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MCL coexpression mm9:401: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0.102214874643271,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.267273341778078,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.764609063350494,0.760491754914107,0.741586013873372,0,0,0,0,0,0,0,0.15068229631276,0.103807782330171,0.0994390598362085,0.677709755083959,0.751143509015826,0.207487332897458,0.170034929556811,0.28312448614836,0.732766388647999,0.609006712671987,0.636781020696569,0.606005372625665,0.613903092435099,0.615474509542399,0.665522736028698,0.581359400489082,0.537160477951037,0.952064222933132,0.931747596043227,0.806558725892495,0,0.0316393102377815,0,0,0,0,0,0,0.0570741246689917,0,0,0,0.107781924973909,0,0,0,0,0,0,0.00454915296751848,0,0,0.00129980849867767,0.115432590314795,0,0,0,0,0,0,0,0,0,0,0,1.0661036052128,1.08280961336163,0,0,0,0,0.676214797611143,0.451786805560604,0.513454444184122,0.313694668824925,0.35766376392443,0.622747261319776,0.607046424739322,0.0228672672794184,0,0,0.0829439327499637,0.0156743091299177,0.0898705446131073,0.133578586898209,0.189020470373144,0.242641168091658,0.306405674159287,0.265599679938124,0.349274827662687,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.33751246443929,0.307291919424198,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.046982063026719,0,0,0.0185823829841138,0.0294389011296462,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.618371407331294,0.553720087736703,0,0,0.119093565942036,0.143151860801801,0.0847275925579778,0,0,0,0,0.111348509539896,0,0.358940419539848,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.12724725138213,0,0,0.0843392403965415,0.0614872842776838,0.132495872273197,0.174247988899791,0.115432414129512,0,0,0,0,0,0,0,0,0,0.598440833598049,0,0,0,0,0,0,0,0,0,0,0,0,0.0167595348081429,0,0,0.054943952156948,0.034489466458534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.328278395983124,0.376754964798171,0.331587424856164,0.405974145903856,0.226621173458704,0.399810008829701,0.224020645200257,0.371245906776716,0.325325934556122,0.407098602473158,0.0428854115575944,0.145825435924841,0.268031959483673,0.210221653661541,0.152051658298929,0.135986724295729,0.159715578577694,0.225735302620479,0.215330413983256,0.0978461107777356,0.178101321237085,0.244154700692047,0.185179281878848,0.214910449956623,0.197102582129624,0.169172763866184,0.165403796547116,0.145259206245058,0.14986111676545,0.201068050435521,0.128033729919821,0.131923786075207,0.169342968499384,0.219276043371841,0.138756502969784,0.142488712893808,0.189990830607665,0.18359421108913,0.195627075216568,0.193442483447008,0.168656579551575,0.201677520895557,0.148982201447044,0.191477766108308,0.141704700595215,0.397742527884853,0.229200662570381,0.216063761676531,0.196967476487388,0.0865703124974023,0
|gostat_on_MCL_coexpression=GO:0060134;prepulse inhibition;0.000470719502175586;242443,14804!GO:0048585;negative regulation of response to stimulus;0.000470719502175586;242443,14804!GO:0032102;negative regulation of response to external stimulus;0.000470719502175586;242443,14804!GO:0032101;regulation of response to external stimulus;0.000604812928979771;242443,14804!GO:0001964;startle response;0.00088618439085382;242443,14804!GO:0005216;ion channel activity;0.00103108625907904;56808,242443,14804,243043!GO:0022838;substrate specific channel activity;0.00103108625907904;56808,242443,14804,243043!GO:0004970;ionotropic glutamate receptor activity;0.00103108625907904;242443,14804!GO:0022803;passive transmembrane transporter activity;0.00103108625907904;56808,242443,14804,243043!GO:0015267;channel activity;0.00103108625907904;56808,242443,14804,243043!GO:0008066;glutamate receptor activity;0.00488962419320737;242443,14804!GO:0048583;regulation of response to stimulus;0.00488962419320737;242443,14804!GO:0005261;cation channel