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MCL coexpression mm9:493: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000160!8.39e-27!31;UBERON:0005409!9.96e-21!47;UBERON:0000344!6.80e-16!15;UBERON:0001242!3.45e-13!13;UBERON:0000060!3.45e-13!13;UBERON:0001262!3.45e-13!13;UBERON:0004786!3.45e-13!13;UBERON:0004923!1.49e-08!24;UBERON:0003350!4.26e-08!9;UBERON:0004808!4.26e-08!9;UBERON:0001277!4.26e-08!9
|ontology_enrichment_uberon=UBERON:0000160!8.39e-27!31;UBERON:0005409!9.96e-21!47;UBERON:0000344!6.80e-16!15;UBERON:0001242!3.45e-13!13;UBERON:0000060!3.45e-13!13;UBERON:0001262!3.45e-13!13;UBERON:0004786!3.45e-13!13;UBERON:0004923!1.49e-08!24;UBERON:0003350!4.26e-08!9;UBERON:0004808!4.26e-08!9;UBERON:0001277!4.26e-08!9
|tfbs_overrepresentation_for_novel_motifs=0.206403,1.44067,0.548514,0.238864,0.110365,0.698129,0.324772,0.210111,0.837665,0.198502,0.288187,0.314655,0.210446,0.335151,0.383709,0,1.26156,0.105493,0.1896,0.670858,0.160516,1.053,0.334384,0.353775,0.192505,0.942903,1.09305,0.736859,0.139679,0.125189,0.710801,0.598971,1.14573,0.634402,0.384512,0.0584849,0.0985485,0.311629,0.0859217,0.247011,0.710516,0.259911,0.121081,0.122151,0.823347,0.230148,0.433813,0.279902,0.356013,0.8599,0.48979,0.381972,0.832043,0.732469,0.749094,0.904193,0.147717,0.303999,0.166653,0.339495,0.580338,0.390204,0.516848,0.479581,0.925321,0.516415,0.880067,1.22155,0.576002,1.07689,0.515225,0.823515,0.303663,0.781142,0.158223,0.951256,1.41018,0.423705,0.564426,0.163487,0.82829,0.521544,0.388944,0.0546645,0.671442,0.0442211,0.127322,0.125355,0.438181,1.38183,0.947651,0.676142,0.610915,0.365956,0.595467,0.0741053,0.206664,0.613539,0.43404,0.0236008,0.0985954,0.59871,0.715894,0.490329,0.489372,0.719532,0.543989,0.276621,0.499786,0.161774,0.582521,0.717588,0.164285,0.292444,0.954503,1.16365,0.964922,0.241826,0.506861,0.096357,0.786314,1.16518,0.360259,0.422901,1.00724,0.567849,0.331666,1.4708,0.8786,0.115924,0.699779,0.233152,0.850049,0.9301,0.975524,1.03933,0.212784,1.3312,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,0.260275,0.436593,1.7082,0.214583,0.111457,0.128142,0.434542,0.733963,0.077277,0.352111,0.81211,0.382849,0.128633,0.204546,0.60983,0.93695,0.670634,0.568261,0.199399,0.480505,0.345769,0.0978842,0.313326,0.0488031
|tfbs_overrepresentation_for_novel_motifs=0.206403,1.44067,0.548514,0.238864,0.110365,0.698129,0.324772,0.210111,0.837665,0.198502,0.288187,0.314655,0.210446,0.335151,0.383709,0,1.26156,0.105493,0.1896,0.670858,0.160516,1.053,0.334384,0.353775,0.192505,0.942903,1.09305,0.736859,0.139679,0.125189,0.710801,0.598971,1.14573,0.634402,0.384512,0.0584849,0.0985485,0.311629,0.0859217,0.247011,0.710516,0.259911,0.121081,0.122151,0.823347,0.230148,0.433813,0.279902,0.356013,0.8599,0.48979,0.381972,0.832043,0.732469,0.749094,0.904193,0.147717,0.303999,0.166653,0.339495,0.580338,0.390204,0.516848,0.479581,0.925321,0.516415,0.880067,1.22155,0.576002,1.07689,0.515225,0.823515,0.303663,0.781142,0.158223,0.951256,1.41018,0.423