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MCL coexpression mm9:210: Difference between revisions

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{{MCL_coexpression_mm9
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response;0.00826053774179675;15945,20715,66537,18034!GO:0002376;immune system process;0.0201741699337101;15945,20715,66537,18034!GO:0005634;nucleus;0.0240180846587962;11910,20715,66537,18034,66213,14281,70686!GO:0005667;transcription factor complex;0.0240180846587962;11910,66213,14281!GO:0002266;follicular dendritic cell activation;0.0240180846587962;18034!GO:0002268;follicular dendritic cell differentiation;0.0240180846587962;18034!GO:0004867;serine-type endopeptidase inhibitor activity;0.0240180846587962;20715,238393!GO:0044451;nucleoplasm part;0.0316694213930111;11910,66213,14281!GO:0005654;nucleoplasm;0.0316694213930111;11910,66213,14281!GO:0004866;endopeptidase inhibitor activity;0.0316694213930111;20715,238393!GO:0030414;protease inhibitor activity;0.0316694213930111;20715,238393!GO:0031981;nuclear lumen;0.0370814706951127;11910,66213,14281!GO:0002467;germinal center formation;0.0370814706951127;18034!GO:0048536;spleen development;0.0370814706951127;18034!GO:0046983;protein dimerization activity;0.0370814706951127;11910,14281!GO:0004857;enzyme inhibitor activity;0.0370814706951127;20715,238393!GO:0000188;inactivation of MAPK activity;0.0370814706951127;70686!GO:0031974;membrane-enclosed lumen;0.0370814706951127;11910,66213,14281!GO:0043233;organelle lumen;0.0370814706951127;11910,66213,14281!GO:0043234;protein complex;0.0370814706951127;11910,66537,66213,14281!GO:0003700;transcription factor activity;0.0440768544957696;11910,18034,14281!GO:0006355;regulation of transcription, DNA-dependent;0.0479074026411149;11910,18034,66213,14281!GO:0006351;transcription, DNA-dependent;0.0479074026411149;11910,18034,66213,14281!GO:0032774;RNA biosynthetic process;0.0479074026411149;11910,18034,66213,14281!GO:0043407;negative regulation of MAP kinase activity;0.0479074026411149;70686!GO:0048535;lymph node development;0.0479074026411149;18034!GO:0006094;gluconeogenesis;0.0479074026411149;11910!GO:0045449;regulation of transcription;0.0479074026411149;11910,18034,66213,14281!GO:0043231;intracellular membrane-bound organelle;0.0479074026411149;11910,20715,66537,18034,66213,14281,70686!GO:0043227;membrane-bound organelle;0.0479074026411149;11910,20715,66537,18034,66213,14281,70686!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0479074026411149;11910,18034,66213,14281!GO:0044428;nuclear part;0.0479074026411149;11910,66213,14281!GO:0006350;transcription;0.0479074026411149;11910,18034,66213,14281!GO:0006090;pyruvate metabolic process;0.0479074026411149;11910!GO:0032991;macromolecular complex;0.0485576093868489;11910,66537,66213,14281!GO:0019319;hexose biosynthetic process;0.0485576093868489;11910!GO:0010468;regulation of gene expression;0.0485576093868489;11910,18034,66213,14281!GO:0046165;alcohol biosynthetic process;0.0485576093868489;11910!GO:0046364;monosaccharide biosynthetic