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MCL coexpression mm9:264: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0276058484853454;20742,11641!GO:0007527;adult somatic muscle development;0.0276058484853454;22288!GO:0030036;actin cytoskeleton organization and biogenesis;0.0276058484853454;20742,11641!GO:0030029;actin filament-based process;0.0276058484853454;20742,11641!GO:0007525;somatic muscle development;0.0276058484853454;22288!GO:0007184;SMAD protein nuclear translocation;0.0306698039093664;20742!GO:0004499;flavin-containing monooxygenase activity;0.0328569034321639;14261!GO:0003779;actin binding;0.0358052730957127;20742,22288!GO:0007167;enzyme linked receptor protein signaling pathway;0.0367876359540371;20742,11641!GO:0051018;protein kinase A binding;0.0367876359540371;11641!GO:0007182;common-partner SMAD protein phosphorylation;0.0376195958943488;20742!GO:0050661;NADP binding;0.0393980510213329;14261!GO:0008092;cytoskeletal protein binding;0.0393980510213329;20742,22288!GO:0016010;dystrophin-associated glycoprotein complex;0.0393980510213329;22288!GO:0031594;neuromuscular junction;0.039831442055262;22288!GO:0000060;protein import into nucleus, translocation;0.0404043651360832;20742!GO:0051016;barbed-end actin filament capping;0.0404043651360832;20742!GO:0030835;negative regulation of actin filament depolymerization;0.0404043651360832;20742!GO:0051693;actin filament capping;0.0404043651360832;20742!GO:0005624;membrane fraction;0.0404043651360832;22288,14261!GO:0007010;cytoskeleton organization and biogenesis;0.0404043651360832;20742,11641!GO:0030834;regulation of actin filament depolymerization;0.0404043651360832;20742!GO:0030042;actin filament depolymerization;0.0404043651360832;20742!GO:0007165;signal transduction;0.0404043651360832;20742,11641,22288,224792!GO:0016709;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen;0.0404043651360832;14261!GO:0031227;intrinsic to endoplasmic reticulum membrane;0.0406118255343949;14261!GO:0000267;cell fraction;0.0421358455079084;22288,14261!GO:0005605;basal lamina;0.0421358455079084;22288!GO:0007154;cell communication;0.0421358455079084;20742,11641,22288,224792!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0421358455079084;20742!GO:0051261;protein depolymerization;0.0421358455079084;20742!GO:0032535;regulation of cellular component size;0.0421358455079084;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0421358455079084;20742!GO:0030832;regulation of actin filament length;0.0421358455079084;20742!GO:0051129;negative regulation of cellular component organization and biogenesis;0.0421358455079084;20742!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0421358455079084;20742!GO:0033043;regulation of organelle organization and biogenesis;0.0421358455079084;20742!GO:0008154;actin polymerization and/or depolymerization;0.0469985389384137;20742!GO:0007015;actin filament organization;0.0469985389384137;11641!}}
{{MCL_coexpression_mm9
|coexpression_dpi_cluster_scores_mean=0.000615977173006441,-0.0245577200522807,-0.0171841641132251,-0.0292429544404435,-0.0329450769801615,-0.0285968221132588,-0.0329450769801615,-0.0263241563837972,-0.0276241068402713,-0.0112745354814016,-0.024391237544677,-0.0297960615778914,-0.0150244118980563,-0.0210018319531156,0.00314997111892581,0.001742287952234,-0.00582486364428974,0.016810744429861,0.0167093517220397,0.012257016060998,0.0502978909984114,-0.0190269930205292,-0.0264428905630125,-0.0098164970402709,0.000727817630909609,-0.0202309656049533,-0.0279267738860298,-0.0220102789694256,-0.0168760085878243,-0.0240779796704585,-0.0249973195404726,-0.0329450769801615,-0