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MCL coexpression mm9:730: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000970!6.27e-18!9;UBERON:0000019!6.27e-18!9;UBERON:0000047!6.27e-18!9;UBERON:0010312!6.27e-18!9;UBERON:0004088!6.27e-18!9;UBERON:0002104!6.27e-18!9;UBERON:0001456!6.27e-18!9;UBERON:0003072!6.27e-18!9;UBERON:0004128!6.27e-18!9;UBERON:0003071!6.27e-18!9;UBERON:0001444!2.89e-14!11;UBERON:0000020!6.80e-13!12;UBERON:0001032!6.80e-13!12;UBERON:0004456!6.80e-13!12;UBERON:0000033!9.81e-12!13;UBERON:0005085!9.81e-12!13;UBERON:0000014!1.06e-10!5;UBERON:0001003!1.06e-10!5;UBERON:0002097!1.06e-10!5;UBERON:0002199!1.06e-10!5;UBERON:0007029!1.06e-10!5;UBERON:0007376!1.06e-10!5;UBERON:0002416!1.06e-10!5;UBERON:0007383!1.06e-10!5
|ontology_enrichment_uberon=UBERON:0000970!6.27e-18!9;UBERON:0000019!6.27e-18!9;UBERON:0000047!6.27e-18!9;UBERON:0010312!6.27e-18!9;UBERON:0004088!6.27e-18!9;UBERON:0002104!6.27e-18!9;UBERON:0001456!6.27e-18!9;UBERON:0003072!6.27e-18!9;UBERON:0004128!6.27e-18!9;UBERON:0003071!6.27e-18!9;UBERON:0001444!2.89e-14!11;UBERON:0000020!6.80e-13!12;UBERON:0001032!6.80e-13!12;UBERON:0004456!6.80e-13!12;UBERON:0000033!9.81e-12!13;UBERON:0005085!9.81e-12!13;UBERON:0000014!1.06e-10!5;UBERON:0001003!1.06e-10!5;UBERON:0002097!1.06e-10!5;UBERON:0002199!1.06e-10!5;UBERON:0007029!1.06e-10!5;UBERON:0007376!1.06e-10!5;UBERON:0002416!1.06e-10!5;UBERON:0007383!1.06e-10!5
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.178895,0.807108,0.360062,1.09907,0.373426,0.458558,0.124431,0.411053,0.10445,0.417132,1.13606,0.124608,0.470194,0.214197,0,0.656089,0.564478,0.113609,0.205418,0.26524,0.0365724,0.469335,0.198877,0.304728,0.496413,0.107695,0.392919,0.238759,0.0790295,0.379806,1.78376,0.191698,0.0942651,0.214608,0.218093,0.184038,0.443753,0.166348,0.143746,1.08585,0.38461,0.307718,0.215898,0.0081642,0.349801,0.578773,1.05036,1.12721,0.241306,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.695271,0.435119,0.101408,0.47505,0.735292,0.531188,0.140453,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.128829,0.03967,0.944464,0.0968968,0.623453,0.313198,0.567793,0.718494,0.268962,0.80832,0.673009,0.529804,0.380754,0.830765,0.0122854,0.0697823,0.271714,0.583509,1.55487,1.11522,0.835661,1.80968,0.205117,0.163126,0.455999,0.122617,0.770215,0.57902,0.234357,0.541671,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.845852,0.878738,0.26996,0.421988,1.12221,1.07996,0.0187247,0.363536,0.657356,0.181004,0.949798,0.607824,1.24551,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,2.12779,1.14365,15.1463,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.201635,0.580497,0.0316649,0.895708,0.153911,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.18312,0.445669,0.0054279
}}
}}

Revision as of 18:49, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr14:118412218..118412229,-p@chr14:118412218..118412229
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Mm9::chr14:118429907..118429909,-p@chr14:118429907..118429909
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Mm9::chr14:118451457..118451475,-p1@Dct
Mm9::chr15:10930471..10930491,+p1@Slc45a2
Mm9::chr15:10930503..10930518,+p2@Slc45a2
Mm9::chr19:29772395..29772417,+p1@Mlana
Mm9::chr4:80480108..80480125,+p1@Tyrp1
Mm9::chr4:80480190..80480199,+p5@Tyrp1
Mm9::chr4:80480202..80480217,+p3@Tyrp1
Mm9::chr6:97941770..97941784,+p4@Mitf


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:0006583melanin biosynthetic process from tyrosine6.78820209071475e-09
GO:0006582melanin metabolic process1.35741721685762e-08
GO:0042438melanin biosynthetic process1.35741721685762e-08
GO:0006570tyrosine metabolic process2.42608404590985e-08
GO:0009072aromatic amino acid family metabolic process1.46956811269265e-07
GO:0046148pigment biosynthetic process1.46956811269265e-07
GO:0048066pigmentation during development1.77004589903175e-07
GO:0042440pigment metabolic process1.90510097451336e-07
GO:0019748secondary metabolic process4.64698917360445e-07
GO:0006725aromatic compound metabolic process7.9118639122626e-06
GO:0006520amino acid metabolic process4.92698596534237e-05
GO:0006519amino acid and derivative metabolic process0.000103407251882155
GO:0009308amine metabolic process0.000150135472305523
GO:0006807nitrogen compound metabolic process0.000173712652337567
GO:0019752carboxylic acid metabolic process0.000310035712120609
GO:0006082organic acid metabolic process0.000310035712120609
GO:0004167dopachrome isomerase activity0.000991906161063647
GO:0043437butanoic acid metabolic process0.000991906161063647
GO:0043438acetoacetic acid metabolic process0.000991906161063647
GO:0044249cellular biosynthetic process0.00161887872627728
GO:0009058biosynthetic process0.00377523513334822
GO:0032438melanosome organization and biogenesis0.00409565704379738
GO:0048753pigment granule organization and biogenesis0.00409565704379738
GO:0033059cellular pigmentation0.0070626860823427
GO:0016863intramolecular oxidoreductase activity, transposing C



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
eye6.27e-189
camera-type eye6.27e-189
simple eye6.27e-189
immature eye6.27e-189
ocular region6.27e-189
visual system6.27e-189
face6.27e-189
optic cup6.27e-189
optic vesicle6.27e-189
eye primordium6.27e-189
subdivision of head2.89e-1411
sense organ6.80e-1312
sensory system6.80e-1312
entire sense organ system6.80e-1312
head9.81e-1213
ectodermal placode9.81e-1213
zone of skin1.06e-105
skin epidermis1.06e-105
skin of body1.06e-105
integument1.06e-105
surface1.06e-105
outer epithelium1.06e-105
integumental system1.06e-105
enveloping layer of ectoderm1.06e-105


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}}}

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