process;0.0485576093868489;11910!GO:0005515;protein 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|gostat_on_MCL_coexpression=GO:0006955;immune response;0.00826053774179675;15945,20715,66537,18034!GO:0002376;immune system process;0.0201741699337101;15945,20715,66537,18034!GO:0005634;nucleus;0.0240180846587962;11910,20715,66537,18034,66213,14281,70686!GO:0005667;transcription factor complex;0.0240180846587962;11910,66213,14281!GO:0002266;follicular dendritic cell activation;0.0240180846587962;18034!GO:0002268;follicular dendritic cell differentiation;0.0240180846587962;18034!GO:0004867;serine-type endopeptidase inhibitor activity;0.0240180846587962;20715,238393!GO:0044451;nucleoplasm part;0.0316694213930111;11910,66213,14281!GO:0005654;nucleoplasm;0.0316694213930111;11910,66213,14281!GO:0004866;endopeptidase inhibitor activity;0.0316694213930111;20715,238393!GO:0030414;protease inhibitor activity;0.0316694213930111;20715,238393!GO:0031981;nuclear lumen;0.0370814706951127;11910,66213,14281!GO:0002467;germinal center formation;0.0370814706951127;18034!GO:0048536;spleen development;0.0370814706951127;18034!GO:0046983;protein dimerization activity;0.0370814706951127;11910,14281!GO:0004857;enzyme inhibitor activity;0.0370814706951127;20715,238393!GO:0000188;inactivation of MAPK activity;0.0370814706951127;70686!GO:0031974;membrane-enclosed lumen;0.0370814706951127;11910,66213,14281!GO:0043233;organelle lumen;0.0370814706951127;11910,66213,14281!GO:0043234;protein complex;0.0370814706951127;11910,66537,66213,14281!GO:0003700;transcription factor activity;0.0440768544957696;11910,18034,14281!GO:0006355;regulation of transcription, DNA-dependent;0.0479074026411149;11910,18034,66213,14281!GO:0006351;transcription, DNA-dependent;0.0479074026411149;11910,18034,66213,14281!GO:0032774;RNA biosynthetic process;0.0479074026411149;11910,18034,66213,14281!GO:0043407;negative regulation of MAP kinase activity;0.0479074026411149;70686!GO:0048535;lymph node development;0.0479074026411149;18034!GO:0006094;gluconeogenesis;0.0479074026411149;11910!GO:0045449;regulation of transcription;0.0479074026411149;11910,18034,66213,14281!GO:0043231;intracellular membrane-bound organelle;0.0479074026411149;11910,20715,66537,18034,66213,14281,70686!GO:0043227;membrane-bound organelle;0.0479074026411149;11910,20715,66537,18034,66213,14281,70686!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0479074026411149;11910,18034,66213,14281!GO:0044428;nuclear part;0.0479074026411149;11910,66213,14281!GO:0006350;transcription;0.0479074026411149;11910,18034,66213,14281!GO:0006090;pyruvate metabolic process;0.0479074026411149;11910!GO:0032991;macromolecular complex;0.0485576093868489;11910,66537,66213,14281!GO:0019319;hexose biosynthetic process;0.0485576093868489;11910!GO:0010468;regulation of gene expression;0.0485576093868489;11910,18034,66213,14281!GO:0046165;alcohol biosynthetic process;0.0485576093868489;11910!GO:0046364;monosaccharide biosynthetic process;0.0485576093868489;11910!GO:0005515;protein binding;0.0485576093868489;15945,11910,18034,66213,14281,70686!
