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MCL coexpression mm9:230: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0386786870175947,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.722674373467553,0.783106157334932,0.881252412391429,0,0,0,0,0.0568996784870888,0,0,0,0,0.180274689346406,0.154371145613237,0.180605254120548,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00546532438442093,0,0.0394784708464508,0,0,0,0,0,0,0.0683455646190839,0.100296779313498,0,0,0,0,0,0,0,0,0.00588596731853538,0,0,0,0,0,0,0.0482820047261801,0,0,0.0586534975690397,0,0.0788495922528223,0.0644753106405114,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0805105854221362,0.0509235292940968,0,0,0,0,0,0,0.055406237837571,0,0.0388988969149198,0.0593840335866131,0,0,0,0.00471350169361161,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0360345119948964,0,0,0.0338533374824575,0.0592603993571966,0,0.0546921007390138,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0266298923127834,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00143769692539705,0,0,0,0,0.0672592169170953,0,0.0774164737207147,0.117937132941773,0.086880916817156,0.0642538110976656,0,0,0.0586723554240733,0,0,0,0,0,0,0.065928707415698,0,0,0,0,0,0,0,0,0,0,0,0.0576433181427177,0,0,0.123832128606708,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0910996096540711,0.0380940468056394,0.0254340553719351,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0132772188565915,0,0,0.054943952156948,0.034489466458534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.045863710440145,0,0,0,0.00845268861174908,0.0509416601409318,0.0730404042754446,0.0788367770143961,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0240810981784332,0.0269518943326477,0.0242538736058389,0,0,0,0,0,0,0.0375293082098077,0,0,0.0390607415003592,0.0352754493378881,0.0300728901825809,0,0.0540268771520897,0,0,0.0408018333703219,0,0,0,0.0968441960560167,0,0.0793066429689401,0.0571564262804498,0,0.0905641158318875
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0386786870175947,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.722674373467553,0.783106157334932,0.881252412391429,0,0,0,0,0.0568996784870888,0,0,0,0,0.180274689346406,0.154371145613237,0.180605254120548,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00546532438442093,0,0.0394784708464508,0,0,0,0,0,0,0.0683455646190839,0.100296779313498,0,0,0,0,0,0,0,0,0.00588596731853538,0,0,0,0,0,0,0.0482820047261801,0,0,0.0586534975690397,0,0.0788495922528223,0.0644753106405114,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0805105854221362,0.0509235292940968,0,0,0,0,0,0,0.055406237837571,0,0.0388988969149198,0.0593840335866131,0,0,0,0.00471350169361161,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0360345119948964,0,0,0.0338533374824575,0.0592603993571966,0,0.0546921007390138,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0266298923127834,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00143769692539705,0,0,0,0,0.0672592169170953,0,0.0774164737207147,0.117937132941773,0.086880916817156,0.0642538110976656,0,0,0.0586723554240733,0,0,0,0,0,0,0.065928707415698,0,0,0,0,0,0,0,0,0,0,0,0.0576433181427177,0,0,0.123832128606708,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0910996096540711,0.0380940468056394,0.0254340553719351,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0132772188565915,0,0,0.054943952156948,0.034489466458534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.045863710440145,0,0,0,0.00845268861174908,0.0509416601409318,0.0730404042754446,0.0788367770143961,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0240810981784332,0.0269518943326477,0.0242538736058389,0,0,0,0,0,0,0.0375293082098077,0,0,0.0390607415003592,0.0352754493378881,0.0300728901825809,0,0.0540268771520897,0,0,0.0408018333703219,0,0,0,0.0968441960560167,0,0.0793066429689401,0.0571564262804498,0,0.0905641158318875