705,0.564426,0.163487,0.82829,0.521544,0.388944,0.0546645,0.671442,0.0442211,0.127322,0.125355,0.438181,1.38183,0.947651,0.676142,0.610915,0.365956,0.595467,0.0741053,0.206664,0.613539,0.43404,0.0236008,0.0985954,0.59871,0.715894,0.490329,0.489372,0.719532,0.543989,0.276621,0.499786,0.161774,0.582521,0.717588,0.164285,0.292444,0.954503,1.16365,0.964922,0.241826,0.506861,0.096357,0.786314,1.16518,0.360259,0.422901,1.00724,0.567849,0.331666,1.4708,0.8786,0.115924,0.699779,0.233152,0.850049,0.9301,0.975524,1.03933,0.212784,1.3312,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,0.260275,0.436593,1.7082,0.214583,0.111457,0.128142,0.434542,0.733963,0.077277,0.352111,0.81211,0.382849,0.128633,0.204546,0.60983,0.93695,0.670634,0.568261,0.199399,0.480505,0.345769,0.0978842,0.313326,0.0488031
|tfbs_overrepresentation_jaspar=MA0003.1;0.985719,MA0004.1;0.67248,MA0006.1;0.37642,MA0007.1;0.227553,MA0009.1;0.623671,MA0014.1;0.0468601,MA0017.1;0.420732,MA0019.1;0.456268,MA0024.1;0.582844,MA0025.1;0.845702,MA0027.1;2.24512,MA0028.1;0.393672,MA0029.1;0.562703,MA0030.1;0.568779,MA0031.1;0.535959,MA0038.1;0.942753,MA0040.1;0.635404,MA0041.1;0.18185,MA0042.1;0.172351,MA0043.1;0.71494,MA0046.1;0.657417,MA0048.1;0.0239691,MA0050.1;0.270164,MA0051.1;0.366328,MA0052.1;0.642973,MA0055.1;0.0154075,MA0056.1;0,MA0057.1;0.0204801,MA0058.1;0.501197,MA0059.1;0.176308,MA0060.1;0.071412,MA0061.1;0.295622,MA0063.1;0,MA0066.1;2.49109,MA0067.1;0.953264,MA0068.1;0.235061,MA0069.1;0.643292,MA0070.1;0.634186,MA0071.1;0.269487,MA0072.1;0.626238,MA0073.1;0.115588,MA0074.1;1.54107,MA0076.1;0.148159,MA0077.1;0.605975,MA0078.1;0.395048,MA0081.1;0.193203,MA0083.1;0.714187,MA0084.1;1.27474,MA0087.1;0.673355,MA0088.1;1.07775,MA0089.1;0,MA0090.1;0.212772,MA0091.1;0.24961,MA0092.1;1.14922,MA0093.1;0.809981,MA0095.1;0,MA0098.1;0,MA0100.1;0.309116,MA0101.1;0.538493,MA0103.1;0.14251,MA0105.1;0.341877,MA0106.1;0.401864,MA0107.1;0.428571,MA0108.2;0.476838,MA0109.1;0,MA0111.1;0.223614,MA0113.1;0.377232,MA0114.1;2.08276,MA0115.1;0.717599,MA0116.1;0.37608,MA0117.1;0.686999,MA0119.1;1.03177,MA0122.1;0.705806,MA0124.1;0.901619,MA0125.1;0.830088,MA0130.1;0,MA0131.1;0.452196,MA0132.1;0,MA0133.1;0,MA0135.1;0.749615,MA0136.1;0.335579,MA0139.1;0.45049,MA0140.1;0.30902,MA0141.1;1.47359,MA0142.1;0.522654,MA0143.1;0.391481,MA0144.1;1.53402,MA0145.1;1.15108,MA0146.1;0.56368,MA0147.1;0.651622,MA0148.1;0.70223,MA0149.1;0.18682,MA0062.2;0.154316,MA0035.2;0.84095,MA0039.2;0.611885,MA0138.2;0.445088,MA0002.2;1.21215,MA0137.2;0.467774,MA0104.2;0.495875,MA0047.2;0.941296,MA0112.2;0.320682,MA0065.2;1.96086,MA0150.1;0.227466,MA0151.1;0,MA0152.1;0.358055,MA0153.1;0.765498,MA0154.1;0.247047,MA0155.1;0.369691,MA0156.1;0.147567,MA0157.1;0.493416,MA0158.1;0,MA0159.1;1.12623,MA0160.1;0.707761,MA0161.1;0,MA0162.1;0.0853381,MA0163.1;0.00798568,MA0164.1;0.335886,MA0080.2;0.430071,MA0018.2;0.344133,MA0099.2;0.439458,MA0079.2;2.17938e-06,MA0102.2;1.32652,MA0258.1;0.572032,MA0259.1;0.621948,MA0442.1;0
}}
}}

