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MCL coexpression mm9:587: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!5.47e-13!118;UBERON:0000925!5.47e-13!118;UBERON:0006595!5.47e-13!118;UBERON:0001007!1.96e-12!116;UBERON:0001555!1.96e-12!116;UBERON:0007026!1.96e-12!116;UBERON:0004921!1.25e-11!114;UBERON:0005409!1.57e-09!47;UBERON:0000160!1.59e-09!31;UBERON:0007023!1.48e-08!51;UBERON:0004923!6.64e-08!24;UBERON:0000344!7.76e-07!15
|ontology_enrichment_uberon=UBERON:0004119!5.47e-13!118;UBERON:0000925!5.47e-13!118;UBERON:0006595!5.47e-13!118;UBERON:0001007!1.96e-12!116;UBERON:0001555!1.96e-12!116;UBERON:0007026!1.96e-12!116;UBERON:0004921!1.25e-11!114;UBERON:0005409!1.57e-09!47;UBERON:0000160!1.59e-09!31;UBERON:0007023!1.48e-08!51;UBERON:0004923!6.64e-08!24;UBERON:0000344!7.76e-07!15
|tfbs_overrepresentation_for_novel_motifs=0.737036,0.409645,0.686572,0.303186,0.1565,0.315748,0.396495,0.630239,0.0967611,0.852117,0.939294,0.385627,0.630954,0.407615,0.169024,0,1.43434,0.150639,0.279039,0.33293,0.215242,0.725792,1.04849,0.155356,0.251585,0.432737,0.265362,0.888376,0.558665,0.766158,0.321757,0.683831,0.891038,0.234079,0.505829,0.406983,0.438297,0.382372,0.126724,0.347926,0.466602,1.56774,0.668798,0.170547,0.283915,0.797213,1.27535,0.919381,0.337012,0.564214,0.570705,2.01928,0.187938,0.82076,0.837732,0.414119,0.200484,0.37415,0.250759,1.86649,0.664611,0.46618,0.340458,0.560059,1.08652,0.598412,0.970969,1.3158,0.660133,1.17005,0.650349,0.313987,0.251765,0.870406,1.84724,1.76375,0.866433,0.50152,0.648171,0.218647,0.0952669,0.60374,0.464847,0.61111,0.758319,2.31993,0.237482,0.198381,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,1.27589,0.11194,0.0892768,0.698838,0.512384,1.04626,0.142282,0.683562,0.803823,0.571268,0.57027,1.56637,2.57485,0.344504,0.63348,1.16343,0.723377,0.805555,0.219561,2.55104,1.04639,0.152197,1.04217,0.826326,0.58848,0.139554,0.875675,0.540309,1.10848,0.500675,1.09972,0.651709,0.403884,1.64843,0.969481,0.49047,0.787341,0.296885,0.940498,0.426575,1.06766,0.092963,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.871748,0.515065,1.80426,0.276297,0.927992,0.777047,0.404179,0.822286,2.41964,0.425729,0.901933,0.458393,0.178202,0.265096,2.11874,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.436256,0.384198,4.96856
}}
}}

Revision as of 18:35, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:121023786..121023859,-p1@Tbk1
Mm9::chr10:79459200..79459220,+p2@Abca7
Mm9::chr11:120486287..120486312,-p1@Sirt7
Mm9::chr11:69224513..69224543,-p@chr11:69224513..69224543
-
Mm9::chr1:95721847..95721882,+p2@D2hgdh
Mm9::chr2:181316679..181316695,-p1@Uckl1
Mm9::chr3:35653043..35653057,+p1@Atp11b
Mm9::chr4:134479531..134479543,+p1@D4Wsu53e
Mm9::chr4:154998962..154999038,+p1@Cdk11b
Mm9::chr6:56664885..56664945,+p1@Avl9
Mm9::chr8:86222994..86223105,-p1@Pkn1
Mm9::chr9:96531906..96531973,-p1@Rasa2


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:0030554adenyl nucleotide binding0.000581269972159091
GO:0017076purine nucleotide binding0.000999727131268797
GO:0000166nucleotide binding0.00137670865549461
GO:0005524ATP binding0.00243065589320011
GO:0032559adenyl ribonucleotide binding0.00243065589320011
GO:0032553ribonucleotide binding0.00499779722893616
GO:0032555purine ribonucleotide binding0.00499779722893616
GO:0051990(R)-2-hydroxyglutarate dehydrogenase activity0.0076699720593875
GO:0032025response to cobalt ion0.0076699720593875
GO:0010042response to manganese ion0.0076699720593875
GO:0010043response to zinc ion0.0139427295764083
GO:0006972hyperosmotic response0.0255518688309197
GO:0004849uridine kinase activity0.0294772723990682
GO:0005677chromatin silencing complex0.0437696187419012
GO:0010038response to metal ion0.045218395249302
GO:0016301kinase activity0.045218395249302
GO:0006970response to osmotic stress0.045218395249302
GO:0019206nucleoside kinase activity0.045218395249302
GO:0016887ATPase activity0.045218395249302
GO:0010035response to inorganic substance0.045218395249302
GO:0006342chromatin silencing0.045218395249302
GO:0031507heterochromatin formation0.045218395249302
GO:0045814negative regulation of gene expression, epigenetic0.0476710522172964
GO:0004697protein kinase C activity0.0476710522172964
GO:0016772transferase activity, transferring phosphorus-containing groups0.0476710522172964
GO:0016787hydrolase activity0.0481444912763527
GO:0001565phorbol ester receptor activity0.0481444912763527



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
endoderm-derived structure5.47e-13118
endoderm5.47e-13118
presumptive endoderm5.47e-13118
digestive system1.96e-12116
digestive tract1.96e-12116
primitive gut1.96e-12116
subdivision of digestive tract1.25e-11114
gastrointestinal system1.57e-0947
intestine1.59e-0931
adult organism1.48e-0851
organ component layer6.64e-0824
mucosa7.76e-0715


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}}}