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MCL coexpression mm9:789: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005409!3.56e-13!47;UBERON:0000160!5.49e-13!31;UBERON:0004119!8.61e-10!118;UBERON:0000925!8.61e-10!118;UBERON:0006595!8.61e-10!118;UBERON:0007023!1.30e-09!51;UBERON:0001007!2.72e-09!116;UBERON:0001555!2.72e-09!116;UBERON:0007026!2.72e-09!116;UBERON:0004921!1.58e-08!114;UBERON:0000344!8.14e-08!15;UBERON:0004923!8.44e-08!24;UBERON:0001242!8.97e-07!13;UBERON:0000060!8.97e-07!13;UBERON:0001262!8.97e-07!13;UBERON:0004786!8.97e-07!13
|ontology_enrichment_uberon=UBERON:0005409!3.56e-13!47;UBERON:0000160!5.49e-13!31;UBERON:0004119!8.61e-10!118;UBERON:0000925!8.61e-10!118;UBERON:0006595!8.61e-10!118;UBERON:0007023!1.30e-09!51;UBERON:0001007!2.72e-09!116;UBERON:0001555!2.72e-09!116;UBERON:0007026!2.72e-09!116;UBERON:0004921!1.58e-08!114;UBERON:0000344!8.14e-08!15;UBERON:0004923!8.44e-08!24;UBERON:0001242!8.97e-07!13;UBERON:0000060!8.97e-07!13;UBERON:0001262!8.97e-07!13;UBERON:0004786!8.97e-07!13
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.706384,0.330161,0.394491,0.645379,0.40827,0.495658,0.146465,0.468136,0.573183,0.453212,0.484001,0.146657,0.507558,0.24249,0,0.696644,0.22065,0.419123,0.902262,0.296085,0.403891,0.50668,0.64218,0.337218,0.534339,1.30297,0.428336,0.739731,1.09271,1.06602,0.796599,0.624261,0.364174,2.74163,0.137663,0.210533,0.480503,0.191662,0.967553,0.224094,0.419787,0.163087,0.244285,0.536558,0.383899,0.618203,0.443479,0.133514,0.745859,0.679429,0.560572,0.0915709,0.937018,0.954342,0.514504,0.279148,0.471658,0.12126,0.512521,0.776777,0.569793,0.952934,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,1.51902,0.460931,0.191038,0.987652,0.371787,0.710896,0.364033,0.607043,0.759798,0.299972,0.152219,0.713779,0.568383,0.436063,0.873141,0.967095,0.231102,0.0965007,0.623015,1.60001,1.15927,2.03711,0.809272,0.232894,0.551605,0.17334,0.444003,0.812053,0.618454,0.0816605,0.605162,0.796322,0.919715,0.680015,0.678976,0.419366,1.74861,0.439611,0.30446,1.46548,0.348012,0.921485,0.301014,0.458194,1.16629,0.633313,0.265919,0.398075,0.697928,0.207304,0.993019,1.56109,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,0.177062,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.32395,0.161645,0.938577,1.01208,0.526881,1.01974,1.38016,0.253271,0.352329,0.362302,2.58709,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.976805
}}
}}

Revision as of 18:55, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:61080643..61080656,-p2@Aldh3a2
Mm9::chr11:98822047..98822072,+p9@Rara
Mm9::chr16:93712197..93712253,+p1@Dopey2
Mm9::chr19:21547042..21547096,-p1@Gda
Mm9::chr2:29643002..29643031,+p5@Coq4
Mm9::chr2:29643841..29643855,+p2@Coq4
Mm9::chr4:43591581..43591644,+p2@Rgp1
Mm9::chr4:45985209..45985237,+p1@Tdrd7
Mm9::chr8:84927102..84927126,-p1@Il15


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:0045062extrathymic T cell selection0.0167780638799102
GO:0050691regulation of defense response to virus by host0.0167780638799102
GO:0008892guanine deaminase activity0.0167780638799102
GO:0033078extrathymic T cell differentiation0.0167780638799102
GO:0003708retinoic acid receptor activity0.0191717784505482
GO:0050688regulation of defense response to virus0.0191717784505482
GO:0001866NK T cell proliferation0.0191717784505482
GO:0004030aldehyde dehydrogenase [NAD(P)+] activity0.041917589897169
GO:0055012ventricular cardiac muscle cell differentiation0.0447047472996375
GO:0004029aldehyde dehydrogenase (NAD) activity0.0469322700537544



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
gastrointestinal system3.56e-1347
intestine5.49e-1331
endoderm-derived structure8.61e-10118
endoderm8.61e-10118
presumptive endoderm8.61e-10118
adult organism1.30e-0951
digestive system2.72e-09116
digestive tract2.72e-09116
primitive gut2.72e-09116
subdivision of digestive tract1.58e-08114
mucosa8.14e-0815
organ component layer8.44e-0824
intestinal mucosa8.97e-0713
anatomical wall8.97e-0713
wall of intestine8.97e-0713
gastrointestinal system mucosa8.97e-0713


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}}}