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MCL coexpression mm9:173: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002113!2.18e-22!14;UBERON:0003918!2.18e-22!14;UBERON:0011143!2.18e-22!14;UBERON:0005095!2.18e-22!14;UBERON:0007687!2.18e-22!14;UBERON:0006554!7.29e-17!18;UBERON:0001008!7.59e-16!19;UBERON:0000489!4.20e-14!21
|tfbs_overrepresentation_for_novel_motifs=0.244077,1.0564,0.20042,0.322992,0.551837,0.882841,0.129441,0.0660164,0.864552,0.146126,1.08087,0.844687,0.604135,0.139319,0.62811,0,0.339509,0.0571397,0.369859,0.612439,0.925879,0.40397,0.138579,0.544986,0.377843,1.46194,1.79101,0.0805072,0.35387,0.108756,0.0721666,0.472387,0.341188,0.253009,0.630383,0.215663,0.311861,0.521973,0.0778574,0.175004,0.225486,0.193797,0.971611,0.873411,0.0688642,0.780217,0.902931,0.703929,0.568687,0.362356,0.0961001,0.187558,1.3581,0.243357,0.25518,0.145251,0.233729,0.110621,0.416818,0.143545,0.44482,0.0531464,0.165266,0.631946,0.355731,0.109539,1.66588,0.646267,0.438473,1.2876,0.313358,0.0139323,0.00736362,1.39544,1.31854,0.327668,0.166121,0.506786,0.421662,1.25689,0.0358212,0.361149,0.432862,0.563312,0.583779,0.0503736,1.61861,1.2205,0.538507,0.79385,0.408631,0.204735,0.163079,0.249098,0.236942,0.302655,0.297907,0.956452,0.07057,0.255367,0.312105,0.919148,0.654997,0.65681,0.0958958,0.0162974,0.124252,0.0878574,0.293048,0.148771,0.914944,0.232932,0.28464,0.466987,0.414266,1.5586,0.171521,0.165964,0.104628,0.860146,0.282295,0.280605,1.47057,1.30855,0.458262,0.137605,0.915283,0.159232,0.352977,0.592041,0.628947,0.308597,1.58312,0.645289,0.431675,0.0220423,0.449062,0.380729,0.392345,1.14356,0.764457,0.357745,0.395364,2.15822,0.0930391,0.0754316,0.535003,1.10524,1.00064,0.775654,0.266966,0.00128726,0.244412,0.471435,0.642858,0.815343,0.188516,0.17926,0.114214,0.124672,0.399868,0.201084,0.42721,0.904257,0.634074,1.39112,0.463194,0.839216,1.0707
|tfbs_overrepresentation_jaspar=MA0003.1;0.0632004,MA0004.1;0.0607877,MA0006.1;0.0292022,MA0007.1;0.50283,MA0009.1;0.170945,MA0014.1;0.0164305,MA0017.1;0.994527,MA0019.1;0.0803114,MA0024.1;0.448499,MA0025.1;0.327256,MA0027.1;1.63269,MA0028.1;0.00954418,MA0029.1;0.419177,MA0030.1;0.427961,MA0031.1;0.381168,MA0038.1;0.371249,MA0040.1;0.5276,MA0041.1;0.0868238,MA0042.1;0.0248852,MA0043.1;0.231094,MA0046.1;7.87961,MA0048.1;0.0389331,MA0050.1;0.210299,MA0051.1;0.170797,MA0052.1;0.539275,MA0055.1;0.0439036,MA0056.1;0,MA0057.1;0.673068,MA0058.1;0.0229365,MA0059.1;0.323426,MA0060.1;0.783891,MA0061.1;0.0815299,MA0063.1;0,MA0066.1;0.0390959,MA0067.1;0.413246,MA0068.1;0.0314929,MA0069.1;0.539768,MA0070.1;0.525728,MA0071.1;0.662772,MA0072.1;2.24041,MA0073.1;0.470194,MA0074.1;0.294981,MA0076.1;0.0160419,MA0077.1;0.48287,MA0078.1;0.202037,MA0081.1;0.21415,MA0083.1;0.230572,MA0084.1;0.694709,MA0087.1;0.586802,MA0088.1;0.0261873,MA0089.1;0,MA0090.1;2.6121,MA0091.1;0.585728,MA0092.1;0.259553,MA0093.1;0.0377307,MA0095.1;0,MA0098.1;0,MA0100.1;0.115136,MA0101.1;0.344922,MA0103.1;0.366015,MA0105.1;0.340614,MA0106.1;0.0575433,MA0107.1;0.532491,MA0108.2;0.301323,MA0109.1;0,MA0111.1;0.13969,MA0113.1;0.408727,MA0114.1;1.5364,MA0115.1;0.657769,MA0116.1;0.0741332,MA0117.1;0.211999,MA0119.1;0.802969,MA0122.1;0.638661,MA0124.1;0.371289,MA0125.1;0.315245,MA0130.1;0,MA0131.1;0.0784825,MA0132.1;0,MA0133.1;0,MA0135.1;0.255553,MA0136.1;0.0349259,MA0139.1;0.00333956,MA0140.1;0.821535,MA0141.1;0.425213,MA0142.1;0.362679,MA0143.1;0.198046,MA0144.1;0.000395324,MA0145.1;0.0980963,MA0146.1;0.0146845,MA0147.1;0.0447292,MA0148.1;0.357007,MA0149.1;0.00567616,MA0062.2;0.000197992,MA0035.2;0.284279,MA0039.2;4.14159e-06,MA0138.2;0.940196,MA0002.2;0.198411,MA0137.2;0.0179716,MA0104.2;0.0163237,MA0047.2;0.660823,MA0112.2;0.391566,MA0065.2;1.34514,MA0150.1;0.053269,MA0151.1;0,MA0152.1;0.0419416,MA0153.1;3.79865,MA0154.1;0.250513,MA0155.1;0.647901,MA0156.1;0.015853,MA0157.1;0.323092,MA0158.1;0,MA0159.1;0.326045,MA0160.1;0.363284,MA0161.1;0,MA0162.1;0.00563035,MA0163.1;0.00667394,MA0164.1;0.327018,MA0080.2;0.0447291,MA0018.2;0.148115,MA0099.2;0.254183,MA0079.2;0.1243,MA0102.2;0.742404,MA0258.1;0.669205,MA0259.1;0.0134254,MA0442.1;0