|gostat_on_MCL_coexpression=GO:0044421;extracellular region part;0.0263871369384338;21826,18295,16195,16170,23892,18414,216725,268977!GO:0045625;regulation of T-helper 1 cell differentiation;0.0386373874983721;56468!GO:0045627;positive regulation of T-helper 1 cell differentiation;0.0386373874983721;56468!GO:0004924;oncostatin-M receptor activity;0.0386373874983721;18414!GO:0004896;hematopoietin/interferon-class (D200-domain) cytokine receptor activity;0.0386373874983721;16195,18414!GO:0005102;receptor binding;0.0386373874983721;56468,18295,16170,23892!GO:0005515;protein binding;0.0386373874983721;56468,18295,16195,245007,330171,23892,268977,21826,16709,16170!GO:0007167;enzyme linked receptor protein signaling pathway;0.0386373874983721;56468,23892,268977!GO:0005578;proteinaceous extracellular matrix;0.0386373874983721;18295,216725,268977!GO:0045629;negative regulation of T-helper 2 cell differentiation;0.0386373874983721;56468!GO:0045624;positive regulation of T-helper cell differentiation;0.0386373874983721;56468!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0386373874983721;23892,268977!GO:0007166;cell surface receptor linked signal transduction;0.0386373874983721;56468,16195,23892,71111,18414,216725,268977!GO:0009966;regulation of signal transduction;0.0386373874983721;56468,16195,23892!GO:0009968;negative regulation of signal transduction;0.0386373874983721;56468,23892!GO:0045628;regulation of T-helper 2 cell differentiation;0.0386373874983721;56468!GO:0045063;T-helper 1 cell differentiation;0.0386373874983721;56468!GO:0017074;procollagen N-endopeptidase activity;0.0386373874983721;216725!GO:0045623;negative regulation of T-helper cell differentiation;0.0386373874983721;56468!GO:0045064;T-helper 2 cell differentiation;0.041147959075257;56468!GO:0008593;regulation of Notch signaling pathway;0.041147959075257;16195!GO:0045622;regulation of T-helper cell differentiation;0.041147959075257;56468!GO:0007165;signal transduction;0.041147959075257;56468,68842,16195,23892,71111,18414,216725,268977!GO:0005615;extracellular space;0.041147959075257;21826,16195,16170,23892,18414,268977!GO:0042092;T-helper 2 type immune response;0.0476555594886153;56468!GO:0007154;cell communication;0.0476555594886153;56468,68842,16195,23892,71111,18414,216725,268977!GO:0050920;regulation of chemotaxis;0.0476555594886153;16170!GO:0050926;regulation of positive chemotaxis;0.0476555594886153;16170!GO:0050921;positive regulation of chemotaxis;0.0476555594886153;16170!GO:0005154;epidermal growth factor receptor binding;0.0476555594886153;56468!GO:0050927;positive regulation of positive chemotaxis;0.0476555594886153;16170!GO:0050930;induction of positive chemotaxis;0.0476555594886153;16170!GO:0002294;CD4-positive, alpha-beta T cell differentiation during immune response;0.0476555594886153;56468!GO:0042088;T-helper 1 type immune response;0.0476555594886153;56468!GO:0002286;T cell activation during immune response;0.0476555594886153;56468!GO:0002292;T cell differentiation during immune response;0.0476555594886153;56468!GO:0042093;T-helper cell differentiation;0.0476555594886153;56468!GO:0019894;kinesin binding;0.0476555594886153;16709!GO:0002285;lymphocyte activation during immune response;0.0476555594886153;56468!GO:0002293;alpha-beta T cell differentiation during immune response;0.0476555594886153;56468!GO:0050918;positive chemotaxis;0.0476555594886153;16170!GO:0051605;protein maturation via proteolysis;0.0499379591277511;216725!GO:0002366;leukocyte activation during immune response;0.0499379591277511;56468!GO:0002263;cell activation during immune response;0.0499379591277511;56468!
|gostat_on_MCL_coexpression=GO:0044421;extracellular region part;0.0263871369384338;21826,18295,16195,16170,23892,18414,216725,268977!GO:0045625;regulation of T-helper 1 cell differentiation;0.0386373874983721;56468!GO:0045627;positive regulation of T-helper 1 cell differentiation;0.0386373874983721;56468!GO:0004924;oncostatin-M receptor activity;0.0386373874983721;18414!GO:0004896;hematopoietin/interferon-class (D200-domain) cytokine receptor activity;0.0386373874983721;16195,18414!GO:0005102;receptor binding;0.0386373874983721;56468,18295,16170,23892!GO:0005515;protein binding;0.0386373874983721;56468,18295,16195,245007,330171,23892,268977,21826,16709,16170!GO:0007167;enzyme linked receptor protein signaling pathway;0.0386373874983721;56468,23892,268977!GO:0005578;proteinaceous extracellular matrix;0.0386373874983721;18295,216725,268977!GO:0045629;negative regulation of T-helper 2 cell differentiation;0.0386373874983721;56468!GO:0045624;positive regulation of T-helper cell differentiation;0.0386373874983721;56468!