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MCL coexpression mm9:597: Difference between revisions

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{{MCL_coexpression_mm9
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localization;0.0320997394001498;69162,69608,66913,21405!GO:0033036;macromolecule localization;0.0320997394001498;69162,69608,66913,21405!GO:0046483;heterocycle metabolic process;0.0320997394001498;18453,21405!GO:0043691;reverse cholesterol transport;0.0320997394001498;21405!GO:0005046;KDEL sequence binding;0.0320997394001498;66913!GO:0015721;bile acid and bile salt transport;0.0320997394001498;21405!GO:0004656;procollagen-proline 4-dioxygenase activity;0.0320997394001498;18453!GO:0018401;peptidyl-proline hydroxylation to 4-hydroxy-L-proline;0.0320997394001498;18453!GO:0019511;peptidyl-proline hydroxylation;0.0320997394001498;18453!GO:0031545;peptidyl-proline 4-dioxygenase activity;0.0320997394001498;18453!GO:0046923;ER retention sequence binding;0.0320997394001498;66913!GO:0006621;protein retention in ER;0.0320997394001498;66913!GO:0019471;4-hydroxyproline metabolic process;0.0320997394001498;18453!GO:0009743;response to carbohydrate stimulus;0.0320997394001498;21405!GO:0006699;bile acid biosynthetic process;0.0320997394001498;21405!GO:0009746;response to hexose stimulus;0.0320997394001498;21405!GO:0009749;response to glucose stimulus;0.0320997394001498;21405!GO:0018208;peptidyl-proline modification;0.0320997394001498;18453!GO:0006810;transport;0.0320997394001498;69162,69608,20535,66913,21405!GO:0015908;fatty acid transport;0.0320997394001498;21405!GO:0051234;establishment of localization;0.0320997394001498;69162,69608,20535,66913,21405!GO:0015031;protein transport;0.0320997394001498;69162,69608,66913!GO:0048341;paraxial mesoderm formation;0.0320997394001498;21405!GO:0031543;peptidyl-proline dioxygenase activity;0.0320997394001498;18453!GO:0019798;procollagen-proline dioxygenase activity;0.0320997394001498;18453!GO:0015718;monocarboxylic acid transport;0.0320997394001498;21405!GO:0032507;maintenance of cellular protein localization;0.0320997394001498;66913!GO:0042802;identical protein binding;0.0320997394001498;73137,21405!GO:0045184;establishment of protein localization;0.0320997394001498;69162,69608,66913!GO:0016864;intramolecular oxidoreductase activity, transposing S-S bonds;0.0320997394001498;18453!GO:0003756;protein disulfide isomerase activity;0.0320997394001498;18453!GO:0031018;endocrine pancreas development;0.0320997394001498;21405!GO:0005783;endoplasmic reticulum;0.0326021141895586;69162,18453,66913!GO:0051651;maintenance of cellular localization;0.0326021141895586;66913!GO:0016862;intramolecular oxidoreductase activity, interconverting keto- and enol-groups;0.0326021141895586;18453!GO:0005452;inorganic anion exchanger activity;0.0326021141895586;20535!GO:0005048;signal sequence binding;0.0338486238688349;66913!GO:0048340;paraxial mesoderm morphogenesis;0.0338486238688349;21405!GO:0045185;maintenance of protein localization;0.0338486238688349;66913!GO:0051179;localization;0.0343283832004196;69162,69608,20535,66913,21405!GO:0015380;anion exchanger activity;0.0350596560803832;20535!GO:0008206;bile acid metabolic process;0.0350596560803832;21405!GO:0015106;bicarbonate transmembrane transporter activity;0.0350596560803832;20535!GO:0050796;regulation of insulin secretion;0.0350596560803832;21405!GO:0015301;anion:anion antiporter activity;0.0350596560803832;20535!GO:0006783;heme biosynthetic process;0.0350596560803832;21405!GO:0015108;chloride transmembrane transporter activity;0.0373555961627596;20535!GO:0006779;porphyrin biosynthetic