.0329450769801615,-0.0329450769801615,-0.0201692500593789,-0.00993816016061508,-0.0171814476929429,0.0187433168566151,0.00523897266683459,0.00244509599724976,0.007660762381974,0.0201723836651974,-0.00530349217145016,0.0128531063270873,0.0248040797141397,0.0115547095221085,-0.0329450769801615,-0.0223488778830144,-0.00776348673201894,-0.0169276535908318,-0.0221450940957942,-0.0329450769801615,0.00445215537982952,-0.0127458925065476,-0.0248265641786151,0.024049412716798,-0.00168435913778159,0.0594016318304806,-0.0159748392601055,0.000960124821752559,-0.0191897712201322,-0.0247689383194101,-0.0329450769801615,-0.0329450769801615,-0.0329450769801615,-0.0329450769801615,-0.0256025131346462,-0.0249583190057648,0.014176169274718,0.000661196976694232,-0.0131502280876461,-0.00185817697556758,0.00414791245552141,-0.00980596077113803,-0.00331275528933485,-0.0329450769801615,0.00416402502088561,0.037468783236274,0.0513680065982709,-0.0211790689332628,0.00643600903594862,-0.0094477249991652,0.0224609534672128,0.0148345724393523,0.0576430571503035,0.0554547631733495,0.0357588748152641,-0.00143493157800592,-0.0086077503715213,-0.0154439160881367,0.21483496766535,0.0564583187803158,-0.0329450769801615,0.053049821384757,0.073314734836971,0.0443494605520573,0.00897563414163471,-0.00213245487923854,-0.00241762624558815,-0.0127395212479803,0.00306467875716736,-0.0108249698588247,-0.00762080523606927,-0.0329450769801615,0.00840427552177323,-0.00146826076638293,0.0215729307198815,0.0117834877743889,0.0385460935668504,0.0723689987428777,0.0483457460397654,0.106638700893137,0.0430098117625931,0.137067279806242,0.186654491771462,0.0812320865356235,0.0878630368309329,0.043206485846545,0.0114455066339203,0.0840481997726558,0.173900179183278,0.0943571290606217,-0.00346375309380233,0.0878253769449964,0.0605740131658257,0.0408605829598175,-0.00467514652603428,-0.0197777492554619,-0.00608121595995905,0.0364998147375577,0.0397782653040074,0.0129929838511826,0.0174814167261181,0.043770190064062,0.0502806649679067,0.0672640385539803,0.121619613032187,0.0747726534902889,0.0329089264990834,0.0317901324858522,0.0401137894415806,0.00198623914507805,-0.00378153265491946,0.118733878091753,0.0619433155833068,0.0925329382671457,0.0535991052264756,0.161847031426754,-0.00465277448928374,0.0218402834206141,0.0412450424533539,0.0133656587431393,0.124785688605711,0.0627641321391967,0.0679365707489176,0.0878842893759232,-0.0329450769801615,-0.0271281277778974,-0.00632073749874059,0.0484376448757887,0.157556658530615,0.150054664961789,0.0717128431839066,0.17106324610445,0.263992843524751,0.293654838801753,0.166532897976292,0.240853813551572,0.19617302666417,0.428311661925212,0.204889982950227,0.192828866552231,0.243683971057498,0.169944316225581,0.0311498188156698,0.0578774680939621,0.0191238103930553,-0.00993498060117687,0.076634127146162,0.114496198226373,0.0197139520643549,0.0197780420156638,0.0443409116746058,0.0184483206263203,0.0307977697062698,0.0840781538383474,0.10633308265854,0.0600880282065119,0.0992579689573714,0.0263842764422017,0.130426681888611,0.0691854888683442,-0.0215010201563324,0.110717564532774,0.0258798047840452,0.180385827054083,0.178260693802052,0.192950647852026,0.194223308911029,0.229435549464482,0.271855837443227,0.089847613465179,0.0236109032445923,-0.00960398853148705,-0.00102950135253944,0.0101411786877046,-0.00857677709988597,0.012413365440356,0.0365239041773286,0.0477183234133008,0.125998609099097,0.147594917425588,0.904476688288492,0.174319355252922,0.156790254675303,0.104317429883432,0.0801569350835679,0.0913085766694483,0.310072187772608,-7.95667064728025e-06,0.0486522972986742,0