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0386373874983721;23892,268977!GO:0007166;cell surface receptor linked signal transduction;0.0386373874983721;56468,16195,23892,71111,18414,216725,268977!GO:0009966;regulation of signal transduction;0.0386373874983721;56468,16195,23892!GO:0009968;negative regulation of signal transduction;0.0386373874983721;56468,23892!GO:0045628;regulation of T-helper 2 cell differentiation;0.0386373874983721;56468!GO:0045063;T-helper 1 cell differentiation;0.0386373874983721;56468!GO:0017074;procollagen N-endopeptidase activity;0.0386373874983721;216725!GO:0045623;negative regulation of T-helper cell differentiation;0.0386373874983721;56468!GO:0045064;T-helper 2 cell differentiation;0.041147959075257;56468!GO:0008593;regulation of Notch signaling pathway;0.041147959075257;16195!GO:0045622;regulation of T-helper cell differentiation;0.041147959075257;56468!GO:0007165;signal transduction;0.041147959075257;56468,68842,16195,23892,71111,18414,216725,268977!GO:0005615;extracellular space;0.041147959075257;21826,16195,16170,23892,18414,268977!GO:0042092;T-helper 2 type immune response;0.0476555594886153;56468!GO:0007154;cell communication;0.0476555594886153;56468,68842,16195,23892,71111,18414,216725,268977!GO:0050920;regulation of chemotaxis;0.0476555594886153;16170!GO:0050926;regulation of positive chemotaxis;0.0476555594886153;16170!GO:0050921;positive regulation of chemotaxis;0.0476555594886153;16170!GO:0005154;epidermal growth factor receptor binding;0.0476555594886153;56468!GO:0050927;positive regulation of positive chemotaxis;0.0476555594886153;16170!GO:0050930;induction of positive chemotaxis;0.0476555594886153;16170!GO:0002294;CD4-positive, alpha-beta T cell differentiation during immune response;0.0476555594886153;56468!GO:0042088;T-helper 1 type immune response;0.0476555594886153;56468!GO:0002286;T cell activation during immune response;0.0476555594886153;56468!GO:0002292;T cell differentiation during immune response;0.0476555594886153;56468!GO:0042093;T-helper cell differentiation;0.0476555594886153;56468!GO:0019894;kinesin binding;0.0476555594886153;16709!GO:0002285;lymphocyte activation during immune response;0.0476555594886153;56468!GO:0002293;alpha-beta T cell differentiation during immune response;0.0476555594886153;56468!GO:0050918;positive chemotaxis;0.0476555594886153;16170!GO:0051605;protein maturation via proteolysis;0.0499379591277511;216725!GO:0002366;leukocyte activation during immune response;0.0499379591277511;56468!GO:0002263;cell activation during immune response;0.0499379591277511;56468!
|ontology_enrichment_celltype=CL:0000222!2.04e-12!7;CL:0000680!2.12e-11!6;CL:0000183!2.12e-11!6;CL:0000187!2.12e-11!6;CL:0000056!2.12e-11!6;CL:0000355!3.37e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000055!7.96e-09!5;UBERON:0007500!7.96e-09!5;UBERON:0001981!7.96e-09!5;UBERON:0002049!7.96e-09!5;UBERON:0007798!7.96e-09!5;UBERON:0004537!7.96e-09!5;UBERON:0006965!7.96e-09!5;UBERON:0004535!7.39e-08!23;UBERON:0001009!7.39e-08!23;UBERON:0000947!8.48e-08!4;UBERON:0001637!8.48e-08!4;UBERON:0004573!8.48e-08!4;UBERON:0003509!8.48e-08!4;UBERON:0004571!8.48e-08!4;UBERON:0010191!8.48e-08!4;UBERON:0004572!8.48e-08!4;UBERON:0001134!3.37e-07!9;UBERON:0002036!3.37e-07!9;UBERON:0002385!3.37e-07!9;UBERON:0000486!3.37e-07!9;UBERON:0007503!3.37e-07!9;UBERON:0001015!3.37e-07!9;UBERON:0002329!3.37e-07!9;UBERON:0003082!3.37e-07!9;UBERON:0003059!3.37e-07!9;UBERON:0007282!3.37e-07!9;UBERON:0004290!3.37e-07!9;UBERON:0009618!3.37e-07!9
}}
}}

Revision as of 18:14, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:16801833..16801838,+p@chr11:16801833..16801838
+
Mm9::chr11:50416871..50416882,+p5@Adamts2
Mm9::chr11:86417559..86417568,+p@chr11:86417559..86417568
+
Mm9::chr13:113253807..113253846,+p4@Il6st
Mm9::chr13:119579287..119579292,+p@chr13:119579287..119579292
+
Mm9::chr13:49704496..49704539,+p3@Ogn
Mm9::chr13:96374858..96374868,-p@chr13:96374858..96374868
-
Mm9::chr14:48268074..48268102,+p@chr14:48268074..48268102
+
Mm9::chr15:6824231..6824248,-p2@Osmr
Mm9::chr17:14813242..14813246,-p@chr17:14813242..14813246
-
Mm9::chr17:14831089..14831106,-p1@Thbs2
Mm9::chr17:29227828..29227839,-p@chr17:29227828..29227839
-
Mm9::chr17:6106908..6106922,+p5@Tulp4
Mm9::chr17:75577989..75578000,+p11@Ltbp1
Mm9::chr17:75578018..75578028,+p14@Ltbp1
Mm9::chr17:75578058..75578071,+p8@Ltbp1