process;0.0373555961627596;21405!GO:0048339;paraxial mesoderm development;0.0373555961627596;21405!GO:0033014;tetrapyrrole biosynthetic process;0.0373555961627596;21405!GO:0031016;pancreas development;0.0373555961627596;21405!GO:0045120;pronucleus;0.0385486000284395;21405!GO:0030301;cholesterol transport;0.0385486000284395;21405!GO:0015918;sterol transport;0.0385486000284395;21405!GO:0051235;maintenance of localization;0.0385486000284395;66913!GO:0045453;bone resorption;0.0385486000284395;21405!GO:0001750;photoreceptor outer 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|gostat_on_MCL_coexpression=GO:0008104;protein localization;0.0320997394001498;69162,69608,66913,21405!GO:0033036;macromolecule localization;0.0320997394001498;69162,69608,66913,21405!GO:0046483;heterocycle metabolic process;0.0320997394001498;18453,21405!GO:0043691;reverse cholesterol transport;0.0320997394001498;21405!GO:0005046;KDEL sequence binding;0.0320997394001498;66913!GO:0015721;bile acid and bile salt transport;0.0320997394001498;21405!GO:0004656;procollagen-proline 4-dioxygenase activity;0.0320997394001498;18453!GO:0018401;peptidyl-proline hydroxylation to 4-hydroxy-L-proline;0.0320997394001498;18453!GO:0019511;peptidyl-proline hydroxylation;0.0320997394001498;18453!GO:0031545;peptidyl-proline 4-dioxygenase activity;0.0320997394001498;18453!GO:0046923;ER retention sequence binding;0.0320997394001498;66913!GO:0006621;protein retention in ER;0.0320997394001498;66913!GO:0019471;4-hydroxyproline metabolic process;0.0320997394001498;18453!GO:0009743;response to carbohydrate stimulus;0.0320997394001498;21405!GO:0006699;bile acid biosynthetic process;0.0320997394001498;21405!GO:0009746;response to hexose stimulus;0.0320997394001498;21405!GO:0009749;response to glucose stimulus;0.0320997394001498;21405!GO:0018208;peptidyl-proline modification;0.0320997394001498;18453!GO:0006810;transport;0.0320997394001498;69162,69608,20535,66913,21405!GO:0015908;fatty acid transport;0.0320997394001498;21405!GO:0051234;establishment of localization;0.0320997394001498;69162,69608,20535,66913,21405!GO:0015031;protein transport;0.0320997394001498;69162,69608,66913!GO:0048341;paraxial mesoderm formation;0.0320997394001498;21405!GO:0031543;peptidyl-proline dioxygenase activity;0.0320997394001498;18453!GO:0019798;procollagen-proline dioxygenase activity;0.0320997394001498;18453!GO:0015718;monocarboxylic acid transport;0.0320997394001498;21405!GO:0032507;maintenance of cellular protein localization;0.0320997394001498;66913!GO:0042802;identical protein binding;0.0320997394001498;73137,21405!GO:0045184;establishment of protein localization;0.0320997394001498;69162,69608,66913!GO:0016864;intramolecular oxidoreductase activity, transposing S-S bonds;0.0320997394001498;18453!GO:0003756;protein disulfide isomerase activity;0.0320997394001498;18453!GO:0031018;endocrine pancreas development;0.0320997394001498;21405!GO:0005783;endoplasmic reticulum;0.0326021141895586;69162,18453,66913!GO:0051651;maintenance of cellular localization;0.0326021141895586;66913!GO:0016862;intramolecular oxidoreductase activity, interconverting keto- and enol-groups;0.0326021141895586;18453!GO:0005452;inorganic anion exchanger activity;0.0326021141895586;20535!GO:0005048;signal sequence binding;0.0338486238688349;66913!GO:0048340;paraxial mesoderm morphogenesis;0.0338486238688349;21405!GO:0045185;maintenance of protein localization;0.0338486238688349;66913!GO:0051179;localization;0.0343283832004196;69162,69608,20535,66913,21405!GO:0015380;anion exchanger activity;0.0350596560803832;20535!GO:0008206;bile acid metabolic process;0.0350596560803832;21405!GO:0015106;bicarbonate transmembrane