activity;0.00488962419320737;56808,242443,243043!GO:0050905;neuromuscular process;0.00488962419320737;242443,14804!GO:0015075;ion transmembrane transporter activity;0.00488962419320737;56808,242443,14804,243043!GO:0022836;gated channel activity;0.00546079721263632;56808,14804,243043!GO:0043025;cell soma;0.00578478784144084;242443,227325!GO:0006811;ion transport;0.00578478784144084;56808,242443,14804,243043!GO:0046873;metal ion transmembrane transporter activity;0.00578478784144084;56808,242443,243043!GO:0045179;apical cortex;0.00578478784144084;18762!GO:0022891;substrate-specific transmembrane transporter activity;0.00578478784144084;56808,242443,14804,243043!GO:0048741;skeletal muscle fiber development;0.00578478784144084;56808,227325!GO:0048747;muscle fiber development;0.00578478784144084;56808,227325!GO:0005262;calcium channel activity;0.00607398701555443;56808,242443!GO:0022857;transmembrane transporter activity;0.0087235199092231;56808,242443,14804,243043!GO:0004700;atypical protein kinase C activity;0.00945423206658046;18762!GO:0030001;metal ion transport;0.0102199130653923;56808,242443,243043!GO:0007519;skeletal muscle development;0.0102199130653923;56808,227325!GO:0044425;membrane part;0.0102199130653923;56808,18762,14804,214058,242443,64540,243043,13483,227325!GO:0022892;substrate-specific transporter activity;0.0102199130653923;56808,242443,14804,243043!GO:0006816;calcium ion transport;0.0110408241806702;56808,242443!GO:0007220;Notch receptor processing;0.0115191890431605;227325!GO:0045211;postsynaptic membrane;0.0115985942305008;242443,14804!GO:0022843;voltage-gated cation channel activity;0.0125769220468412;56808,243043!GO:0008324;cation transmembrane transporter activity;0.0125769220468412;56808,242443,243043!GO:0006812;cation transport;0.0125769220468412;56808,242443,243043!GO:0044456;synapse part;0.0125769220468412;242443,14804!GO:0014706;striated muscle development;0.0125769220468412;56808,227325!GO:0060024;rhythmic synaptic transmission;0.0125987378246049;56808!GO:0015674;di-, tri-valent inorganic cation transport;0.0141581877252212;56808,242443!GO:0004972;N-methyl-D-aspartate selective glutamate receptor activity;0.0175386307102534;242443!GO:0005112;Notch binding;0.0175386307102534;227325!GO:0004274;dipeptidyl-peptidase IV activity;0.0192244577366487;13483!GO:0007517;muscle development;0.0192244577366487;56808,227325!GO:0022832;voltage-gated channel activity;0.0192244577366487;56808,243043!GO:0005244;voltage-gated ion channel activity;0.0192244577366487;56808,243043!GO:0016021;integral to membrane;0.0225795367769959;56808,14804,214058,242443,64540,243043,13483,227325!GO:0051605;protein maturation via proteolysis;0.0225795367769959;227325!GO:0031224;intrinsic to membrane;0.0225795367769959;56808,14804,214058,242443,64540,243043,13483,227325!GO:0051604;protein maturation;0.0245271979983456;227325!GO:0008239;dipeptidyl-peptidase activity;0.0282851177934602;13483!GO:0016806;dipeptidyl-peptidase and tripeptidyl-peptidase activity;0.0282851177934602;13483!GO:0005891;voltage-gated calcium channel complex;0.032247943507392;56808!GO:0044459;plasma membrane part;0.032247943507392;56808,18762,14804,243043!GO:0004697;protein kinase C activity;0.033400420144724;18762!GO:0016020;membrane;0.0342180268267809;56808,18762,14804,214058,242443,64540,243043,13483,227325!GO:0005515;protein binding;0.0342180268267809;18762,242443,64540,320311,14804,243043,227325!GO:0001565;phorbol ester receptor activity;0.0352681340964569;18762!GO:0005234;extracellular-glutamate-gated ion channel activity;0.0352681340964569;14804!GO:0051969;regulation of transmission of nerve impulse;0.0394518387140763;56808!GO:0007528;neuromuscular junction development;0.0394518387140763;56808!GO:0050804;regulation of synaptic transmission;0.0394518387140763;56808!GO:0005245;voltage-gated calcium channel activity;0.0407557438701065;56808!GO:0031644;regulation of neurological process;0.0496031471657009;56808!