}}

Latest revision as of 14:49, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:102508936..102508939,-p@chr10:102508936..102508939
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Mm9::chr10:102607555..102607564,-p@chr10:102607555..102607564
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Mm9::chr10:102607602..102607613,-p@chr10:102607602..102607613
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Mm9::chr10:102608111..102608126,-p@chr10:102608111..102608126
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Mm9::chr10:39251651..39251690,+p@chr10:39251651..39251690
+
Mm9::chr10:45527339..45527346,+p4@D030045P18Rik
Mm9::chr10:45527364..45527375,+p3@D030045P18Rik
Mm9::chr10:50614300..50614322,-p@chr10:50614300..50614322
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Mm9::chr10:50614546..50614568,+p1@Sim1
Mm9::chr10:68587785..68587793,-p@chr10:68587785..68587793
-
Mm9::chr10:79277411..79277429,+p@chr10:79277411..79277429
+
Mm9::chr11:75720175..75720186,-p@chr11:75720175..75720186
-
Mm9::chr11:75720190..75720216,-p@chr11:75720190..75720216
-
Mm9::chr11:96112414..96112425,+p3@ENSMUST00000129907
Mm9::chr11:96153767..96153822,+p1@Hoxb6
Mm9::chr11:96168431..96168442,+p@chr11:96168431..96168442
+
Mm9::chr11:96168445..96168469,+p@chr11:96168445..96168469
+
Mm9::chr13:108834249..108834299,+p3@2810008M24Rik
Mm9::chr13:94853445..94853455,+p19@Lhfpl2
Mm9::chr17:86199756..86199767,-p@chr17:86199756..86199767
-
Mm9::chr19:44821081..44821112,+p@chr19:44821081..44821112
+
Mm9::chr19:44821149..44821161,+p@chr19:44821149..44821161
+
Mm9::chr19:44821192..44821202,+p@chr19:44821192..44821202
+
Mm9::chr19:44825291..44825299,-p@chr19:44825291..44825299
-
Mm9::chr19:44831187..44831204,+p@chr19:44831187..44831204
+
Mm9::chr19:44911831..44911835,+p@chr19:44911831..44911835
+
Mm9::chr1:14294623..14294631,-p14@Eya1
Mm9::chr1:75014856..75014870,-p@chr1:75014856..75014870
-
Mm9::chr2:160787107..160787116,-p6@Chd6
Mm9::chr2:163317391..163317413,+p@chr2:163317391..163317413
+
Mm9::chr2:33743382..33743397,-p6@Fam125b
Mm9::chr2:62250373..62250392,-p6@Dpp4
Mm9::chr2:74971729..74971738,-p@chr2:74971729..74971738
-
Mm9::chr2:74971765..74971779,-p@chr2:74971765..74971779
-
Mm9::chr2:74971811..74971824,-p@chr2:74971811..74971824
-
Mm9::chr3:29912058..29912071,-p6@Mecom
Mm9::chr3:98231695..98231716,+p@chr3:98231695..98231716
+
Mm9::chr4:82667033..82667039,-p10@Frem1
Mm9::chr5:103854739..103854748,-p@chr5:103854739..103854748
-
Mm9::chr5:103854767..103854780,-p@chr5:103854767..103854780
-
Mm9::chr5:140023924..140023936,+p@chr5:140023924..140023936
+
Mm9::chr5:140023949..140023958,+p@chr5:140023949..140023958
+
Mm9::chr5:142332646..142332665,+p6@Sdk1
Mm9::chr5:24755801..24755819,+p@chr5:24755801..24755819
+
Mm9::chr5:68004442..68004462,+p@chr5:68004442..68004462
+
Mm9::chr5:96803539..96803550,+p@chr5:96803539..96803550
+
Mm9::chr6:139450428..139450439,-p3@Rergl
Mm9::chr6:139450442..139450454,-p2@Rergl
Mm9::chr6:18285749..18285759,+p@chr6:18285749..18285759
+
Mm9::chr6:21936887..21936917,+p9@A430107O13Rik
