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MCL coexpression mm9:409: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0754257438189354,0.108683913498975,0.327783284444535,0.383275722246235,0.389649260204035,0.367640248092631,0.577221386973884,0.199638874161908,0.118594524292246,0.0731640704872308,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0388749848471105,0.0269518943326477,0.0242538736058389,0,0.0476191773904887,0,0,0.0596387295197733,0,0.0354759961767123,0,0.0294684307081759,0.0195303707501796,0,0,0,0.0276517186754466,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0030511;positive regulation of transforming growth factor beta receptor signaling pathway;0.0256382161274507;114249!GO:0017015;regulation of transforming growth factor beta receptor signaling pathway;0.0421083748790152;114249!GO:0001658;ureteric bud branching;0.0421083748790152;114249!GO:0005178;integrin binding;0.0421083748790152;114249!GO:0001657;ureteric bud development;0.0421083748790152;114249!GO:0001656;metanephros development;0.0421083748790152;114249!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0421083748790152;114249!GO:0032403;protein complex binding;0.0421083748790152;114249!GO:0048754;branching morphogenesis of a tube;0.0421083748790152;114249!GO:0001763;morphogenesis of a branching structure;0.0421083748790152;114249!GO:0007160;cell-matrix adhesion;0.0421083748790152;114249!GO:0009967;positive regulation of signal transduction;0.0421083748790152;114249!GO:0031589;cell-substrate adhesion;0.0421083748790152;114249!GO:0001822;kidney development;0.0421083748790152;114249!GO:0001655;urogenital system development;0.0421083748790152;114249!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0421083748790152;114249!
|gostat_on_MCL_coexpression=GO:0030511;positive regulation of transforming growth factor beta receptor signaling pathway;0.0256382161274507;114249!GO:0017015;regulation of transforming growth factor beta receptor signaling pathway;0.0421083748790152;114249!GO:0001658;ureteric bud branching;0.0421083748790152;114249!GO:0005178;integrin binding;0.0421083748790152;114249!GO:0001657;ureteric bud development;0.0421083748790152;114249!GO:0001656;metanephros development;0.0421083748790152;114249!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0421083748790152;114249!GO:0032403;protein complex binding;0.0421083748790152;114249!GO:0048754;branching morphogenesis of a tube;0.0421083748790152;114249!GO:0001763;morphogenesis of a branching structure;0.0421083748790152;114249!GO:0007160;cell-matrix adhesion;0.0421083748790152;114249!GO:0009967;positive regulation of signal transduction;0.0421083748790152;114249!GO:0031589;cell-substrate adhesion;0.0421083748790152;114249!GO:0001822;kidney development;0.0421083748790152;114249!GO:0001655;urogenital system development;0.0421083748790152;114249!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0421083748790152;114249!
}}
}}

Revision as of 12:41, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:102491237..102491291,-p2@Alx1
Mm9::chr10:45588552..45588568,+p@chr10:45588552..45588568
+
Mm9::chr10:50622895..50622905,+p@chr10:50622895..50622905
+
Mm9::chr12:37259377..37259386,+p@chr12:37259377..37259386
+
Mm9::chr13:115892012..115892032,-p10@Itga1
Mm9::chr13:7174912..7174917,-p@chr13:7174912..7174917
-
Mm9::chr15:98639918..98639923,-p@chr15:98639918..98639923
-
Mm9::chr2:113205651..113205663,+p@chr2:113205651..113205663
+
Mm9::chr3:132528811..132528861,+p@chr3:132528811..132528861
+
Mm9::chr3:132546346..132546356,-p@chr3:132546346..132546356
-
Mm9::chr3:54490675..54490702,-p@chr3:54490675..54490702
-
Mm9::chr3:54490730..54490743,-p@chr3:54490730..54490743
-
Mm9::chr5:16903685..16903695,-p@chr5:16903685..16903695
-
Mm9::chr5:16903720..16903727,-p@chr5:16903720..16903727
-
Mm9::chr5:53400291..53400314,-p@chr5:53400291..53400314
-
Mm9::chr7:31992851..31992858,+p@chr7:31992851..31992858
+
Mm9::chr8:108119034..108119056,+p@chr8:108119034..108119056
+
Mm9::chr8:47515509..47515529,-p@chr8:47515509..47515529
-


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:0030511positive regulation of transforming growth factor beta receptor signaling pathway0.0256382161274507
GO:0017015regulation of transforming growth factor beta receptor signaling pathway0.0421083748790152
GO:0001658ureteric bud branching0.0421083748790152
GO:0005178integrin binding0.0421083748790152
GO:0001657ureteric bud development0.0421083748790152
GO:0001656metanephros development0.0421083748790152
GO:0007179transforming growth factor beta receptor signaling pathway0.0421083748790152
GO:0032403protein complex binding0.0421083748790152
GO:0048754branching morphogenesis of a tube0.0421083748790152
GO:0001763morphogenesis of a branching structure0.0421083748790152
GO:0007160cell-matrix adhesion0.0421083748790152
GO:0009967positive regulation of signal transduction0.0421083748790152
GO:0031589cell-substrate adhesion0.0421083748790152
GO:0001822kidney development0.0421083748790152
GO:0001655urogenital system development0.0421083748790152
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0421083748790152



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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