|ontology_enrichment_celltype=CL:0002563!5.45e-16!9;CL:0002251!5.45e-16!9;CL:0000239!1.49e-12!6;CL:0000677!1.49e-12!6;CL:0000212!1.49e-12!6;CL:0000584!1.49e-12!6;CL:0000075!9.89e-11!7;CL:0000066!1.02e-10!25;CL:0000988!1.66e-10!32;CL:0002032!1.66e-10!32;CL:0000037!1.66e-10!32;CL:0000566!1.66e-10!32;CL:0000837!1.66e-10!32;CL:0002076!2.94e-09!15;CL:0000223!5.88e-09!20;CL:0002371!6.40e-09!118;CL:0000548!3.13e-08!115;CL:0000255!3.13e-08!115;CL:0002320!3.64e-08!46;CL:0000134!3.64e-08!46;CL:0000034!1.50e-07!97
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003350!5.45e-16!9;UBERON:0004808!5.45e-16!9;UBERON:0001277!5.45e-16!9;UBERON:0000485!6.23e-13!11;UBERON:0001242!8.20e-11!13;UBERON:0000060!8.20e-11!13;UBERON:0001262!8.20e-11!13;UBERON:0004786!8.20e-11!13;UBERON:0000344!2.94e-09!15;UBERON:0002384!3.64e-08!46
|tfbs_overrepresentation_for_novel_motifs=0.265401,0.195464,1.03458,0.144193,0.195431,0.157279,0.0718138,0.0661182,0.42176,0.518723,0.447974,0.237602,0.0256018,0.265233,0.225204,0,0.176334,0.527154,0.492321,0.346427,0.578036,0.367278,0.264183,0.346887,0.236835,0.298017,0.0998,0.705582,0.482078,0.406379,0.373023,0.241883,0.0808269,0.140896,0.623839,0.1246,0.300023,0.503895,0.247039,0.0934258,0.188547,0.680187,0.304947,0.0375952,0.633443,0.0333208,0.812691,0.428539,0.204696,0.286874,0.497135,0.678642,0.372939,0.345318,0.358841,0.2736,0.788966,0.837773,1.30871,0.271202,0.646878,1.15519,0.469608,0.480792,0.599924,0.540314,0.469298,0.779659,0.639531,0.645209,0.385974,0.595585,1.10312,0.385253,0.0350744,0.216072,1.4891,0.39364,0.21687,0.180201,0.601779,1.65333,0.696443,0.986569,0.296819,0.293951,0.092357,0.569541,0.41582,0.932016,1.31029,0.300486,0.699119,0.0955531,0.595299,0.0421883,0.375569,0.25267,0.409447,0.00367388,0.300223,0.678177,0.331962,0.498003,0.496465,0.043853,0.202468,0.188857,0.365753,0.177001,0.769313,0.333321,0.595581,0.796092,0.534653,0.535089,0.374803,0.341748,0.177127,0.157424,0.389556,0.14722,0.30024,0.124234,0.581865,0.219311,1.40488,0.246028,0.468027,0.591365,0.319105,0.137799,0.443426,0.605306,0.553389,0.0620373,0.115854,0.385005,1.2728,1.28785,0.901817,0.473251,0.0949151,0.69537,0.161761,0.383255,0.819982,1.24909,0.282602,0.56382,0.101942,0.1375,0.915958,0.772179,0.603323,1.05804,0.680878,0.118702,0.261535,0.516289,0.519098,0.29619,0.626457,0.250896,0.936375,0.587532,0.0232209,0.066474,0.917317
|tfbs_overrepresentation_jaspar=MA0003.1;0.22497,MA0004.1;1.36286,MA0006.1;0.604557,MA0007.1;0.310419,MA0009.1;0.260251,MA0014.1;0.0217988,MA0017.1;0.462126,MA0019.1;0.144464,MA0024.1;0.65113,MA0025.1;2.91725,MA0027.1;1.78014,MA0028.1;1.62801,MA0029.1;0.215644,MA0030.1;0.219976,MA0031.1;0.196896,MA0038.1;0.619614,MA0040.1;0.741478,MA0041.1;0.0853046,MA0042.1;0.0766617,MA0043.1;1.58516,MA0046.1;0.285948,MA0048.1;0.20449,MA0050.1;2.06963,MA0051.1;1.57613,MA0052.1;3.86179,MA0055.1;0.050436,MA0056.1;0,MA0057