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MCL coexpression mm9:2001: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.257056954190279,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.32698366624965,1.24584906907213,1.24693472336387,0,0,0,0,0,0,0,0.0214234775414374,0.0274990668782,0,0.485744360992031,0.686988739492235,0.0250913949416665,0.0198746585451445,0,0.322458878535173,0.397627241672108,0.361130742874007,1.10944129025684,0.919966648697359,1.0474606352831,0.681744727264156,0.761674789470675,0.597412607154421,0.668568224353718,0.67145364782559,1.0211791910281,0,0,0,0,0,0,0,0,0.0822927832744084,0,0,0,0,0,0,0,0,0,0,0.0681426399143868,0,0,0.125725757341388,0.0577162951573975,0.224288318617122,0,0.0458646709052479,0,0,0,0,0,0,0,0,1.14201106171899,1.04988227466744,0,0,0,0,0.520228021773391,0,0.0743847601857175,0,0,0.360310158376858,0.169628842227326,0,0,0,0,0.0531247310291112,0.0449352723065536,0.102741730119667,0.0304819657131131,0,0.0261764406050477,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0828894264954325,0.021268976479071,0,0,0.0419819959588466,0,0,0,0,0,0,0,0,0,0,0,0,0,1.52145269025156,1.34586376845778,1.38843604743193,1.21438622239347,1.14996017096616,1.17754919852255,0.313771558545724,0.225487823327682,0.143103035125604,0.234111174858286,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0753613107413788,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.340629187459647,0.3110408004214,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0355847379748454,0.0327687501780757,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.129738448591673,0.217615633477148,0.119636201452401,0.0709019855629759,0.0712812415377886,0.0948573962131381,0,0,0,0,0,0,0,0,0,0,0.23849840977779,0,0,0,0,0,0,0,0,0,0,0,0.192500065883259,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0265784939468031,0.0216534965544966,0.0469880747817416,0,0,0.0400832080528911,0,0,0,0,0,0,0,0.015947867244644,0.020859375746038,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.875234345531339,0.995282685268208,0.653138110911947,0.463062108387213,0.378923921517796,0.472979908468883,0.300382622867388,0.215436292038279,0.325750660612702,0.245041507634362,0.307082459001251,0.280159070816815,0.368270460989428,0.356935725746205,0.386536328941417,0.377754105675354,0.40620303430498,0.427206818670058,0.481809255996476,0.386003911915605,0.396262068328163,0.313279388776319,0.381909527297276,0.34354934110874,0.304684410746654,0.341259975147143,0.345075763579416,0.101427320830301,0.395813168911119,0.163401805547804,0.388223578098135,0.344308485405452,0.259704250749409,0.35015004469672,0.369664102778283,0.451339280443902,0.251538439074035,0.2878762464921,0.168828349421515,0,0
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.257056954190279,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1.32698366624965,1.24584906907213,1.24693472336387,0,0,0,0,0,0,0,0.0214234775414374,0.0274990668782,0,0.485744360992031,0.686988739492235,0.0250913949416665,0.0198746585451445,0,0.322458878535173,0.397627241672108,0.361130742874007,1.10944129025684,0.919966648697359,1.0474606352831,0.681744727264156,0.761674789470675,0.597412607154421,0.668568224353718,0.67145364782559,1.0211791910281,0,0,0,0,0,0,0,0,0.0822927832744084,0,0,0,0,0,0,0,0,0,0,0.0681426399143868,0,0,0.125725757341388,0.0577162951573975,0.224288318617122,0,0.0458646709052479,0,0,0,0,0,0,0,0,1.14201106171899,1.04988227466744,0,0,0,0,0.520228021773391,0,0.0743847601857175,0,0,0.360310158376858,0.169628842227326,0,0,0,0,0.0531247310291112,0.0449352723065536,0.102741730119667,0.0304819657131131,0,0.0261764406050477,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0828894264954325,0.021268976479071,0,0,0.0419819959588466,0,0,0,0,0,0,0,0,0,0,0,0,0,1.52145269025156,1.34586376845778,1.38843604743193,1.21438622239347,1.14996017096616,1.17754919852255,0.313771558545724,0.225487823327682,0.143103035125604,0.234111174858286,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0753613107413788,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.340629187459647,0.3110408004214,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0355847379748454,0.0327687501780757,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.129738448591673,0.217615633477148,0.119636201452401,0.0709019855629759,0.0712812415377886,0.0948573962131381,0,0,0,0,0,0,0,0,0,0,0.23849840977779,0,0,0,0,0,0,0,0,0,0,0,0.192500065883259,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0265784939468031,0.0216534965544