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MCL coexpression mm9:252: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0986886653414259,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0469568706916304,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.046982063026719,0,0.20708313509219,0.372482540320573,0.340901754499126,0.734524417069462,0.612764059597706,0.459992957186366,0.349077655346599,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0269518943326477,0.0242538736058389,0,0,0,0,0,0,0,0,0,0,0.0352754493378881,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0045079;negative regulation of chemokine biosynthetic process;0.0243214367362558;24058!GO:0004662;CAAX-protein geranylgeranyltransferase activity;0.0243214367362558;225467!GO:0001960;negative regulation of cytokine and chemokine mediated signaling pathway;0.0243214367362558;24058!GO:0001959;regulation of cytokine and chemokine mediated signaling pathway;0.0273578686066375;24058!GO:0004661;protein geranylgeranyltransferase activity;0.0319000303945271;225467!GO:0050755;chemokine metabolic process;0.0319000303945271;24058!GO:0045073;regulation of chemokine biosynthetic process;0.0319000303945271;24058!GO:0042033;chemokine biosynthetic process;0.0319000303945271;24058!GO:0032602;chemokine production;0.032401941583357;24058!GO:0042036;negative regulation of cytokine biosynthetic process;0.0364421998452786;24058!GO:0008318;protein prenyltransferase activity;0.0397442381751995;225467!
|gostat_on_MCL_coexpression=GO:0045079;negative regulation of chemokine biosynthetic process;0.0243214367362558;24058!GO:0004662;CAAX-protein geranylgeranyltransferase activity;0.0243214367362558;225467!GO:0001960;negative regulation of cytokine and chemokine mediated signaling pathway;0.0243214367362558;24058!GO:0001959;regulation of cytokine and chemokine mediated signaling pathway;0.0273578686066375;24058!GO:0004661;protein geranylgeranyltransferase activity;0.0319000303945271;225467!GO:0050755;chemokine metabolic process;0.0319000303945271;24058!GO:0045073;regulation of chemokine biosynthetic process;0.0319000303945271;24058!GO:0042033;chemokine biosynthetic process;0.0319000303945271;24058!GO:0032602;chemokine production;0.032401941583357;24058!GO:0042036;negative regulation of cytokine biosynthetic process;0.0364421998452786;24058!GO:0008318;protein prenyltransferase activity;0.0397442381751995;225467!
}}
}}

Revision as of 12:39, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127286945..127286957,+p1@Rdh19
Mm9::chr10:127286959..127286970,+p3@Rdh19
Mm9::chr10:127286973..127286982,+p2@Rdh19
Mm9::chr10:75036237..75036246,+p20@Ggt1
Mm9::chr10:75036945..75036970,+p@chr10:75036945..75036970
+
Mm9::chr12:70892340..70892351,-p@chr12:70892340..70892351
-
Mm9::chr13:29449543..29449564,-p@chr13:29449543..29449564
-
Mm9::chr14:65994176..65994223,+p9@Zfp395
Mm9::chr14:77873677..77873682,+p@chr14:77873677..77873682
+
Mm9::chr15:6330615..6330624,+p@chr15:6330615..6330624
+
Mm9::chr16:36561687..36561700,-p3@Casr
Mm9::chr16:86806603..86806613,-p1@uc007ztx.1
Mm9::chr19:17554168..17554181,+p@chr19:17554168..17554181
+
Mm9::chr19:44825248..44825255,-p@chr19:44825248..44825255
-
Mm9::chr1:108438515..108438553,+p1@ENSMUST00000144260
p1@ENSMUST00000149909
p1@uc007cgx.1
Mm9::chr2:29107203..29107216,-p8@6530402F18Rik
Mm9::chr3:132400383..132400390,+p@chr3:132400383..132400390
+
Mm9::chr3:28715165..28715176,-p@chr3:28715165..28715176
-
Mm9::chr3:28715186..28715197,-p@chr3:28715186..28715197
-
Mm9::chr3:57936042..57936071,-p@chr3:57936042..57936071
-
Mm9::chr3:63243166..63243186,+p@chr3:63243166..63243186
+
Mm9::chr3:68310831..68310837,+p@chr3:68310831..68310837
+
Mm9::chr4:114361321..114361337,-p@chr4:114361321..114361337
-
Mm9::chr4:19664510..19664529,+p@chr4:19664510..19664529
+
Mm9::chr5:123795864..123795869,-p@chr5:123795864..123795869
-
Mm9::chr6:117811962..117811990,+p5@Zfp239
Mm9::chr6:92766630..92766649,-p@chr6:92766630..92766649
-
Mm9::chr7:148280772..148280783,-p@chr7:148280772..148280783
-
Mm9::chr8:24425161..24425163,+p@chr8:24425161..24425163
+
Mm9::chr9:67114707..67114717,-p@chr9:67114707..67114717
-
Mm9::chr9:67114726..67114737,-p@chr9:67114726..67114737
-
Mm9::chr9:70616610..70616624,+p@chr9:70616610..70616624
+
Mm9::chr9:76894068..76894073,-p7@Tinag


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:0045079negative regulation of chemokine biosynthetic process0.0243214367362558
GO:0004662CAAX-protein geranylgeranyltransferase activity0.0243214367362558
GO:0001960negative regulation of cytokine and chemokine mediated signaling pathway0.0243214367362558
GO:0001959regulation of cytokine and chemokine mediated signaling pathway0.0273578686066375
GO:0004661protein geranylgeranyltransferase activity0.0319000303945271
GO:0050755chemokine metabolic process0.0319000303945271
GO:0045073regulation of chemokine biosynthetic process0.0319000303945271
GO:0042033chemokine biosynthetic process0.0319000303945271
GO:0032602chemokine production0.032401941583357
GO:0042036negative regulation of cytokine biosynthetic process0.0364421998452786
GO:0008318protein prenyltransferase activity0.0397442381751995



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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