Mm9::chr6:37996994..37996998,-p1@Svopl
Mm9::chr6:61154837..61154845,+p@chr6:61154837..61154845
+
Mm9::chr7:103681210..103681217,+p@chr7:103681210..103681217
+
Mm9::chr7:103681228..103681249,+p@chr7:103681228..103681249
+
Mm9::chr7:137720372..137720385,+p@chr7:137720372..137720385
+
Mm9::chr8:113605037..113605048,-p@chr8:113605037..113605048
-
Mm9::chr8:113605595..113605630,-p1@Clec18a
Mm9::chr8:113605713..113605724,-p5@Clec18a
Mm9::chr8:113605798..113605816,-p2@Clec18a
Mm9::chr8:118959620..118959632,-p@chr8:118959620..118959632
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Mm9::chr8:86545343..86545374,+p1@Palm3
Mm9::chr8:91566534..91566554,-p@chr8:91566534..91566554
-


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:0001657ureteric bud development0.0187279281203433
GO:0001656metanephros development0.0187279281203433
GO:0031129inductive cell-cell signaling0.0231115008345079
GO:0001822kidney development0.0231115008345079
GO:0001655urogenital system development0.0231115008345079
GO:0045165cell fate commitment0.0307770024211147
GO:0004287prolyl oligopeptidase activity0.0498376918235744



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
kidney2.18e-2214
kidney mesenchyme2.18e-2214
upper urinary tract2.18e-2214
kidney rudiment2.18e-2214
kidney field2.18e-2214
urinary system structure7.29e-1718
renal system7.59e-1619
cavitated compound organ4.20e-1421


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)
MA0003.10.0632004
MA0004.10.0607877
MA0006.10.0292022
MA0007.10.50283
MA0009.10.170945
MA0014.10.0164305
MA0017.10.994527
MA0019.10.0803114
MA0024.10.448499
MA0025.10.327256
MA0027.11.63269
MA0028.10.00954418
MA0029.10.419177
MA0030.10.427961
MA0031.10.381168
MA0038.10.371249
MA0040.10.5276
MA0041.10.0868238
MA0042.10.0248852
MA0043.10.231094
MA0046.17.87961
MA0048.10.0389331
MA0050.10.210299
MA0051.10.170797
MA0052.10.539275
MA0055.10.0439036
MA0056.10
MA0057.10.673068
MA0058.10.0229365
MA0059.10.323426
MA0060.10.783891
MA0061.10.0815299
MA0063.10
MA0066.10.0390959
MA0067.10.413246
MA0068.10.0314929
MA0069.10.539768
MA0070.10.525728
MA0071.10.662772
MA0072.12.24041
MA0073.10.470194
MA0074.10.294981
MA0076.10.0160419
MA0077.10.48287
MA0078.10.202037
MA0081.10.21415
MA0083.10.230572
MA0084.10.694709
MA0087.10.586802
MA0088.10.0261873
MA0089.10
MA0090.12.6121
MA0091.10.585728
MA0092.10.259553
MA0093.10.0377307
MA0095.10
MA0098.10
MA0100.10.115136
MA0101.10.344922
MA0103.10.366015
MA0105.10.340614
MA0106.10.0575433
MA0107.10.532491
MA0108.20.301323
MA0109.10
MA0111.10.13969
MA0113.10.408727
MA0114.11.5364
MA0115.10.657769
MA0116.10.0741332
MA0117.10.211999
MA0119.10.802969
MA0122.10.638661
MA0124.10.371289
MA0125.10.315245
MA0130.10
MA0131.10.0784825
MA0132.10
MA0133.10
MA0135.10.255553
MA0136.10.0349259
MA0139.10.00333956
MA0140.10.821535
MA0141.10.425213
MA0142.10.362679
MA0143.10.198046
MA0144.10.000395324
MA0145.10.0980963
MA0146.10.0146845
MA0147.10.0447292
MA0148.10.357007
MA0149.10.00567616
MA0062.20.000197992
MA0035.20.284279
MA0039.24.14159e-06
MA0138.20.940196
MA0002.20.198411
MA0137.20.0179716
MA0104.20.0163237
MA0047.20.660823
MA0112.20.391566
MA0065.21.34514
MA0150.10.053269
MA0151.10
MA0152.10.0419416
MA0153.13.79865
MA0154.10.250513
MA0155.10.647901
MA0156.10.015853
MA0157.10.323092
MA0158.10
MA0159.10.326045
MA0160.10.363284
MA0161.10
MA0162.10.00563035
MA0163.10.00667394
MA0164.10.327018
MA0080.20.0447291
MA0018.20.148115
MA0099.20.254183
MA0079.20.1243
MA0102.20.742404
MA0258.10.669205
MA0259.10.0134254
MA0442.10
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