
larynx9.60e-149
upper respiratory tract5.82e-1319
extraembryonic structure2.27e-1224
chorion1.37e-117
endoderm-derived structure4.76e-09160
endoderm4.76e-09160
presumptive endoderm4.76e-09160
subdivision of digestive tract5.39e-09118
foregut7.78e-0987
multi-tissue structure3.81e-08342
digestive system7.44e-08145
digestive tract7.44e-08145
primitive gut7.44e-08145
mesenchyme9.16e-08160
entire embryonic mesenchyme9.16e-08160
placenta2.17e-074
allantois2.17e-074
segment of respiratory tract3.41e-0747
organ component layer7.07e-0766
organism subdivision9.44e-07264


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
EGR1#1958231.821081256835450.001803058739523370.0109089127387951



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