|gostat_on_MCL_coexpression=GO:0060134;prepulse inhibition;0.000470719502175586;242443,14804!GO:0048585;negative regulation of response to stimulus;0.000470719502175586;242443,14804!GO:0032102;negative regulation of response to external stimulus;0.000470719502175586;242443,14804!GO:0032101;regulation of response to external stimulus;0.000604812928979771;242443,14804!GO:0001964;startle response;0.00088618439085382;242443,14804!GO:0005216;ion channel activity;0.00103108625907904;56808,242443,14804,243043!GO:0022838;substrate specific channel activity;0.00103108625907904;56808,242443,14804,243043!GO:0004970;ionotropic glutamate receptor activity;0.00103108625907904;242443,14804!GO:0022803;passive transmembrane transporter activity;0.00103108625907904;56808,242443,14804,243043!GO:0015267;channel activity;0.00103108625907904;56808,242443,14804,243043!GO:0008066;glutamate receptor activity;0.00488962419320737;242443,14804!GO:0048583;regulation of response to stimulus;0.00488962419320737;242443,14804!GO:0005261;cation channel activity;0.00488962419320737;56808,242443,243043!GO:0050905;neuromuscular process;0.00488962419320737;242443,14804!GO:0015075;ion transmembrane transporter activity;0.00488962419320737;56808,242443,14804,243043!GO:0022836;gated channel activity;0.00546079721263632;56808,14804,243043!GO:0043025;cell soma;0.00578478784144084;242443,227325!GO:0006811;ion transport;0.00578478784144084;56808,242443,14804,243043!GO:0046873;metal ion transmembrane transporter activity;0.00578478784144084;56808,242443,243043!GO:0045179;apical cortex;0.00578478784144084;18762!GO:0022891;substrate-specific transmembrane transporter activity;0.00578478784144084;56808,242443,14804,243043!GO:0048741;skeletal muscle fiber development;0.00578478784144084;56808,227325!GO:0048747;muscle fiber development;0.00578478784144084;56808,227325!GO:0005262;calcium channel activity;0.00607398701555443;56808,242443!GO:0022857;transmembrane transporter activity;0.0087235199092231;56808,242443,14804,243043!GO:0004700;atypical protein kinase C activity;0.00945423206658046;18762!GO:0030001;metal ion transport;0.0102199130653923;56808,242443,243043!GO:0007519;skeletal muscle development;0.0102199130653923;56808,227325!GO:0044425;membrane part;0.0102199130653923;56808,18762,14804,214058,242443,64540,243043,13483,227325!GO:0022892;substrate-specific transporter activity;0.0102199130653923;56808,242443,14804,243043!GO:0006816;calcium ion transport;0.0110408241806702;56808,242443!GO:0007220;Notch receptor processing;0.0115191890431605;227325!GO:0045211;postsynaptic membrane;0.0115985942305008;242443,14804!GO:0022843;voltage-gated cation channel activity;0.0125769220468412;56808,243043!GO:0008324;cation transmembrane transporter activity;0.0125769220468412;56808,242443,243043!GO:0006812;cation transport;0.0125769220468412;56808,242443,243043!GO:0044456;synapse part;0.0125769220468412;242443,14804!GO:0014706;striated muscle development;0.0125769220468412;56808,227325!GO:0060024;rhythmic synaptic transmission;0.0125987378246049;56808!GO:0015674;di-, tri-valent inorganic cation transport;0.0141581877252212;56808,242443!GO:0004972;N-methyl-D-aspartate selective glutamate receptor activity;0.0175386307102534;242443!GO:0005112;Notch