966,0.0469880747817416,0,0,0.0400832080528911,0,0,0,0,0,0,0,0.015947867244644,0.020859375746038,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.875234345531339,0.995282685268208,0.653138110911947,0.463062108387213,0.378923921517796,0.472979908468883,0.300382622867388,0.215436292038279,0.325750660612702,0.245041507634362,0.307082459001251,0.280159070816815,0.368270460989428,0.356935725746205,0.386536328941417,0.377754105675354,0.40620303430498,0.427206818670058,0.481809255996476,0.386003911915605,0.396262068328163,0.313279388776319,0.381909527297276,0.34354934110874,0.304684410746654,0.341259975147143,0.345075763579416,0.101427320830301,0.395813168911119,0.163401805547804,0.388223578098135,0.344308485405452,0.259704250749409,0.35015004469672,0.369664102778283,0.451339280443902,0.251538439074035,0.2878762464921,0.168828349421515,0,0
|gostat_on_MCL_coexpression=GO:0001706;endoderm formation;0.00751056046497468;16869!GO:0005667;transcription factor complex;0.00751056046497468;16869!GO:0021937;Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation;0.00751056046497468;16869!GO:0044451;nucleoplasm part;0.00751056046497468;16869!GO:0005654;nucleoplasm;0.00751056046497468;16869!GO:0021692;cerebellar Purkinje cell layer morphogenesis;0.00751056046497468;16869!GO:0021940;positive regulation of granule cell precursor proliferation;0.00751056046497468;16869!GO:0021694;cerebellar Purkinje cell layer formation;0.00751056046497468;16869!GO:0021936;regulation of granule cell precursor proliferation;0.00751056046497468;16869!GO:0021702;cerebellar Purkinje cell differentiation;0.00751056046497468;16869!GO:0021534;cell proliferation in hindbrain;0.00751056046497468;16869!GO:0021930;granule cell precursor proliferation;0.00751056046497468;16869!GO:0021924;cell proliferation in the external granule layer;0.00751056046497468;16869!GO:0021697;cerebellar cortex formation;0.00751056046497468;16869!GO:0021533;cell differentiation in hindbrain;0.00751056046497468;16869!GO:0031981;nuclear lumen;0.00751056046497468;16869!GO:0021680;cerebellar Purkinje cell layer development;0.00751056046497468;16869!GO:0021696;cerebellar cortex morphogenesis;0.00751056046497468;16869!GO:0031974;membrane-enclosed lumen;0.00751056046497468;16869!GO:0043233;organelle lumen;0.00751056046497468;16869!GO:0021587;cerebellum morphogenesis;0.00751056046497468;16869!GO:0021575;hindbrain morphogenesis;0.00757002253337944;16869!GO:0007492;endoderm development;0.00757002253337944;16869!GO:0003700;transcription factor activity;0.00757002253337944;16869!GO:0021695;cerebellar cortex development;0.00757002253337944;16869!GO:0022037;metencephalon development;0.00895507505215965;16869!GO:0021549;cerebellum development;0.00895507505215965;16869!GO:0044428;nuclear part;0.00973301948905536;16869!GO:0001704;formation of primary germ layer;0.00978640769926849;16869!GO:0009791;post-embryonic development;0.0105101741671494;16869!GO:0001702;gastrulation with mouth forming second;0.0105101741671494;16869!GO:0030902;hindbrain development;0.0137904433531285;16869!GO:0007369;gastrulation;0.0197296049695444;16869!GO:0043234;protein complex;0.0205590795987763;16869!GO:0006355;regulation of transcription, DNA-dependent;0.0258268232098056;16869!GO:0006351;transcription, DNA-dependent;0.0258268232098056;16869!GO:0032774;RNA biosynthetic process;0.0258268232098056;16869!GO:0003677;DNA binding;0.0258268232098056;16869!GO:0045449;regulation of transcription;0.0259339862375044;16869!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0262942375471823;16869!GO:0006350;transcription;0.0263286738552209;16869!GO:0032991;macromolecular complex;0.0264238765307082;16869!GO:0010468;regulation of gene expression;0.0268185410295017;16869!GO:0031323;regulation of cellular metabolic process;0.0284016674325537;16869!GO:0019222;regulation of metabolic process;0.0298621036708348;16869!GO:0016070;RNA metabolic process;0.0307754304918284;16869!GO:0044446;intracellular organelle part;0.0316054068440399;16869!GO:0044422;organelle part;0.0316054068440399;16869!GO:0008284;positive regulation of cell proliferation;0.0376007537088389;16869!GO:0007420;brain development;0.0381683309718694;16869!GO:0048646;anatomical structure formation;0.0381683309718694;16869!GO:0010467;gene expression;0.0389882682277188;16869!GO:0003676;nucleic acid binding;0.0401208433633189;16869!GO:0007417;central nervous system development;0.0447136566776892;16869!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0449011665679947;16869!
