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MCL coexpression mm9:341: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0048500;signal recognition particle;0.00597732630773684;217337,67398!GO:0005786;signal recognition particle, endoplasmic reticulum targeting;0.00597732630773684;217337,67398!GO:0005783;endoplasmic reticulum;0.00597732630773684;81910,53421,106200,67398,19035!GO:0065002;intracellular protein transport across a membrane;0.0260779050019175;81910,53421!GO:0005047;signal recognition particle binding;0.0260779050019175;67398!GO:0005789;endoplasmic reticulum membrane;0.0315120351101235;81910,67398!GO:0042175;nuclear envelope-endoplasmic reticulum network;0.0315120351101235;81910,67398!GO:0005785;signal recognition particle receptor complex;0.0315120351101235;67398!GO:0044432;endoplasmic reticulum part;0.0315120351101235;81910,67398!GO:0006886;intracellular protein transport;0.0400770095428246;81910,53421,67398!GO:0008312;7S RNA binding;0.0400770095428246;67398!GO:0005791;rough endoplasmic reticulum;0.0400770095428246;67398!GO:0030867;rough endoplasmic reticulum membrane;0.0400770095428246;67398!
|gostat_on_MCL_coexpression=GO:0048500;signal recognition particle;0.00597732630773684;217337,67398!GO:0005786;signal recognition particle, endoplasmic reticulum targeting;0.00597732630773684;217337,67398!GO:0005783;endoplasmic reticulum;0.00597732630773684;81910,53421,106200,67398,19035!GO:0065002;intracellular protein transport across a membrane;0.0260779050019175;81910,53421!GO:0005047;signal recognition particle binding;0.0260779050019175;67398!GO:0005789;endoplasmic reticulum membrane;0.0315120351101235;81910,67398!GO:0042175;nuclear envelope-endoplasmic reticulum network;0.0315120351101235;81910,67398!GO:0005785;signal recognition particle receptor complex;0.0315120351101235;67398!GO:0044432;endoplasmic reticulum part;0.0315120351101235;81910,67398!GO:0006886;intracellular protein transport;0.0400770095428246;81910,53421,67398!GO:0008312;7S RNA binding;0.0400770095428246;67398!GO:0005791;rough endoplasmic reticulum;0.0400770095428246;67398!GO:0030867;rough endoplasmic reticulum membrane;0.0400770095428246;67398!
}}
}}

Revision as of 12:40, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:116135416..116135452,-p1@Srp68
Mm9::chr12:60230744..60230805,+p3@Ctage5
Mm9::chr13:73741583..73741594,+p3@Clptm1l
Mm9::chr16:11134590..11134605,-p4@Txndc11
Mm9::chr16:38562934..38562974,+p1@Tmem39a
Mm9::chr1:13579798..13579985,-p1@Tram1
Mm9::chr1:75432577..75432588,+p2@Gmppa
Mm9::chr2:143836938..143836972,-p1@Rrbp1
Mm9::chr3:115710258..115710314,-p1@Slc30a7
Mm9::chr3:58329035..58329050,+p@chr3:58329035..58329050
+
Mm9::chr3:58329639..58329650,-p3@Serp1
Mm9::chr3:58329664..58329683,-p1@Serp1
Mm9::chr3:58329690..58329710,-p2@Serp1
Mm9::chr5:115608144..115608168,-p1@Mlec
Mm9::chr5:130698198..130698260,+p1@0610007L01Rik
Mm9::chr5:31171996..31172037,+p1@Tmem214
Mm9::chr6:88468729..88468751,-p2@Sec61a1
Mm9::chr8:26830514..26830525,+p3@Ppapdc1b
Mm9::chr8:26830526..26830571,+p1@Ppapdc1b
Mm9::chr9:103965379..103965476,-p1@Uba5
Mm9::chr9:35018762..35018809,+p1@Srpr
Mm9::chr9:35018814..35018833,+p2@Srpr
Mm9::chr9:65908002..65908080,+p1@Ppib


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:0048500signal recognition particle0.00597732630773684
GO:0005786signal recognition particle, endoplasmic reticulum targeting0.00597732630773684
GO:0005783endoplasmic reticulum0.00597732630773684
GO:0065002intracellular protein transport across a membrane0.0260779050019175
GO:0005047signal recognition particle binding0.0260779050019175
GO:0005789endoplasmic reticulum membrane0.0315120351101235
GO:0042175nuclear envelope-endoplasmic reticulum network0.0315120351101235
GO:0005785signal recognition particle receptor complex0.0315120351101235
GO:0044432endoplasmic reticulum part0.0315120351101235
GO:0006886intracellular protein transport0.0400770095428246
GO:00083127S RNA binding0.0400770095428246
GO:0005791rough endoplasmic reticulum0.0400770095428246
GO:0030867rough endoplasmic reticulum membrane0.0400770095428246



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>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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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