binding;0.0175386307102534;227325!GO:0004274;dipeptidyl-peptidase IV activity;0.0192244577366487;13483!GO:0007517;muscle development;0.0192244577366487;56808,227325!GO:0022832;voltage-gated channel activity;0.0192244577366487;56808,243043!GO:0005244;voltage-gated ion channel activity;0.0192244577366487;56808,243043!GO:0016021;integral to membrane;0.0225795367769959;56808,14804,214058,242443,64540,243043,13483,227325!GO:0051605;protein maturation via proteolysis;0.0225795367769959;227325!GO:0031224;intrinsic to membrane;0.0225795367769959;56808,14804,214058,242443,64540,243043,13483,227325!GO:0051604;protein maturation;0.0245271979983456;227325!GO:0008239;dipeptidyl-peptidase activity;0.0282851177934602;13483!GO:0016806;dipeptidyl-peptidase and tripeptidyl-peptidase activity;0.0282851177934602;13483!GO:0005891;voltage-gated calcium channel complex;0.032247943507392;56808!GO:0044459;plasma membrane part;0.032247943507392;56808,18762,14804,243043!GO:0004697;protein kinase C activity;0.033400420144724;18762!GO:0016020;membrane;0.0342180268267809;56808,18762,14804,214058,242443,64540,243043,13483,227325!GO:0005515;protein binding;0.0342180268267809;18762,242443,64540,320311,14804,243043,227325!GO:0001565;phorbol ester receptor activity;0.0352681340964569;18762!GO:0005234;extracellular-glutamate-gated ion channel activity;0.0352681340964569;14804!GO:0051969;regulation of transmission of nerve impulse;0.0394518387140763;56808!GO:0007528;neuromuscular junction development;0.0394518387140763;56808!GO:0050804;regulation of synaptic transmission;0.0394518387140763;56808!GO:0005245;voltage-gated calcium channel activity;0.0407557438701065;56808!GO:0031644;regulation of neurological process;0.0496031471657009;56808!
}}
}}

Revision as of 12:41, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr12:106575390..106575401,+p2@uc007oyh.1
Mm9::chr12:91051249..91051258,+p4@LOC100505240
p5@Nrxn3
Mm9::chr15:4325574..4325623,+p2@Plcxd3
Mm9::chr1:107253057..107253093,-p2@Rnf152
Mm9::chr1:84692551..84692569,-p2@Dner
Mm9::chr1:84692741..84692753,-p7@Dner
Mm9::chr1:84692757..84692777,-p3@Dner
Mm9::chr3:97692834..97692852,-p14@Pde4dip
Mm9::chr4:154719787..154719798,-p5@Prkcz
Mm9::chr4:49857757..49857759,-p@chr4:49857757..49857759
-
Mm9::chr5:151062497..151062511,+p7@Fry
Mm9::chr5:27231364..27231415,+p5@Dpp6
Mm9::chr5:69732910..69732924,-p2@Kctd8
Mm9::chr5:69732938..69732953,-p3@Kctd8
Mm9::chr6:63206101..63206120,+p3@Grid2
Mm9::chr7:148667927..148667985,+p@chr7:148667927..148667985
+
Mm9::chr9:107302127..107302180,+p1@Cacna2d2
Mm9::chr9:107302189..107302203,+p3@Cacna2d2
Mm9::chr9:64233453..64233464,+p2@Megf11


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:0060134prepulse inhibition0.000470719502175586
GO:0048585negative regulation of response to stimulus0.000470719502175586
GO:0032102negative regulation of response to external stimulus0.000470719502175586
GO:0032101regulation of response to external stimulus0.000604812928979771
GO:0001964startle response0.00088618439085382
GO:0005216ion channel activity0.00103108625907904
GO:0022838substrate specific channel activity0.00103108625907904
GO:0004970ionotropic glutamate receptor activity0.00103108625907904
GO:0022803passive transmembrane transporter activity0.00103108625907904