|gostat_on_MCL_coexpression=GO:0001706;endoderm formation;0.00751056046497468;16869!GO:0005667;transcription factor complex;0.00751056046497468;16869!GO:0021937;Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation;0.00751056046497468;16869!GO:0044451;nucleoplasm part;0.00751056046497468;16869!GO:0005654;nucleoplasm;0.00751056046497468;16869!GO:0021692;cerebellar Purkinje cell layer morphogenesis;0.00751056046497468;16869!GO:0021940;positive regulation of granule cell precursor proliferation;0.00751056046497468;16869!GO:0021694;cerebellar Purkinje cell layer formation;0.00751056046497468;16869!GO:0021936;regulation of granule cell precursor proliferation;0.00751056046497468;16869!GO:0021702;cerebellar Purkinje cell differentiation;0.00751056046497468;16869!GO:0021534;cell proliferation in hindbrain;0.00751056046497468;16869!GO:0021930;granule cell precursor proliferation;0.00751056046497468;16869!GO:0021924;cell proliferation in the external granule layer;0.00751056046497468;16869!GO:0021697;cerebellar cortex formation;0.00751056046497468;16869!GO:0021533;cell differentiation in hindbrain;0.00751056046497468;16869!GO:0031981;nuclear lumen;0.00751056046497468;16869!GO:0021680;cerebellar Purkinje cell layer development;0.00751056046497468;16869!GO:0021696;cerebellar cortex morphogenesis;0.00751056046497468;16869!GO:0031974;membrane-enclosed lumen;0.00751056046497468;16869!GO:0043233;organelle lumen;0.00751056046497468;16869!GO:0021587;cerebellum morphogenesis;0.00751056046497468;16869!GO:0021575;hindbrain morphogenesis;0.00757002253337944;16869!GO:0007492;endoderm development;0.00757002253337944;16869!GO:0003700;transcription factor activity;0.00757002253337944;16869!GO:0021695;cerebellar cortex development;0.00757002253337944;16869!GO:0022037;metencephalon development;0.00895507505215965;16869!GO:0021549;cerebellum development;0.00895507505215965;16869!GO:0044428;nuclear part;0.00973301948905536;16869!GO:0001704;formation of primary germ layer;0.00978640769926849;16869!GO:0009791;post-embryonic development;0.0105101741671494;16869!GO:0001702;gastrulation with mouth forming second;0.0105101741671494;16869!GO:0030902;hindbrain development;0.0137904433531285;16869!GO:0007369;gastrulation;0.0197296049695444;16869!GO:0043234;protein complex;0.0205590795987763;16869!GO:0006355;regulation of transcription, DNA-dependent;0.0258268232098056;16869!GO:0006351;transcription, DNA-dependent;0.0258268232098056;16869!GO:0032774;RNA biosynthetic process;0.0258268232098056;16869!GO:0003677;DNA binding;0.0258268232098056;16869!GO:0045449;regulation of transcription;0.0259339862375044;16869!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0262942375471823;16869!GO:0006350;transcription;0.0263286738552209;16869!GO:0032991;macromolecular complex;0.0264238765307082;16869!GO:0010468;regulation of gene expression;0.0268185410295017;16869!GO:0031323;regulation of cellular metabolic process;0.0284016674325537;16869!GO:0019222;regulation of metabolic process;0.0298621036708348;16869!GO:0016070;RNA metabolic process;0.0307754304918284;16869!GO:0044446;intracellular organelle part;0.0316054068440399;16869!GO:0044422;organelle part;0.0316054068440399;16869!GO:0008284;positive regulation of cell proliferation;0.0376007537088389;16869!GO:0007420;brain development;0.0381683309718694;16869!GO:0048646;anatomical structure formation;0.0381683309718694;16869!GO:0010467;gene expression;0.0389882682277188;16869!GO:0003676;nucleic acid binding;0.0401208433633189;16869!GO:0007417;central nervous system development;0.0447136566776892;16869!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0449011665679947;16869!