.153634539482566,0.239444002363592,0.137809373276924,0.147319977251711,0.371207336490305,0.345973193868231,0.517222768665141,0.470244349225534,0.6790816180746,0.603552406019789,0.517117895091556,-0.020064030565779,0.0431494823465984,0.0509828990485891,0.0451385908432497,0.052748366175246,0.0468025486278585,-0.0160237379802125,0.112247027210399,0.0196464509243605,0.018326540729279,0.0407479341468967,0.00240831587187,0.0236658990017584,-0.00920001214587358,-0.0246357955529881,0.0213761681195549,0.0148709521943952,0.0403083306760025,0.0533214068955076,0.022324506529184,0.0780849872003248,0.0622937884638305,-0.0211102183331783,0.0411050950270654,0.0397627221798359,0.0588696698283018,-0.0090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|gostat_on_MCL_coexpression=GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0276058484853454;20742,11641!GO:0007527;adult somatic muscle development;0.0276058484853454;22288!GO:0030036;actin cytoskeleton organization and biogenesis;0.0276058484853454;20742,11641!GO:0030029;actin filament-based process;0.0276058484853454;20742,11641!GO:0007525;somatic muscle development;0.0276058484853454;22288!GO:0007184;SMAD protein nuclear translocation;0.0306698039093664;20742!GO:0004499;flavin-containing monooxygenase activity;0.0328569034321639;14261!GO:0003779;actin binding;0.0358052730957127;20742,22288!GO:0007167;enzyme linked receptor protein signaling pathway;0.0367876359540371;20742,11641!GO:0051018;protein kinase A binding;0.0367876359540371;11641!GO:0007182;common-partner SMAD protein phosphorylation;0.0376195958943488;20742!GO:0050661;NADP binding;0.0393980510213329;14261!GO:0008092;cytoskeletal protein binding;0.0393980510213329;20742,22288!GO:0016010;dystrophin-associated glycoprotein complex;0.0393980510213329;22288!GO:0031594;neuromuscular junction;0.039831442055262;22288!GO:0000060;protein import into nucleus, translocation;0.0404043651360832;20742!GO:0051016;barbed-end actin filament capping;0.0404043651360832;20742!GO:0030835;negative regulation of actin filament depolymerization;0.0404043651360832;20742!GO:0051693;actin filament capping;0.0404043651360832;20742!GO:0005624;membrane fraction;0.0404043651360832;22288,14261!GO:0007010;cytoskeleton organization and biogenesis;0.0404043651360832;20742,11641!GO:0030834;regulation of actin filament depolymerization;0.0404043651360832;20742!GO:0030042;actin filament depolymerization;0.0404043651360832;20742!GO:0007165;signal transduction;0.0404043651360832;20742,11641,22288,224792!GO:0016709;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen;0.0404043651360832;14261!GO:0031227;intrinsic to endoplasmic reticulum membrane;0.0406118255343949;14261!GO:0000267;cell fraction;0.0421358455079084;22288,14261!GO:0005605;basal lamina;0.0421358455079084;22288!GO:0007154;cell communication;0.0421358455079084;20742,11641,22288,224792!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0421358455079084;20742!GO:0051261;protein depolymerization;0.0421358455079084;20742!GO:0032535;regulation of cellular component size;0.0421358455079084;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0421358455079084;20742!GO:0030832;regulation of actin filament length;0.0421358455079084;20742!GO:0051129;negative regulation of cellular component organization and biogenesis;0.0421358455079084;20742!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0421358455079084;20742!GO:0033043;regulation of organelle organization and biogenesis;0.0421358455079084;20742!GO:0008154;actin polymerization and/or depolymerization;0.0469985389384137;20742!GO:0007015;actin filament organization;0.0469985389384137;11641!