transporter activity;0.0350596560803832;20535!GO:0050796;regulation of insulin secretion;0.0350596560803832;21405!GO:0015301;anion:anion antiporter activity;0.0350596560803832;20535!GO:0006783;heme biosynthetic process;0.0350596560803832;21405!GO:0015108;chloride transmembrane transporter activity;0.0373555961627596;20535!GO:0006779;porphyrin biosynthetic process;0.0373555961627596;21405!GO:0048339;paraxial mesoderm development;0.0373555961627596;21405!GO:0033014;tetrapyrrole biosynthetic process;0.0373555961627596;21405!GO:0031016;pancreas development;0.0373555961627596;21405!GO:0045120;pronucleus;0.0385486000284395;21405!GO:0030301;cholesterol transport;0.0385486000284395;21405!GO:0015918;sterol transport;0.0385486000284395;21405!GO:0051235;maintenance of localization;0.0385486000284395;66913!GO:0045453;bone resorption;0.0385486000284395;21405!GO:0001750;photoreceptor outer segment;0.0385486000284395;21405!GO:0042168;heme metabolic process;0.0404007155440419;21405!GO:0031513;nonmotile primary cilium;0.0421889621772222;21405!GO:0033013;tetrapyrrole metabolic process;0.0431965906050089;21405!GO:0006778;porphyrin metabolic process;0.0431965906050089;21405!GO:0046883;regulation of hormone secretion;0.0472013970439534;21405!GO:0001889;liver development;0.0484875740425892;21405!GO:0042592;homeostatic process;0.0484875740425892;18453,21405!GO:0030111;regulation of Wnt receptor signaling pathway;0.049503468730572;21405!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!2.54e-13!31;UBERON:0005409!1.92e-12!47;UBERON:0002365!6.26e-10!25;UBERON:0002330!6.26e-10!25;UBERON:0009854!2.63e-09!23;UBERON:0009856!2.63e-09!23;UBERON:0004119!3.27e-09!118;UBERON:0000925!3.27e-09!118;UBERON:0006595!3.27e-09!118;UBERON:0002107!4.87e-09!22;UBERON:0007499!4.87e-09!22;UBERON:0006925!4.87e-09!22;UBERON:0009497!4.87e-09!22;UBERON:0000015!4.87e-09!22;UBERON:0002423!4.87e-09!22;UBERON:0006235!4.87e-09!22;UBERON:0008835!4.87e-09!22;UBERON:0003894!4.87e-09!22;UBERON:0004161!4.87e-09!22;UBERON:0008836!4.87e-09!22;UBERON:0005177!7.35e-09!79;UBERON:0001007!1.30e-08!116;UBERON:0001555!1.30e-08!116;UBERON:0007026!1.30e-08!116;UBERON:0002100!1.66e-08!90;UBERON:0000466!5.77e-08!79;UBERON:0004921!6.87e-08!114;UBERON:0005256!2.47e-07!45;UBERON:0000344!2.84e-07!15;UBERON:0001264!8.12e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.737036,0.918622,0.245304,0.303186,0.1565,0.315748,1.02601,0.303924,0.320069,0.336879,0.939294,1.00221,0.630954,1.05028,0.169024,0,0.587245,0.150639,0.586013,0.602977,0.215242,0.447169,1.04849,0.471175,0.701128,0.432737,0.561494,0.334131,0.558665,0.438367,0.321757,0.683831,0.891038,0.0658632,0.975762,0.056009,0.142225,0.382372,0.79515,0.347926,0.153518,0.870859,0.0834993,0.170547,0.685271,0.293566,0.512146,0.34807,0.0642028,1.07257,1.39948,0.457464,0.419161,1.91948,0.837732,1.06445,0.200484,0.37415,0.912284,1.0604,0.664611,0.46618,0.694361,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.650349,0.313987,4.24726,0.870406,0.51601,0.835139,0.504564,0.50152,0.648171,0.218647,0.0952669,0.60374,0.464847,0.0868537,0.758319,0.580776,1.25973,0.053731,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,0.391609,0.11194,0.299765,0.698838,0.512384,1.48367,0.142282,0.683562,1.88464,0.571268,0.57027,0.3259,1.51783,0.344504,0.222586,1.16343,0.723377,0.805555,0.626352,2.55104,1.04639,0.152197,1.39764,1.49689,0.58848,0.43155,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,0.689622,0.969481,0.163147,0.787341,0.296885,0.940498,0.426575,1.06766,0.0212043,0.274293,0.873625,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,0.757925,0.157809,0.445509,3.90631,0.822286,0.747142,0.425729,0.901933,0.458393,0.178202,0.265096,0.752802,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.436256,0.384198,2.50591