|ontology_enrichment_celltype=CL:0000117!5.12e-15!23;CL:0000337!5.12e-15!23;CL:0000540!2.85e-08!33;CL:0000047!2.85e-08!33;CL:0000031!2.85e-08!33;CL:0000404!2.85e-08!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!4.45e-10!54;UBERON:0000489!1.19e-09!21;UBERON:0001049!6.65e-09!52;UBERON:0005068!6.65e-09!52;UBERON:0006241!6.65e-09!52;UBERON:0007135!6.65e-09!52;UBERON:0002346!3.37e-08!64;UBERON:0003075!3.37e-08!64;UBERON:0007284!3.37e-08!64;UBERON:0001017!7.95e-08!73;UBERON:0003076!2.16e-07!12;UBERON:0003057!2.16e-07!12;UBERON:0001016!2.46e-07!75
}}
}}

Revision as of 17:46, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:84339016..84339044,-p1@Lhx1
Mm9::chr5:140019816..140019825,+p3@Uncx
Mm9::chr5:140019843..140019858,+p2@Uncx
Mm9::chr5:140019865..140019886,+p1@Uncx


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:0001706endoderm formation0.00751056046497468
GO:0005667transcription factor complex0.00751056046497468
GO:0021937Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation0.00751056046497468
GO:0044451nucleoplasm part0.00751056046497468
GO:0005654nucleoplasm0.00751056046497468
GO:0021692cerebellar Purkinje cell layer morphogenesis0.00751056046497468
GO:0021940positive regulation of granule cell precursor proliferation0.00751056046497468
GO:0021694cerebellar Purkinje cell layer formation0.00751056046497468
GO:0021936regulation of granule cell precursor proliferation0.00751056046497468
GO:0021702cerebellar Purkinje cell differentiation0.00751056046497468
GO:0021534cell proliferation in hindbrain0.00751056046497468
GO:0021930granule cell precursor proliferation0.00751056046497468
GO:0021924cell proliferation in the external granule layer0.00751056046497468
GO:0021697cerebellar cortex formation0.00751056046497468
GO:0021533cell differentiation in hindbrain0.00751056046497468
GO:0031981nuclear lumen0.00751056046497468
GO:0021680cerebellar Purkinje cell layer development0.00751056046497468
GO:0021696cerebellar cortex morphogenesis0.00751056046497468
GO:0031974membrane-enclosed lumen0.00751056046497468
GO:0043233organelle lumen0.00751056046497468
GO:0021587cerebellum morphogenesis0.00751056046497468
GO:0021575hindbrain morphogenesis0.00757002253337944
GO:0007492endoderm development0.00757002253337944
GO:0003700transcription factor activity0.00757002253337944
GO:0021695cerebellar cortex development0.00757002253337944
GO:0022037metencephalon development0.00895507505215965
GO:0021549cerebellum development0.00895507505215965
GO:0044428nuclear part0.00973301948905536
GO:0001704formation of primary germ layer0.00978640769926849
GO:0009791post-embryonic development0.0105101741671494
GO:0001702gastrulation with mouth forming second0.0105101741671494
GO:0030902hindbrain development0.0137904433531285
GO:0007369gastrulation0.0197296049695444
GO:0043234protein complex0.0205590795987763
GO:0006355regulation of transcription, DNA-dependent0.0258268232098056
GO:0006351transcription, DNA-dependent0.0258268232098056
GO:0032774RNA biosynthetic process0.0258268232098056
GO:0003677DNA binding0.0258268232098056
GO:0045449regulation of transcription0.0259339862375044
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0262942375471823
GO:0006350transcription0.0263286738552209
GO:0032991macromolecular complex0.0264238765307082
GO:0010468regulation of gene expression0.0268185410295017
GO:0031323regulation of cellular metabolic process0.0284016674325537
GO:0019222regulation of metabolic process0.0298621036708348
GO:0016070RNA metabolic process0.0307754304918284
GO:0044446intracellular organelle part0.0316054068440399
GO:0044422organelle part0.0316054068440399
GO:0008284positive regulation of cell proliferation0.0376007537088389
GO:0007420brain development0.0381683309718694
GO:0048646anatomical structure formation0.0381683309718694
GO:0010467gene expression0.0389882682277188
GO:0003676nucleic acid binding0.0401208433633189
GO:0007417central nervous system development0.0447136566776892
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0449011665679947



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
CNS neuron (sensu Vertebrata)5.12e-1523
neuroblast (sensu Vertebrata)5.12e-1523
neuron2.85e-0833
neuronal stem cell2.85e-0833
neuroblast2.85e-0833
electrically signaling cell2.85e-0833

Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.45e-1054
cavitated compound organ1.19e-0921
neural tube6.65e-0952
neural rod6.65e-0952
future spinal cord6.65e-0952
neural keel6.65e-0952
neurectoderm3.37e-0864
neural plate3.37e-0864
presumptive neural plate3.37e-0864
central nervous system7.95e-0873
posterior neural tube2.16e-0712
chordal neural plate2.16e-0712
nervous system2.46e-0775


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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