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MCL coexpression mm9:1609: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.267273341778078,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0570741246689917,0,0,0,0,0,0,0,1.06475968199697,0.908167290436919,1.00429729386248,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0421182837367051,0.096497738357694,0.303388537662931,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0769870445726752,0.0294389011296462,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.299633798006623,0,0.0655375003561515,0.333405124888963,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0489745727197172,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.138417952808354,0.982638705120072,0.268922630346636,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0871588832444397,0,0,0.0978461107777356,0,0.0750453505157095,0,0.0269518943326477,0.0242538736058389,0,0,0,0,0,0,0,0,0.0589368614163519,0,0.0352754493378881,0,0,0,0,0,0.0408018333703219,0,0,0,0,0,0,0,0,0
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.267273341778078,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0570741246689917,0,0,0,0,0,0,0,1.06475968199697,0.908167290436919,1.00429729386248,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0421182837367051,0.096497738357694,0.303388537662931,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0769870445726752,0.0294389011296462,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.299633798006623,0,0.0655375003561515,0.333405124888963,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0489745727197172,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.138417952808354,0.982638705120072,0.268922630346636,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0871588832444397,0,0,0.0978461107777356,0,0.0750453505157095,0,0.0269518943326477,0.0242538736058389,0,0,0,0,0,0,0,0,0.0589368614163519,0,0.0352754493378881,0,0,0,0,0,0.0408018333703219,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0006882;cellular zinc ion homeostasis;0.0312234660803284;72027!GO:0055069;zinc ion homeostasis;0.0312234660803284;72027!GO:0005385;zinc ion transmembrane transporter activity;0.0346889380409686;72027!GO:0000119;mediator complex;0.041610757046365;23989!GO:0006829;zinc ion transport;0.041610757046365;72027!GO:0046915;transition metal ion transmembrane transporter activity;0.041610757046365;72027!GO:0015082;di-, tri-valent inorganic cation transmembrane transporter activity;0.0475447224348353;72027!
|gostat_on_MCL_coexpression=GO:0006882;cellular zinc ion homeostasis;0.0312234660803284;72027!GO:0055069;zinc ion homeostasis;0.0312234660803284;72027!GO:0005385;zinc ion transmembrane transporter activity;0.0346889380409686;72027!GO:0000119;mediator complex;0.041610757046365;23989!GO:0006829;zinc ion transport;0.041610757046365;72027!GO:0046915;transition metal ion transmembrane transporter activity;0.041610757046365;72027!GO:0015082;di-, tri-valent inorganic cation transmembrane transporter activity;0.0475447224348353;72027!
|ontology_enrichment_celltype=CL:0000068!1.25e-12!3;CL:0002202!1.25e-12!3;CL:0000069!1.25e-12!3;CL:0002632!1.25e-12!3;CL:0002368!1.25e-12!3;CL:0000307!1.25e-12!3;CL:0000377!1.25e-12!3
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000474!1.07e-14!9;UBERON:0004175!1.84e-14!9;UBERON:0003126!1.25e-12!3;UBERON:0001005!1.25e-12!3;UBERON:0007196!1.25e-12!3;UBERON:0001558!1.25e-12!3;UBERON:0003100!6.40e-12!11;UBERON:0003134!1.24e-11!8;UBERON:0001301!1.71e-11!3;UBERON:0006555!1.71e-11!3;UBERON:0005103!1.71e-11!3;UBERON:0000083!1.71e-11!3;UBERON:0009201!1.71e-11!3;UBERON:0004819!1.71e-11!3;UBERON:0006553!1.71e-11!3;UBERON:0003074!1.71e-11!3;UBERON:0003060!1.71e-11!3;UBERON:0005156!3.19e-10!26;UBERON:0000990!3.19e-10!26;UBERON:0003133!8.87e-09!24;UBERON:0000080!9.80e-09!4;UBERON:0005904!9.80e-09!4;UBERON:0006947!9.80e-09!4;UBERON:0002120!9.80e-09!4;UBERON:0004054!9.80e-09!4;UBERON:0004875!9.80e-09!4;UBERON:0004876!9.80e-09!4;UBERON:0005721!9.80e-09!4;UBERON:0005754!9.80e-09!4;UBERON:0007297!9.80e-09!4;UBERON:0001343!5.70e-08!2;UBERON:0004910!5.70e-08!2;UBERON:0004909!5.70e-08!2;UBERON:0005154!5.70e-08!2;UBERON:0005295!5.70e-08!2;UBERON:0005297!5.70e-08!2;UBERON:0005294!5.70e-08!2;UBERON:0010141!5.70e-08!2;UBERON:0005891!5.70e-08!2;UBERON:0003975!1.97e-07!5;UBERON:0004122!4.98e-07!5
}}
}}

Revision as of 17:09, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:98568959..98568970,-p2@Med24
Mm9::chr11:98569050..98569057,-p7@Med24
Mm9::chr11:98569071..98569091,-p@chr11:98569071..98569091
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Mm9::chr15:75069502..75069519,-p1@ENSMUST00000089689
Mm9::chr15:76444647..76444681,-p@chr15:76444647..76444681
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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:0006882cellular zinc ion homeostasis0.0312234660803284
GO:0055069zinc ion homeostasis0.0312234660803284
GO:0005385zinc ion transmembrane transporter activity0.0346889380409686
GO:0000119mediator complex0.041610757046365
GO:0006829zinc ion transport0.041610757046365
GO:0046915transition metal ion transmembrane transporter activity0.041610757046365
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.0475447224348353



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>cell_data<br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
female reproductive system1.07e-149
internal genitalia1.84e-149
trachea1.25e-123
respiratory airway1.25e-123
tracheobronchial tree1.25e-123
lower respiratory tract1.25e-123
female organism6.40e-1211
female reproductive organ1.24e-118
epididymis1.71e-113
excretory tube1.71e-113
mesonephric epithelium1.71e-113
mesonephric tubule1.71e-113
nephric duct1.71e-113
kidney epithelium1.71e-113
renal duct1.71e-113
mesonephric duct1.71e-113
pronephric duct1.71e-113
reproductive structure3.19e-1026
reproductive system3.19e-1026
reproductive organ8.87e-0924
mesonephros9.80e-094
duct of male reproductive system9.80e-094
male genital duct9.80e-094
pronephros9.80e-094
internal male genitalia9.80e-094
nephrogenic cord9.80e-094
urogenital ridge9.80e-094
pronephric mesoderm9.80e-094
rostral part of nephrogenic cord9.80e-094
presumptive pronephric mesoderm9.80e-094
seminiferous tubule of testis5.70e-082
epithelium of male gonad5.70e-082
epithelium of gonad5.70e-082
epithelial cord5.70e-082
sex cord5.70e-082
testis sex cord5.70e-082
genital ridge5.70e-082
primitive sex cord of indifferent gonad5.70e-082
coelomic epithelium5.70e-082
internal female genitalia1.97e-075
genitourinary system4.98e-075


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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