}}

Latest revision as of 15:34, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:113612097..113612161,-p3@Cdc42ep4
Mm9::chr11:120434178..120434195,-p1@P4hb
Mm9::chr13:115879674..115879694,+p@chr13:115879674..115879694
+
Mm9::chr13:115879700..115879724,+p@chr13:115879700..115879724
+
Mm9::chr18:57514387..57514451,+p1@Prrc1
Mm9::chr3:122970363..122970418,+p1@Sec24d
Mm9::chr3:40886914..40886946,-p1@Pgrmc2
Mm9::chr4:118217520..118217535,-p@chr4:118217520..118217535
-
Mm9::chr5:100845134..100845301,-p1@Sec31a
Mm9::chr5:115420882..115420896,-p3@Hnf1a
Mm9::chr5:144165498..144165561,+p1@Kdelr2
Mm9::chr5:23934029..23934061,+p3@Slc4a2


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:0008104protein localization0.0320997394001498
GO:0033036macromolecule localization0.0320997394001498
GO:0046483heterocycle metabolic process0.0320997394001498
GO:0043691reverse cholesterol transport0.0320997394001498
GO:0005046KDEL sequence binding0.0320997394001498
GO:0015721bile acid and bile salt transport0.0320997394001498
GO:0004656procollagen-proline 4-dioxygenase activity0.0320997394001498
GO:0018401peptidyl-proline hydroxylation to 4-hydroxy-L-proline0.0320997394001498
GO:0019511peptidyl-proline hydroxylation0.0320997394001498
GO:0031545peptidyl-proline 4-dioxygenase activity0.0320997394001498
GO:0046923ER retention sequence binding0.0320997394001498
GO:0006621protein retention in ER0.0320997394001498
GO:00194714-hydroxyproline metabolic process0.0320997394001498
GO:0009743response to carbohydrate stimulus0.0320997394001498
GO:0006699bile acid biosynthetic process0.0320997394001498
GO:0009746response to hexose stimulus0.0320997394001498
GO:0009749response to glucose stimulus0.0320997394001498
GO:0018208peptidyl-proline modification0.0320997394001498
GO:0006810transport0.0320997394001498
GO:0015908fatty acid transport0.0320997394001498
GO:0051234establishment of localization0.0320997394001498
GO:0015031protein transport0.0320997394001498
GO:0048341paraxial mesoderm formation0.0320997394001498
GO:0031543peptidyl-proline dioxygenase activity0.0320997394001498
GO:0019798procollagen-proline dioxygenase activity0.0320997394001498
GO:0015718monocarboxylic acid transport0.0320997394001498
GO:0032507maintenance of cellular protein localization0.0320997394001498
GO:0042802identical protein binding0.0320997394001498
GO:0045184establishment of protein localization0.0320997394001498
GO:0016864intramolecular oxidoreductase activity, transposing S-S bonds0.0320997394001498
GO:0003756protein disulfide isomerase activity0.0320997394001498
GO:0031018endocrine pancreas development0.0320997394001498
GO:0005783endoplasmic reticulum0.0326021141895586
GO:0051651maintenance of cellular localization0.0326021141895586
GO:0016862intramolecular oxidoreductase activity, interconverting keto- and enol-groups0.0326021141895586
GO:0005452inorganic anion exchanger activity0.0326021141895586
GO:0005048signal sequence binding0.0338486238688349
GO:0048340paraxial mesoderm morphogenesis0.0338486238688349
GO:0045185maintenance of protein localization0.0338486238688349
GO:0051179localization0.0343283832004196
GO:0015380anion exchanger activity0.0350596560803832
GO:0008206bile acid metabolic process0.0350596560803832
GO:0015106bicarbonate transmembrane transporter activity0.0350596560803832
GO:0050796regulation of insulin secretion0.0350596560803832
GO:0015301anion:anion antiporter activity0.0350596560803832
GO:0006783heme biosynthetic process0.0350596560803832
GO:0015108chloride transmembrane transporter activity0.0373555961627596