GO:0015267channel activity0.00103108625907904
GO:0008066glutamate receptor activity0.00488962419320737
GO:0048583regulation of response to stimulus0.00488962419320737
GO:0005261cation channel activity0.00488962419320737
GO:0050905neuromuscular process0.00488962419320737
GO:0015075ion transmembrane transporter activity0.00488962419320737
GO:0022836gated channel activity0.00546079721263632
GO:0043025cell soma0.00578478784144084
GO:0006811ion transport0.00578478784144084
GO:0046873metal ion transmembrane transporter activity0.00578478784144084
GO:0045179apical cortex0.00578478784144084
GO:0022891substrate-specific transmembrane transporter activity0.00578478784144084
GO:0048741skeletal muscle fiber development0.00578478784144084
GO:0048747muscle fiber development0.00578478784144084
GO:0005262calcium channel activity0.00607398701555443
GO:0022857transmembrane transporter activity0.0087235199092231
GO:0004700atypical protein kinase C activity0.00945423206658046
GO:0030001metal ion transport0.0102199130653923
GO:0007519skeletal muscle development0.0102199130653923
GO:0044425membrane part0.0102199130653923
GO:0022892substrate-specific transporter activity0.0102199130653923
GO:0006816calcium ion transport0.0110408241806702
GO:0007220Notch receptor processing0.0115191890431605
GO:0045211postsynaptic membrane0.0115985942305008
GO:0022843voltage-gated cation channel activity0.0125769220468412
GO:0008324cation transmembrane transporter activity0.0125769220468412
GO:0006812cation transport0.0125769220468412
GO:0044456synapse part0.0125769220468412
GO:0014706striated muscle development0.0125769220468412
GO:0060024rhythmic synaptic transmission0.0125987378246049
GO:0015674di-, tri-valent inorganic cation transport0.0141581877252212
GO:0004972N-methyl-D-aspartate selective glutamate receptor activity0.0175386307102534
GO:0005112Notch binding0.0175386307102534
GO:0004274dipeptidyl-peptidase IV activity0.0192244577366487
GO:0007517muscle development0.0192244577366487
GO:0022832voltage-gated channel activity0.0192244577366487
GO:0005244voltage-gated ion channel activity0.0192244577366487
GO:0016021integral to membrane0.0225795367769959
GO:0051605protein maturation via proteolysis0.0225795367769959
GO:0031224intrinsic to membrane0.0225795367769959
GO:0051604protein maturation0.0245271979983456
GO:0008239dipeptidyl-peptidase activity0.0282851177934602
GO:0016806dipeptidyl-peptidase and tripeptidyl-peptidase activity0.0282851177934602
GO:0005891voltage-gated calcium channel complex0.032247943507392
GO:0044459plasma membrane part0.032247943507392
GO:0004697protein kinase C activity0.033400420144724
GO:0016020membrane0.0342180268267809
GO:0005515protein binding0.0342180268267809
GO:0001565phorbol ester receptor activity0.0352681340964569
GO:0005234extracellular-glutamate-gated ion channel activity0.0352681340964569
GO:0051969regulation of transmission of nerve impulse0.0394518387140763
GO:0007528neuromuscular junction development0.0394518387140763
GO:0050804regulation of synaptic transmission0.0394518387140763
GO:0005245voltage-gated calcium channel activity0.0407557438701065
GO:0031644regulation of neurological process0.0496031471657009



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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