.1;1.12335,MA0058.1;1.67524,MA0059.1;0.0802172,MA0060.1;0.188663,MA0061.1;9.12307,MA0063.1;0,MA0066.1;0.284669,MA0067.1;0.533552,MA0068.1;0.180141,MA0069.1;0.27511,MA0070.1;0.268186,MA0071.1;0.180115,MA0072.1;0.262182,MA0073.1;0.0594637,MA0074.1;0.521239,MA0076.1;1.11529,MA0077.1;0.247052,MA0078.1;0.108226,MA0081.1;0.238248,MA0083.1;0.330594,MA0084.1;0.829882,MA0087.1;0.29831,MA0088.1;0.520269,MA0089.1;0,MA0090.1;0.27877,MA0091.1;0.0401384,MA0092.1;0.116091,MA0093.1;1.30955,MA0095.1;0,MA0098.1;0,MA0100.1;0.497838,MA0101.1;7.39609,MA0103.1;0.0520183,MA0105.1;4.56029,MA0106.1;0.729623,MA0107.1;13.0909,MA0108.2;1.48233,MA0109.1;0,MA0111.1;0.301903,MA0113.1;0.666587,MA0114.1;0.411227,MA0115.1;0.333331,MA0116.1;0.384308,MA0117.1;0.309003,MA0119.1;2.30433,MA0122.1;0.323899,MA0124.1;0.488052,MA0125.1;0.426393,MA0130.1;0,MA0131.1;0.437569,MA0132.1;0,MA0133.1;0,MA0135.1;0.359267,MA0136.1;0.562317,MA0139.1;0.129996,MA0140.1;0.230166,MA0141.1;0.840721,MA0142.1;0.550541,MA0143.1;0.106237,MA0144.1;1.88116,MA0145.1;0.447193,MA0146.1;0.10275,MA0147.1;0.15457,MA0148.1;0.364643,MA0149.1;0.0203741,MA0062.2;0.533029,MA0035.2;1.31269,MA0039.2;0.178163,MA0138.2;0.426506,MA0002.2;1.02833,MA0137.2;1.54429,MA0104.2;0.16085,MA0047.2;0.0882619,MA0112.2;0.594441,MA0065.2;0.325578,MA0150.1;1.73983,MA0151.1;0,MA0152.1;0.297119,MA0153.1;0.972944,MA0154.1;0.59388,MA0155.1;0.289243,MA0156.1;0.788033,MA0157.1;0.168226,MA0158.1;0,MA0159.1;0.311625,MA0160.1;0.0419283,MA0161.1;0,MA0162.1;0.38346,MA0163.1;1.48657,MA0164.1;0.0771648,MA0080.2;0.478849,MA0018.2;2.0187,MA0099.2;4.13452,MA0079.2;0.489387,MA0102.2;0.879116,MA0258.1;0.366312,MA0259.1;1.19107,MA0442.1;0
}}

Latest revision as of 14:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:109223249..109223256,+p@chr11:109223249..109223256
+
Mm9::chr11:109223375..109223389,+p@chr11:109223375..109223389
+
Mm9::chr11:46250533..46250552,+p4@Med7
Mm9::chr11:69224327..69224356,+p@chr11:69224327..69224356
+
Mm9::chr11:93856714..93856728,+p@chr11:93856714..93856728
+
Mm9::chr12:105452722..105452742,+p2@Serpina3f
p2@Serpina3g
Mm9::chr12:105452748..105452759,+p1@Serpina3f
p1@Serpina3g
Mm9::chr12:86815252..86815257,+p11@Fos
Mm9::chr12:88177893..88177896,+p@chr12:88177893..88177896
+
Mm9::chr13:53097230..53097239,+p@chr13:53097230..53097239
+
Mm9::chr13:83713633..83713642,+p@chr13:83713633..83713642
+
Mm9::chr13:8994837..8994857,+p@chr13:8994837..8994857
+
Mm9::chr17:29232354..29232361,-p@chr17:29232354..29232361
-
Mm9::chr17:29626175..29626182,+p@chr17:29626175..29626182
+
Mm9::chr17:35188211..35188241,-p@chr17:35188211..35188241
-
Mm9::chr19:46379320..46379329,+p9@Nfkb2
Mm9::chr1:132934560..132934561,-p@chr1:132934560..132934561
-
Mm9::chr1:187027697..187027717,-p@chr1:187027697..187027717
-
Mm9::chr1:193007123..193007139,-p1@Atf3
Mm9::chr1:66863031..66863035,+p@chr1:66863031..66863035
+