GO:0006779porphyrin biosynthetic process0.0373555961627596
GO:0048339paraxial mesoderm development0.0373555961627596
GO:0033014tetrapyrrole biosynthetic process0.0373555961627596
GO:0031016pancreas development0.0373555961627596
GO:0045120pronucleus0.0385486000284395
GO:0030301cholesterol transport0.0385486000284395
GO:0015918sterol transport0.0385486000284395
GO:0051235maintenance of localization0.0385486000284395
GO:0045453bone resorption0.0385486000284395
GO:0001750photoreceptor outer segment0.0385486000284395
GO:0042168heme metabolic process0.0404007155440419
GO:0031513nonmotile primary cilium0.0421889621772222
GO:0033013tetrapyrrole metabolic process0.0431965906050089
GO:0006778porphyrin metabolic process0.0431965906050089
GO:0046883regulation of hormone secretion0.0472013970439534
GO:0001889liver development0.0484875740425892
GO:0042592homeostatic process0.0484875740425892
GO:0030111regulation of Wnt receptor signaling pathway0.049503468730572



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
intestine2.54e-1331
gastrointestinal system1.92e-1247
exocrine gland6.26e-1025
exocrine system6.26e-1025
digestive tract diverticulum2.63e-0923
sac2.63e-0923
endoderm-derived structure3.27e-09118
endoderm3.27e-09118
presumptive endoderm3.27e-09118
liver4.87e-0922
epithelial sac4.87e-0922
digestive gland4.87e-0922
epithelium of foregut-midgut junction4.87e-0922
anatomical boundary4.87e-0922
hepatobiliary system4.87e-0922
foregut-midgut junction4.87e-0922
hepatic diverticulum4.87e-0922
liver primordium4.87e-0922
septum transversum4.87e-0922
liver bud4.87e-0922
trunk region element7.35e-0979
digestive system1.30e-08116
digestive tract1.30e-08116
primitive gut1.30e-08116
trunk1.66e-0890
immaterial anatomical entity5.77e-0879
subdivision of digestive tract6.87e-08114
trunk mesenchyme2.47e-0745
mucosa2.84e-0715
pancreas8.12e-0712


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)
MA0003.10.829197
MA0004.11.48666
MA0006.10.496735
MA0007.10.290695
MA0009.10.709264
MA0014.11.0426
MA0017.11.04297
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.992869
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.11.76106
MA0048.10.168666
MA0050.10.337476
MA0051.11.12244
MA0052.10.729105
MA0055.10.624457
MA0056.10
MA0057.10.630087
MA0058.11.18867
MA0059.11.22696
MA0060.11.17531
MA0061.10.129002
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.157638
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.11.47506
MA0074.11.01196
MA0076.11.10234
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.11.08862
MA0089.10
MA0090.10.27428
MA0091.10.845572
MA0092.10.274547
MA0093.11.61312
MA0095.10
MA0098.10
MA0100.10.989129
MA0101.10.240622
MA0103.10.19444
MA0105.10.846872
MA0106.10.478503
MA0107.10.189625
MA0108.20.557195
MA0109.10
MA0111.10.286331
MA0113.10.452439
MA0114.11.29784
MA0115.10.805567
MA0116.10.959944
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.11.03624
MA0140.10.379562
MA0141.10.603844
MA0142.10.604892
MA0143.10.467531
MA0144.10.406018
MA0145.12.55967
MA0146.10.651503
MA0147.10.845188
MA0148.10.317692
MA0149.10.245177
MA0062.20.870192
MA0035.20.383789
MA0039.24.16319
MA0138.20.523978
MA0002.20.302282
MA0137.20.207733
MA0104.21.63782
MA0047.20.431964
MA0112.21.15536
MA0065.20.79588
MA0150.10.790482
MA0151.10
MA0152.11.1034
MA0153.10.854464
MA0154.10.16541
MA0155.10.555224
MA0156.10.580656
MA0157.10.574484
MA0158.10
MA0159.10.446593
MA0160.10.85749
MA0161.10
MA0162.11.72487
MA0163.10.962545
MA0164.10.408402
MA0080.20.190316
MA0018.20.417217
MA0099.20.518072
MA0079.22.13111
MA0102.21.42135
MA0258.10.376353
MA0259.11.31847
MA0442.10
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