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MCL coexpression mm9:2280: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002365!6.31e-12!25;UBERON:0002330!6.31e-12!25;UBERON:0002107!2.02e-10!22;UBERON:0007499!2.02e-10!22;UBERON:0006925!2.02e-10!22;UBERON:0009497!2.02e-10!22;UBERON:0000015!2.02e-10!22;UBERON:0002423!2.02e-10!22;UBERON:0006235!2.02e-10!22;UBERON:0008835!2.02e-10!22;UBERON:0003894!2.02e-10!22;UBERON:0004161!2.02e-10!22;UBERON:0008836!2.02e-10!22;UBERON:0009854!8.71e-10!23;UBERON:0009856!8.71e-10!23;UBERON:0000014!1.29e-08!5;UBERON:0001003!1.29e-08!5;UBERON:0002097!1.29e-08!5;UBERON:0002199!1.29e-08!5;UBERON:0007029!1.29e-08!5;UBERON:0007376!1.29e-08!5;UBERON:0002416!1.29e-08!5;UBERON:0007383!1.29e-08!5
|ontology_enrichment_uberon=UBERON:0002365!6.31e-12!25;UBERON:0002330!6.31e-12!25;UBERON:0002107!2.02e-10!22;UBERON:0007499!2.02e-10!22;UBERON:0006925!2.02e-10!22;UBERON:0009497!2.02e-10!22;UBERON:0000015!2.02e-10!22;UBERON:0002423!2.02e-10!22;UBERON:0006235!2.02e-10!22;UBERON:0008835!2.02e-10!22;UBERON:0003894!2.02e-10!22;UBERON:0004161!2.02e-10!22;UBERON:0008836!2.02e-10!22;UBERON:0009854!8.71e-10!23;UBERON:0009856!8.71e-10!23;UBERON:0000014!1.29e-08!5;UBERON:0001003!1.29e-08!5;UBERON:0002097!1.29e-08!5;UBERON:0002199!1.29e-08!5;UBERON:0007029!1.29e-08!5;UBERON:0007376!1.29e-08!5;UBERON:0002416!1.29e-08!5;UBERON:0007383!1.29e-08!5
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.128156,0.612053,0.688265,1.21364,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,1.39891,0.197567,0.815872,0.481455,0.620553,0.846564,0.906602,0.727368,0.535752,0.790816,0.711848,1.12823,0.471365,0.318879,0.503207,0.30022,0.460474,0.786577,1.10929,0.40068,0.478558,0.717547,0.544696,0.504971,2.22741,1.61988,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.864765,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.758875,0.808001,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.961641,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.442329,0.692434,1.02384,0.456123,1.33244,2.22508,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,2.65107,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,2.11223,0.79777,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.0824127
}}
}}

Revision as of 21:10, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr1:123224249..123224267,-p9@Insig2
Mm9::chr2:110154372..110154384,-p7@Bbox1
Mm9::chr2:110154391..110154403,-p9@Bbox1
Mm9::chr2:110154423..110154449,-p6@Bbox1


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:0008336gamma-butyrobetaine dioxygenase activity0.00423663040837316
GO:0006991response to sterol depletion0.00423663040837316
GO:0045329carnitine biosynthetic process0.00423663040837316
GO:0009437carnitine metabolic process0.00635459742497994
GO:0042401biogenic amine biosynthetic process0.0254016766960898
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0.0254016766960898
GO:0042398amino acid derivative biosynthetic process0.0254016766960898
GO:0006767water-soluble vitamin metabolic process0.0283527507694216
GO:0009309amine biosynthetic process0.0283527507694216
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0283527507694216
GO:0051213dioxygenase activity0.0283527507694216
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0283527507694216
GO:0006766vitamin metabolic process0.0283527507694216
GO:0008203cholesterol metabolic process0.0283527507694216
GO:0016125sterol metabolic process0.0283527507694216
GO:0006576biogenic amine metabolic process0.0283527507694216
GO:0044271nitrogen compound biosynthetic process0.0283527507694216
GO:0006575amino acid derivative metabolic process0.03064404692869
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0416679741868591
GO:0008202steroid metabolic process0.044316444686879



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
exocrine gland6.31e-1225
exocrine system6.31e-1225
liver2.02e-1022
epithelial sac2.02e-1022
digestive gland2.02e-1022
epithelium of foregut-midgut junction2.02e-1022
anatomical boundary2.02e-1022
hepatobiliary system2.02e-1022
foregut-midgut junction2.02e-1022
hepatic diverticulum2.02e-1022
liver primordium2.02e-1022
septum transversum2.02e-1022
liver bud2.02e-1022
digestive tract diverticulum8.71e-1023
sac8.71e-1023
zone of skin1.29e-085
skin epidermis1.29e-085
skin of body1.29e-085
integument1.29e-085
surface1.29e-085
outer epithelium1.29e-085
integumental system1.29e-085
enveloping layer of ectoderm1.29e-085


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}}}