Mm9::chr1:74342572..74342575,+p@chr1:74342572..74342575
+
Mm9::chr2:11457337..11457348,+p@chr2:11457337..11457348
+
Mm9::chr2:155651874..155651887,+p@chr2:155651874..155651887
+
Mm9::chr2:167209562..167209573,+p@chr2:167209562..167209573
+
Mm9::chr2:167209584..167209596,+p@chr2:167209584..167209596
+
Mm9::chr2:167246951..167246967,-p@chr2:167246951..167246967
-
Mm9::chr3:65762631..65762643,+p@chr3:65762631..65762643
+
Mm9::chr4:129178014..129178028,-p@chr4:129178014..129178028
-
Mm9::chr5:148672261..148672270,+p3@Pomp
Mm9::chr5:92777897..92777912,-p1@Cxcl10
Mm9::chr6:108609658..108609661,+p@chr6:108609658..108609661
+
Mm9::chr6:134742411..134742424,-p4@Dusp16
Mm9::chr6:37682625..37682629,+p@chr6:37682625..37682629
+
Mm9::chr6:53523649..53523653,+p@chr6:53523649..53523653
+
Mm9::chr7:19895040..19895049,-p5@Fosb
Mm9::chr7:20408246..20408265,+p@chr7:20408246..20408265
+
Mm9::chr7:29166897..29166918,-p@chr7:29166897..29166918
-
Mm9::chr7:29166951..29166962,-p@chr7:29166951..29166962
-
Mm9::chr7:29964591..29964598,+p@chr7:29964591..29964598
+
Mm9::chr8:35013053..35013058,-p@chr8:35013053..35013058
-
Mm9::chr8:86716164..86716184,+p@chr8:86716164..86716184
+
Mm9::chr9:32310107..32310119,-p@chr9:32310107..32310119
-
Mm9::chr9:40129323..40129336,+p@chr9:40129323..40129336
+
Mm9::chr9:44318264..44318273,-p@chr9:44318264..44318273
-


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:0006955immune response0.00826053774179675
GO:0002376immune system process0.0201741699337101
GO:0005634nucleus0.0240180846587962
GO:0005667transcription factor complex0.0240180846587962
GO:0002266follicular dendritic cell activation0.0240180846587962
GO:0002268follicular dendritic cell differentiation0.0240180846587962
GO:0004867serine-type endopeptidase inhibitor activity0.0240180846587962
GO:0044451nucleoplasm part0.0316694213930111
GO:0005654nucleoplasm0.0316694213930111
GO:0004866endopeptidase inhibitor activity0.0316694213930111
GO:0030414protease inhibitor activity0.0316694213930111
GO:0031981nuclear lumen0.0370814706951127
GO:0002467germinal center formation0.0370814706951127
GO:0048536spleen development0.0370814706951127
GO:0046983protein dimerization activity0.0370814706951127
GO:0004857enzyme inhibitor activity0.0370814706951127
GO:0000188inactivation of MAPK activity0.0370814706951127
GO:0031974membrane-enclosed lumen0.0370814706951127
GO:0043233organelle lumen0.0370814706951127
GO:0043234protein complex0.0370814706951127
GO:0003700transcription factor activity0.0440768544957696
GO:0006355regulation of transcription, DNA-dependent0.0479074026411149
GO:0006351transcription, DNA-dependent0.0479074026411149
GO:0032774RNA biosynthetic process0.0479074026411149
GO:0043407negative regulation of MAP kinase activity0.0479074026411149
GO:0048535lymph node development0.0479074026411149
GO:0006094gluconeogenesis0.0479074026411149
GO:0045449regulation of transcription0.0479074026411149
