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MCL coexpression mm9:686: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!1.01e-22!29;UBERON:0005057!1.01e-22!29;UBERON:0002370!2.77e-18!23;UBERON:0000974!2.77e-18!23;UBERON:0004807!2.77e-18!23;UBERON:0005058!2.77e-18!23;UBERON:0003351!2.77e-18!23;UBERON:0009113!2.77e-18!23;UBERON:0003295!2.77e-18!23;UBERON:0009722!2.77e-18!23;UBERON:0005562!2.77e-18!23;UBERON:0007690!2.77e-18!23;UBERON:0000077!4.83e-18!35;UBERON:0006562!2.25e-17!24;UBERON:0003408!2.25e-17!24;UBERON:0001557!2.25e-17!24;UBERON:0001042!2.25e-17!24;UBERON:0008814!2.25e-17!24;UBERON:0009145!2.25e-17!24;UBERON:0000072!4.71e-15!27;UBERON:0002390!1.35e-14!45;UBERON:0003061!1.35e-14!45;UBERON:0002193!2.17e-13!48;UBERON:0002405!2.17e-13!48;UBERON:0000063!7.99e-11!35;UBERON:0007811!1.98e-10!36;UBERON:0003081!8.70e-10!87;UBERON:0003929!9.39e-09!55;UBERON:0000065!9.49e-09!41;UBERON:0002368!1.09e-08!60;UBERON:0001004!1.84e-08!42;UBERON:0000153!3.45e-08!43;UBERON:0001041!5.21e-08!80;UBERON:0002530!1.07e-07!65
|ontology_enrichment_uberon=UBERON:0004177!1.01e-22!29;UBERON:0005057!1.01e-22!29;UBERON:0002370!2.77e-18!23;UBERON:0000974!2.77e-18!23;UBERON:0004807!2.77e-18!23;UBERON:0005058!2.77e-18!23;UBERON:0003351!2.77e-18!23;UBERON:0009113!2.77e-18!23;UBERON:0003295!2.77e-18!23;UBERON:0009722!2.77e-18!23;UBERON:0005562!2.77e-18!23;UBERON:0007690!2.77e-18!23;UBERON:0000077!4.83e-18!35;UBERON:0006562!2.25e-17!24;UBERON:0003408!2.25e-17!24;UBERON:0001557!2.25e-17!24;UBERON:0001042!2.25e-17!24;UBERON:0008814!2.25e-17!24;UBERON:0009145!2.25e-17!24;UBERON:0000072!4.71e-15!27;UBERON:0002390!1.35e-14!45;UBERON:0003061!1.35e-14!45;UBERON:0002193!2.17e-13!48;UBERON:0002405!2.17e-13!48;UBERON:0000063!7.99e-11!35;UBERON:0007811!1.98e-10!36;UBERON:0003081!8.70e-10!87;UBERON:0003929!9.39e-09!55;UBERON:0000065!9.49e-09!41;UBERON:0002368!1.09e-08!60;UBERON:0001004!1.84e-08!42;UBERON:0000153!3.45e-08!43;UBERON:0001041!5.21e-08!80;UBERON:0002530!1.07e-07!65
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.883225,0.807108,0.360062,0.580303,0.373426,1.16061,1.27916,0.816027,0.0244487,1.071,1.13606,0.393382,0.470194,1.15381,0,0.656089,0.564478,1.209,0.451901,1.34675,0.954669,0.469335,0.577226,0.822446,0.496413,1.16975,1.01819,0.238759,0.271461,0.379806,0.754912,0.191698,0.0942651,0.214608,0.386349,0.184038,0.443753,0.166348,0.143746,0.196807,0.38461,0.890234,0.215898,0.249283,0.349801,0.578773,1.05036,0.772185,0.677281,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.249055,0.435119,0.68053,1.19606,0.735292,0.531188,0.854737,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.404236,0.639498,0.944464,0.0968968,0.0893951,0.646602,0.567793,0.718494,0.74114,0.80832,0.673009,0.529804,0.764135,0.830765,0.0593483,0.0149522,0.96859,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.163126,1.43327,0.122617,0.770215,0.57902,0.86751,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.26996,1.08155,1.12221,0.195318,0.0839537,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,2.00057,0.353344,1.01535,0.48999,1.14365,0.33206,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,1.27006,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.201635,0.0806411,0.0316649,0.895708,0.153911,0.489108,2.23791,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.53929,0.445669,0.350088
}}
}}

Revision as of 18:45, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:19438492..19438529,-p1@uc007enj.1
Mm9::chr11:88486943..88486975,-p@chr11:88486943..88486975
-
Mm9::chr15:81853206..81853231,+p7@Xrcc6
Mm9::chr15:81853256..81853270,+p9@Xrcc6
Mm9::chr15:81853287..81853302,+p10@Xrcc6
Mm9::chr15:81853353..81853364,+p13@Xrcc6
Mm9::chr15:86065302..86065315,+p@chr15:86065302..86065315
+
Mm9::chr5:114282539..114282554,-p@chr5:114282539..114282554
-
Mm9::chr9:103328951..103328961,+p@chr9:103328951..103328961
+
Mm9::chr9:103328967..103328977,+p@chr9:103328967..103328977
+


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


GO IDGO nameFDR corrected p-value
GO:0005958DNA-dependent protein kinase complex0.00230099161781625
GO:0006303double-strand break repair via nonhomologous end joining0.00402673533117844
GO:0000726non-recombinational repair0.00402673533117844
GO:0005941unlocalized protein complex0.00402673533117844
GO:0004003ATP-dependent DNA helicase activity0.0046019832356325
GO:0003678DNA helicase activity0.00657426176518928
GO:0006302double-strand break repair0.00657426176518928
GO:0008094DNA-dependent ATPase activity0.009203966471265
GO:0006310DNA recombination0.01840793294253
GO:0008026ATP-dependent helicase activity0.01840793294253
GO:0004386helicase activity0.0263568130768043
GO:0006281DNA repair0.0358571193776366
GO:0042623ATPase activity, coupled0.0375349257656276
GO:0006974response to DNA damage stimulus0.0375349257656276
GO:0009719response to endogenous stimulus0.0375349257656276
GO:0016887ATPase activity0.0375349257656276



Relative expression of the co-expression cluster over median <br>Analyst:





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>


Uber Anatomy
Ontology termp-valuen
hemopoietic organ1.01e-2229
immune organ1.01e-2229
thymus2.77e-1823
neck2.77e-1823
respiratory system epithelium2.77e-1823
hemolymphoid system gland2.77e-1823
pharyngeal epithelium2.77e-1823
thymic region2.77e-1823
pharyngeal gland2.77e-1823
entire pharyngeal arch endoderm2.77e-1823
thymus primordium2.77e-1823
early pharyngeal endoderm2.77e-1823
mixed endoderm/mesoderm-derived structure4.83e-1835
pharynx2.25e-1724
gland of gut2.25e-1724
upper respiratory tract2.25e-1724
chordate pharynx2.25e-1724
pharyngeal arch system2.25e-1724
pharyngeal region of foregut2.25e-1724
segment of respiratory tract4.71e-1527
hematopoietic system1.35e-1445
blood island1.35e-1445
hemolymphoid system2.17e-1348
immune system2.17e-1348
organ segment7.99e-1135
craniocervical region1.98e-1036
lateral plate mesoderm8.70e-1087
gut epithelium9.39e-0955
respiratory tract9.49e-0941
endocrine gland1.09e-0860
respiratory system1.84e-0842
anterior region of body3.45e-0843
foregut5.21e-0880
gland1.07e-0765


TFBS overrepresentation<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}}}