Revision as of 11:50, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:80081660..80081667,-p@chr12:80081660..80081667
-
Mm9::chr13:41942916..41942930,-p7@9530008L14Rik
Mm9::chr14:59819868..59819890,+p5@Rcbtb1
Mm9::chr17:34741829..34741866,+p6@Agpat1
Mm9::chr17:34741874..34741896,+p8@Agpat1
Mm9::chr17:34742434..34742443,+p16@Agpat1
Mm9::chr19:32135843..32135852,-p8@Asah2
Mm9::chr19:32135856..32135871,-p5@Asah2
Mm9::chr2:29659138..29659154,+p@chr2:29659138..29659154
+
Mm9::chr2:29659170..29659180,+p@chr2:29659170..29659180
+
Mm9::chr7:52970037..52970048,-p@chr7:52970037..52970048
-
Mm9::chr7:52970050..52970066,-p@chr7:52970050..52970066
-
Mm9::chr7:52970068..52970099,-p4@Sphk2
Mm9::chr8:26864686..26864722,-p2@Ddhd2
Mm9::chr8:26864824..26864896,-p1@Ddhd2


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:0006629lipid metabolic process0.000103886642702824
GO:0006643membrane lipid metabolic process0.00102577637870691
GO:0044255cellular lipid metabolic process0.00102577637870691
GO:0006665sphingolipid metabolic process0.00433710004817991
GO:0046467membrane lipid biosynthetic process0.00771790938475867
GO:0017050D-erythro-sphingosine kinase activity0.00771790938475867
GO:0046511sphinganine biosynthetic process0.00771790938475867
GO:0006669sphinganine-1-phosphate biosynthetic process0.00771790938475867
GO:0006667sphinganine metabolic process0.0112242048383209
GO:0008481sphinganine kinase activity0.0112242048383209
GO:0006668sphinganine-1-phosphate metabolic process0.0112242048383209
GO:0006670sphingosine metabolic process0.0154307449992403
GO:0017040ceramidase activity0.0264396648314999
GO:0046520sphingoid biosynthetic process0.0264396648314999
GO:0008610lipid biosynthetic process0.0346849533115712
GO:00038411-acylglycerol-3-phosphate O-acyltransferase activity0.0346849533115712
GO:0004467long-chain-fatty-acid-CoA ligase activity0.0381467145022446
GO:0007205protein kinase C activation0.0381467145022446
GO:0004143diacylglycerol kinase activity0.0381467145022446
GO:0015645fatty-acid ligase activity0.0381467145022446
GO:0016411acylglycerol O-acyltransferase activity0.0381467145022446
GO:0001676long-chain fatty acid metabolic process0.0392073114929924
GO:0030148sphingolipid biosynthetic process0.0401748033217997
GO:0044238primary metabolic process0.048660483088478



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>

Uber Anatomy
Ontology termp-valuen
intestine8.39e-2731
gastrointestinal system9.96e-2147
mucosa6.80e-1615
intestinal mucosa3.45e-1313
anatomical wall3.45e-1313
wall of intestine3.45e-1313
gastrointestinal system mucosa3.45e-1313
organ component layer1.49e-0824
epithelium of mucosa4.26e-089
gastrointestinal system epithelium4.26e-089
intestinal epithelium4.26e-089


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)
MA0003.10.985719
MA0004.10.67248
MA0006.10.37642
MA0007.10.227553
MA0009.10.623671
MA0014.10.0468601
MA0017.10.420732
MA0019.10.456268
MA0024.10.582844
MA0025.10.845702
MA0027.12.24512
MA0028.10.393672
MA0029.10.562703
MA0030.10.568779
MA0031.10.535959
MA0038.10.942753
MA0040.10.635404
MA0041.10.18185
MA0042.10.172351
MA0043.10.71494
MA0046.10.657417
MA0048.10.0239691
MA0050.10.270164
MA0051.10.366328
MA0052.10.642973
MA0055.10.0154075
MA0056.10
MA0057.10.0204801
MA0058.10.501197
MA0059.10.176308
MA0060.10.071412
MA0061.10.295622
MA0063.10
MA0066.12.49109
MA0067.10.953264
MA0068.10.235061
MA0069.10.643292
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.10.115588
MA0074.11.54107
MA0076.10.148159
MA0077.10.605975
MA0078.10.395048
MA0081.10.193203
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.11.07775
MA0089.10
MA0090.10.212772
MA0091.10.24961
MA0092.11.14922
MA0093.10.809981
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.538493
MA0103.10.14251
MA0105.10.341877
MA0106.10.401864
MA0107.10.428571
MA0108.20.476838
MA0109.10
MA0111.10.223614
MA0113.10.377232
MA0114.12.08276
MA0115.10.717599
MA0116.10.37608
MA0117.10.686999
MA0119.11.03177
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.10.452196
MA0132.10
MA0133.10
MA0135.10.749615
MA0136.10.335579
MA0139.10.45049
MA0140.10.30902
MA0141.11.47359
MA0142.10.522654
MA0143.10.391481
MA0144.11.53402
MA0145.11.15108
MA0146.10.56368
MA0147.10.651622
MA0148.10.70223
MA0149.10.18682
MA0062.20.154316
MA0035.20.84095
MA0039.20.611885
MA0138.20.445088
MA0002.21.21215
MA0137.20.467774
MA0104.20.495875
MA0047.20.941296
MA0112.20.320682
MA0065.21.96086
MA0150.10.227466
MA0151.10
MA0152.10.358055
MA0153.10.765498
MA0154.10.247047
MA0155.10.369691
MA0156.10.147567
MA0157.10.493416
MA0158.10
MA0159.11.12623
MA0160.10.707761
MA0161.10
MA0162.10.0853381
MA0163.10.00798568
MA0164.10.335886
MA0080.20.430071
MA0018.20.344133
MA0099.20.439458
MA0079.22.17938e-06
MA0102.21.32652
MA0258.10.572032
MA0259.10.621948
MA0442.10
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