Mm9::chr17:75578115..75578134,+p9@Ltbp1
Mm9::chr17:75578137..75578164,+p2@Ltbp1
Mm9::chr17:75578174..75578196,+p7@Ltbp1
Mm9::chr17:75578287..75578301,+p5@Ltbp1
Mm9::chr17:87506961..87507024,+p1@Socs5
Mm9::chr17:87507025..87507042,+p3@Socs5
Mm9::chr17:87544959..87544962,+p@chr17:87544959..87544962
+
Mm9::chr1:127573864..127573879,+p10@Gpr39
Mm9::chr1:127574253..127574264,+p@chr1:127574253..127574264
+
Mm9::chr1:165243978..165243992,-p9@Prrx1
Mm9::chr2:113589030..113589077,-p@chr2:113589030..113589077
-
Mm9::chr2:117938827..117938841,+p@chr2:117938827..117938841
+
Mm9::chr2:117943977..117944000,+p@chr2:117943977..117944000
+
Mm9::chr2:178190171..178190178,+p@chr2:178190171..178190178
+
Mm9::chr5:114822634..114822665,-p9@Kctd10
Mm9::chr7:90893343..90893363,-p@chr7:90893343..90893363
-
Mm9::chr7:90894306..90894354,-p2@Il16
Mm9::chr7:91081998..91082010,-p@chr7:91081998..91082010
-
Mm9::chr7:91235004..91235019,-p1@9930013L23Rik
Mm9::chr8:34997222..34997224,-p@chr8:34997222..34997224
-
Mm9::chr9:96632690..96632703,-p20@Zbtb38


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:0044421extracellular region part0.0263871369384338
GO:0045625regulation of T-helper 1 cell differentiation0.0386373874983721
GO:0045627positive regulation of T-helper 1 cell differentiation0.0386373874983721
GO:0004924oncostatin-M receptor activity0.0386373874983721
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0386373874983721
GO:0005102receptor binding0.0386373874983721
GO:0005515protein binding0.0386373874983721
GO:0007167enzyme linked receptor protein signaling pathway0.0386373874983721
GO:0005578proteinaceous extracellular matrix0.0386373874983721
GO:0045629negative regulation of T-helper 2 cell differentiation0.0386373874983721
GO:0045624positive regulation of T-helper cell differentiation0.0386373874983721
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0386373874983721
GO:0007166cell surface receptor linked signal transduction0.0386373874983721
GO:0009966regulation of signal transduction0.0386373874983721
GO:0009968negative regulation of signal transduction0.0386373874983721
GO:0045628regulation of T-helper 2 cell differentiation0.0386373874983721
GO:0045063T-helper 1 cell differentiation0.0386373874983721
GO:0017074procollagen N-endopeptidase activity0.0386373874983721
GO:0045623negative regulation of T-helper cell differentiation0.0386373874983721
GO:0045064T-helper 2 cell differentiation0.041147959075257
GO:0008593regulation of Notch signaling pathway0.041147959075257
GO:0045622regulation of T-helper cell differentiation0.041147959075257
GO:0007165signal transduction0.041147959075257
GO:0005615extracellular space0.041147959075257
GO:0042092T-helper 2 type immune response0.0476555594886153
GO:0007154cell communication0.0476555594886153
GO:0050920regulation of chemotaxis0.0476555594886153
GO:0050926regulation of positive chemotaxis0.0476555594886153
GO:0050921positive regulation of chemotaxis0.0476555594886153
GO:0005154epidermal growth factor receptor binding0.0476555594886153
GO:0050927positive regulation of positive chemotaxis0.0476555594886153
GO:0050930induction of positive chemotaxis0.0476555594886153
GO:0002294CD4-positive, alpha-beta T cell differentiation during immune response0.0476555594886153
GO:0042088T-helper 1 type immune response0.0476555594886153
GO:0002286T cell activation during immune response0.0476555594886153
GO:0002292T cell differentiation during immune response0.0476555594886153
GO:0042093T-helper cell differentiation0.0476555594886153
GO:0019894kinesin binding0.0476555594886153
GO:0002285lymphocyte activation during immune response0.0476555594886153
GO:0002293alpha-beta T cell differentiation during immune response0.0476555594886153
GO:0050918positive chemotaxis0.0476555594886153
GO:0051605protein maturation via proteolysis0.0499379591277511
GO:0002366leukocyte activation during immune response0.0499379591277511
GO:0002263cell activation during immune response0.0499379591277511



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>

Cell Type
Ontology termp-valuen
mesodermal cell2.04e-127
muscle precursor cell2.12e-116
contractile cell2.12e-116
muscle cell2.12e-116
myoblast2.12e-116
multi-potent skeletal muscle stem cell3.37e-079


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)

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