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MCL coexpression mm9:886: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.073830516978053,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.205436104810215,0.0577162951573975,0.0450611899487389,0.03048532897689,0,0,0,0,0,0.0325594900422539,0,0.0858449846883365,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0265623655145556,0,0,0.0304819657131131,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.040876261176449,0.199199636536075,0.0719048481885784,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0419819959588466,0.0906941294286938,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0681780861044218,0,0,0,0,0,0,0,0,0,1.14796986126149,1.03390126855774,0.910176607704148,0.911188115885702,0.716675210635423,0.463431179757021,0.233811088121107,0.0936166775853224,0.10536076625968,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0471972389326998,0,0,0,0,0,0,0,0,0,0,0,0,0.0264159477773836,0,0,0,0,0,0,0.041721220909304,0,0,0,0,0,0,0,0,0.0685090053637401,0,0.164368616077759,0.159425201918028,0.08030228141145,0,0,0,0,0,0.0318857800356453,0,0,0,0,0,0,0,0,0,0,0.0605152268483434,0.0332484050430722,0,0,0,0,0,0,0,0,0,0,0.0212308449966822,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0214427057787972,0.496662055277832,0.336142183686976,0.233541046240123,0.181964973832605,0,0.0435794416222198,0.040679966067952,0.0604381279967265,0,0,0,0.0388749848471105,0.0269518943326477,0.0472245945615809,0,0.0238095886952444,0,0,0.0596387295197733,0,0.0354759961767123,0.0464368173027965,0.0294684307081759,0.0569785733435272,0.017637724668944,0,0,0,0,0.0243442052522616,0.0594496181738161,0,0.0312791175364151,0.109155573003225,0,0,0,0,0,0
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.073830516978053,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.205436104810215,0.0577162951573975,0.0450611899487389,0.03048532897689,0,0,0,0,0,0.0325594900422539,0,0.0858449846883365,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0265623655145556,0,0,0.0304819657131131,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.040876261176449,0.199199636536075,0.0719048481885784,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0419819959588466,0.0906941294286938,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0681780861044218,0,0,0,0,0,0,0,0,0,1.14796986126149,1.03390126855774,0.910176607704148,0.911188115885702,0.716675210635423,0.463431179757021,0.233811088121107,0.0936166775853224,0.10536076625968,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0471972389326998,0,0,0,0,0,0,0,0,0,0,0,0,0.0264159477773836,0,0,0,0,0,0,0.041721220909304,0,0,0,0,0,0,0,0,0.0685090053637401,0,0.164368616077759,0.159425201918028,0.08030228141145,0,0,0,0,0,0.0318857800356453,0,0,0,0,0,0,0,0,0,0,0.0605152268483434,0.0332484050430722,0,0,0,0,0,0,0,0,0,0,0.0212308449966822,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0214427057787972,0.496662055277832,0.336142183686976,0.233541046240123,0.181964973832605,0,0.0435794416222198,0.040679966067952,0.0604381279967265,0,0,0,0.0388749848471105,0.0269518943326477,0.0472245945615809,0,0.0238095886952444,0,0,0.0596387295197733,0,0.0354759961767123,0.0464368173027965,0.0294684307081759,0.0569785733435272,0.017637724668944,0,0,0,0,0.0243442052522616,0.0594496181738161,0,0.0312791175364151,0.109155573003225,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0030125;clathrin vesicle coat;0.0152668967658284;108800!GO:0030665;clathrin coated vesicle membrane;0.0152668967658284;108800!GO:0030119;AP-type membrane coat adaptor complex;0.0152668967658284;108800!GO:0030120;vesicle coat;0.0152668967658284;108800!GO:0030131;clathrin adaptor complex;0.0152668967658284;108800!GO:0030662;coated vesicle membrane;0.0152668967658284;108800!GO:0030100;regulation of endocytosis;0.0152668967658284;108800!GO:0030118;clathrin coat;0.0152668967658284;108800!GO:0030659;cytoplasmic vesicle membrane;0.0152668967658284;108800!GO:0044433;cytoplasmic vesicle part;0.0155759432590639;108800!GO:0030117;membrane coat;0.0155759432590639;108800!GO:0048475;coated membrane;0.0155759432590639;108800!GO:0012506;vesicle membrane;0.0155759432590639;108800!GO:0030136;clathrin-coated vesicle;0.0191123181316574;108800!GO:0051049;regulation of transport;0.0196611515915192;108800!GO:0030135;coated vesicle;0.0196611515915192;108800!GO:0006461;protein complex assembly;0.0265870880209861;108800!GO:0008565;protein transporter activity;0.0287258715462298;108800!GO:0010324;membrane invagination;0.0303730893551745;108800!GO:0006897;endocytosis;0.0303730893551745;108800!GO:0016023;cytoplasmic membrane-bound vesicle;0.031885169561168;108800!GO:0031988;membrane-bound vesicle;0.031885169561168;108800!GO:0016044;membrane organization and biogenesis;0.0366300715308264;108800!GO:0031410;cytoplasmic vesicle;0.0413040638209104;108800!GO:0012505;endomembrane system;0.0413040638209104;108800!GO:0031982;vesicle;0.0413040638209104;108800!GO:0065003;macromolecular complex assembly;0.0421848463266313;108800!GO:0022607;cellular component assembly;0.0479099326138169;108800!GO:0006886;intracellular protein transport;0.0480034458199597;108800!GO:0016192;vesicle-mediated transport;0.0483317810770832;108800!
|gostat_on_MCL_coexpression=GO:0030125;clathrin vesicle coat;0.0152668967658284;108800!GO:0030665;clathrin coated vesicle membrane;0.0152668967658284;108800!GO:0030119;AP-type membrane coat adaptor complex;0.0152668967658284;108800!GO:0030120;vesicle coat;0.0152668967658284;108800!GO:0030131;clathrin adaptor complex;0.0152668967658284;108800!GO:0030662;coated vesicle membrane;0.0152668967658284;108800!GO:0030100;regulation of endocytosis;0.0152668967658284;108800!GO:0030118;clathrin coat;0.0152668967658284;108800!GO:0030659;cytoplasmic vesicle membrane;0.0152668967658284;108800!GO:0044433;cytoplasmic vesicle part;0.0155759432590639;108800!GO:0030117;membrane coat;0.0155759432590639;108800!GO:0048475;coated membrane;0.0155759432590639;108800!GO:0012506;vesicle membrane;0.0155759432590639;108800!GO:0030136;clathrin-coated vesicle;0.0191123181316574;108800!GO:0051049;regulation of transport;0.0196611515915192;108800!GO:0030135;coated vesicle;0.0196611515915192;108800!GO:0006461;protein complex assembly;0.0265870880209861;108800!GO:0008565;protein transporter activity;0.0287258715462298;108800!GO:0010324;membrane invagination;0.0303730893551745;108800!GO:0006897;endocytosis;0.0303730893551745;108800!GO:0016023;cytoplasmic membrane-bound vesicle;0.031885169561168;108800!GO:0031988;membrane-bound vesicle;0.031885169561168;108800!GO:0016044;membrane organization and biogenesis;0.0366300715308264;108800!GO:0031410;cytoplasmic vesicle;0.0413040638209104;108800!GO:0012505;endomembrane system;0.0413040638209104;108800!GO:0031982;vesicle;0.0413040638209104;108800!GO:0065003;macromolecular complex assembly;0.0421848463266313;108800!GO:0022607;cellular component assembly;0.0479099326138169;108800!GO:0006886;intracellular protein transport;0.0480034458199597;108800!GO:0016192;vesicle-mediated transport;0.0483317810770832;108800!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005172!1.20e-07!49;UBERON:0005173!1.20e-07!49;UBERON:0002417!1.20e-07!49;UBERON:0000916!1.20e-07!49
}}
}}