}}

Revision as of 11:05, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:115726435..115726454,+p@chr10:115726435..115726454
+
Mm9::chr10:115783936..115783945,+p@chr10:115783936..115783945
+
Mm9::chr10:115809917..115809921,+p@chr10:115809917..115809921
+
Mm9::chr10:12103662..12103666,-p@chr10:12103662..12103666
-
Mm9::chr11:30000318..30000322,-p@chr11:30000318..30000322
-
Mm9::chr11:30148502..30148509,-p@chr11:30148502..30148509
-
Mm9::chr11:30153416..30153420,-p@chr11:30153416..30153420
-
Mm9::chr13:100017650..100017662,+p@chr13:100017650..100017662
+
Mm9::chr13:115846729..115846733,-p@chr13:115846729..115846733
-
Mm9::chr16:85542827..85542835,-p@chr16:85542827..85542835
-
Mm9::chr16:95581011..95581024,-p@chr16:95581011..95581024
-
Mm9::chr17:13016269..13016283,+p@chr17:13016269..13016283
+
Mm9::chr17:43592386..43592398,+p@chr17:43592386..43592398
+
Mm9::chr17:43592580..43592605,+p@chr17:43592580..43592605
+
Mm9::chr17:47898459..47898487,+p@chr17:47898459..47898487
+
Mm9::chr17:67475291..67475294,-p@chr17:67475291..67475294
-
Mm9::chr17:75919962..75919967,+p@chr17:75919962..75919967
+
Mm9::chr19:21867742..21867746,+p@chr19:21867742..21867746
+
Mm9::chr1:11175335..11175339,+p@chr1:11175335..11175339
+
Mm9::chr1:152644349..152644352,-p@chr1:152644349..152644352
-
Mm9::chr1:164764434..164764438,-p13@Fmo1
Mm9::chr1:59931940..59931964,+p@chr1:59931940..59931964
+
Mm9::chr2:84247734..84247745,-p@chr2:84247734..84247745
-
Mm9::chr4:3706358..3706404,+p@chr4:3706358..3706404
+
Mm9::chr4:57906800..57906812,+p@chr4:57906800..57906812
+
Mm9::chr4:94487460..94487476,+p@chr4:94487460..94487476
+
Mm9::chr5:65546218..65546229,+p@chr5:65546218..65546229
+
Mm9::chr5:65546334..65546342,+p@chr5:65546334..65546342
+
Mm9::chr6:97469086..97469090,-p@chr6:97469086..97469090
-
Mm9::chr7:108156311..108156321,-p@chr7:108156311..108156321
-
Mm9::chr8:37649789..37649792,-p@chr8:37649789..37649792
-


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:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0276058484853454
GO:0007527adult somatic muscle development0.0276058484853454
GO:0030036actin cytoskeleton organization and biogenesis0.0276058484853454
GO:0030029actin filament-based process0.0276058484853454
GO:0007525somatic muscle development0.0276058484853454
GO:0007184SMAD protein nuclear translocation0.0306698039093664
GO:0004499flavin-containing monooxygenase activity0.0328569034321639
GO:0003779actin binding0.0358052730957127
GO:0007167enzyme linked receptor protein signaling pathway0.0367876359540371
GO:0051018protein kinase A binding0.0367876359540371
GO:0007182common-partner SMAD protein phosphorylation0.0376195958943488
GO:0050661NADP binding0.0393980510213329
GO:0008092cytoskeletal protein binding0.0393980510213329
GO:0016010dystrophin-associated glycoprotein complex0.0393980510213329
GO:0031594neuromuscular junction0.039831442055262
GO:0000060protein import into nucleus, translocation0.0404043651360832
GO:0051016barbed-end actin filament capping0.0404043651360832
GO:0030835negative regulation of actin filament depolymerization0.0404043651360832
GO:0051693actin filament capping0.0404043651360832
GO:0005624membrane fraction0.0404043651360832
GO:0007010cytoskeleton organization and biogenesis0.0404043651360832
GO:0030834regulation of actin filament depolymerization0.0404043651360832
GO:0030042actin filament depolymerization0.0404043651360832
GO:0007165signal transduction0.0404043651360832
GO:0016709oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen0.0404043651360832
GO:0031227intrinsic to endoplasmic reticulum membrane0.0406118255343949
GO:0000267cell fraction0.0421358455079084
GO:0005605basal lamina0.0421358455079084
GO:0007154cell communication0.0421358455079084
GO:0008064regulation of actin polymerization and/or depolymerization0.0421358455079084
GO:0051261protein depolymerization0.0421358455079084
GO:0032535regulation of cellular component size0.0421358455079084
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0421358455079084
GO:0030832regulation of actin filament length0.0421358455079084
GO:0051129negative regulation of cellular component organization and biogenesis0.0421358455079084
GO:0051493regulation of cytoskeleton organization and biogenesis0.0421358455079084
GO:0033043regulation of organelle organization and biogenesis0.0421358455079084
GO:0008154actin polymerization and/or depolymerization0.0469985389384137
GO:0007015actin filament organization0.0469985389384137



Relative expression of the co-expression cluster over median <br>Analyst:


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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)

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