GO:0043231intracellular membrane-bound organelle0.0479074026411149
GO:0043227membrane-bound organelle0.0479074026411149
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0479074026411149
GO:0044428nuclear part0.0479074026411149
GO:0006350transcription0.0479074026411149
GO:0006090pyruvate metabolic process0.0479074026411149
GO:0032991macromolecular complex0.0485576093868489
GO:0019319hexose biosynthetic process0.0485576093868489
GO:0010468regulation of gene expression0.0485576093868489
GO:0046165alcohol biosynthetic process0.0485576093868489
GO:0046364monosaccharide biosynthetic process0.0485576093868489
GO:0005515protein binding0.0485576093868489



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>


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)
MA0003.10.22497
MA0004.11.36286
MA0006.10.604557
MA0007.10.310419
MA0009.10.260251
MA0014.10.0217988
MA0017.10.462126
MA0019.10.144464
MA0024.10.65113
MA0025.12.91725
MA0027.11.78014
MA0028.11.62801
MA0029.10.215644
MA0030.10.219976
MA0031.10.196896
MA0038.10.619614
MA0040.10.741478
MA0041.10.0853046
MA0042.10.0766617
MA0043.11.58516
MA0046.10.285948
MA0048.10.20449
MA0050.12.06963
MA0051.11.57613
MA0052.13.86179
MA0055.10.050436
MA0056.10
MA0057.11.12335
MA0058.11.67524
MA0059.10.0802172
MA0060.10.188663
MA0061.19.12307
MA0063.10
MA0066.10.284669
MA0067.10.533552
MA0068.10.180141
MA0069.10.27511
MA0070.10.268186
MA0071.10.180115
MA0072.10.262182
MA0073.10.0594637
MA0074.10.521239
MA0076.11.11529
MA0077.10.247052
MA0078.10.108226
MA0081.10.238248
MA0083.10.330594
MA0084.10.829882
MA0087.10.29831
MA0088.10.520269
MA0089.10
MA0090.10.27877
MA0091.10.0401384
MA0092.10.116091
MA0093.11.30955
MA0095.10
MA0098.10
MA0100.10.497838
MA0101.17.39609
MA0103.10.0520183
MA0105.14.56029
MA0106.10.729623
MA0107.113.0909
MA0108.21.48233
MA0109.10
MA0111.10.301903
MA0113.10.666587
MA0114.10.411227
MA0115.10.333331
MA0116.10.384308
MA0117.10.309003
MA0119.12.30433
MA0122.10.323899
MA0124.10.488052
MA0125.10.426393
MA0130.10
MA0131.10.437569
MA0132.10
MA0133.10
MA0135.10.359267
MA0136.10.562317
MA0139.10.129996
MA0140.10.230166
MA0141.10.840721
MA0142.10.550541
MA0143.10.106237
MA0144.11.88116
MA0145.10.447193
MA0146.10.10275
MA0147.10.15457
MA0148.10.364643
MA0149.10.0203741
MA0062.20.533029
MA0035.21.31269
MA0039.20.178163
MA0138.20.426506
MA0002.21.02833
MA0137.21.54429
MA0104.20.16085
MA0047.20.0882619
MA0112.20.594441
MA0065.20.325578
MA0150.11.73983
MA0151.10
MA0152.10.297119
MA0153.10.972944
MA0154.10.59388
MA0155.10.289243
MA0156.10.788033
MA0157.10.168226
MA0158.10
MA0159.10.311625
MA0160.10.0419283
MA0161.10
MA0162.10.38346
MA0163.11.48657
MA0164.10.0771648
MA0080.20.478849
MA0018.22.0187
MA0099.24.13452
MA0079.20.489387
MA0102.20.879116
MA0258.10.366312
MA0259.11.19107
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:210&oldid=3072209"