Revision as of 21:24, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:105018259..105018270,+p@chr11:105018259..105018270
+
Mm9::chr11:75263386..75263400,-p5@Wdr81
Mm9::chr12:92984460..92984529,-p4@Ston2
Mm9::chr16:12704492..12704509,+p@chr16:12704492..12704509
+
Mm9::chr16:93365564..93365588,-p@chr16:93365564..93365588
-
Mm9::chr19:40844025..40844047,-p@chr19:40844025..40844047
-
Mm9::chr1:158143264..158143294,+p@chr1:158143264..158143294
+
Mm9::chr1:88209180..88209184,+p@chr1:88209180..88209184
+


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:0030125clathrin vesicle coat0.0152668967658284
GO:0030665clathrin coated vesicle membrane0.0152668967658284
GO:0030119AP-type membrane coat adaptor complex0.0152668967658284
GO:0030120vesicle coat0.0152668967658284
GO:0030131clathrin adaptor complex0.0152668967658284
GO:0030662coated vesicle membrane0.0152668967658284
GO:0030100regulation of endocytosis0.0152668967658284
GO:0030118clathrin coat0.0152668967658284
GO:0030659cytoplasmic vesicle membrane0.0152668967658284
GO:0044433cytoplasmic vesicle part0.0155759432590639
GO:0030117membrane coat0.0155759432590639
GO:0048475coated membrane0.0155759432590639
GO:0012506vesicle membrane0.0155759432590639
GO:0030136clathrin-coated vesicle0.0191123181316574
GO:0051049regulation of transport0.0196611515915192
GO:0030135coated vesicle0.0196611515915192
GO:0006461protein complex assembly0.0265870880209861
GO:0008565protein transporter activity0.0287258715462298
GO:0010324membrane invagination0.0303730893551745
GO:0006897endocytosis0.0303730893551745
GO:0016023cytoplasmic membrane-bound vesicle0.031885169561168
GO:0031988membrane-bound vesicle0.031885169561168
GO:0016044membrane organization and biogenesis0.0366300715308264
GO:0031410cytoplasmic vesicle0.0413040638209104
GO:0012505endomembrane system0.0413040638209104
GO:0031982vesicle0.0413040638209104
GO:0065003macromolecular complex assembly0.0421848463266313
GO:0022607cellular component assembly0.0479099326138169
GO:0006886intracellular protein transport0.0480034458199597
GO:0016192vesicle-mediated transport0.0483317810770832



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
abdomen element1.20e-0749
abdominal segment element1.20e-0749
abdominal segment of trunk1.20e-0749
abdomen1.20e-0749


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}}}