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MCL coexpression mm9:901: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002113!1.54e-19!14;UBERON:0003918!1.54e-19!14;UBERON:0011143!1.54e-19!14;UBERON:0005095!1.54e-19!14;UBERON:0007687!1.54e-19!14;UBERON:0006554!1.83e-14!18;UBERON:0001008!1.57e-13!19;UBERON:0000489!6.17e-12!21;UBERON:0003135!1.71e-10!15;UBERON:0003101!1.07e-09!16;UBERON:0000079!1.07e-09!16;UBERON:0000473!6.14e-09!14;UBERON:0000991!3.10e-08!18;UBERON:0005564!3.10e-08!18;UBERON:0003133!4.13e-07!24;UBERON:0004176!4.82e-07!17;UBERON:0009196!4.82e-07!17;UBERON:0009117!4.82e-07!17;UBERON:0001301!9.96e-07!3;UBERON:0006555!9.96e-07!3;UBERON:0005103!9.96e-07!3;UBERON:0000083!9.96e-07!3;UBERON:0009201!9.96e-07!3;UBERON:0004819!9.96e-07!3;UBERON:0006553!9.96e-07!3;UBERON:0003074!9.96e-07!3;UBERON:0003060!9.96e-07!3
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.720982,0.448401,0.538088,0.515265,0.181564,0.0447303,0.494602,0.526159,0.173454,0.550255,1.38589,0,0.742571,1.30041,0.483643,0.620214,0.332107,0.0622758,0.549359,0.258745,0.374936,1.41403,0.153291,0.469052,0.303071,0.757024,0.455168,1.96654,0.250677,0.425071,0.757987,0.60397,0.242032,0.522578,0.221921,0.195877,0.712303,0.460258,0.784847,0.27776,0.209497,0.423266,0.662995,0.484612,0.170971,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.877107,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.922232,1.60452,0.0665967,1.03623,0.433216,0.409836,0.136938,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.968721,0.920903,0.025519,2.70874,4.70749,0.667883,1.65055,1.20871,0.925879,0.856465,1.34857,0.218233,0.202284,0.982739,0.859272,0.663249,0.332938,0.679141,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,1.20804,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.0359654,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,1.09252,1.10792,0.570914,1.23736,0.829188,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,0.766041,0.203102,0.986833,0.598134,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.331912
|tfbs_overrepresentation_jaspar=MA0003.1;0.241599,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.162935,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.335404,MA0050.1;0.472794,MA0051.1;1.43259,MA0052.1;0.890676,MA0055.1;1.2091,MA0056.1;0,MA0057.1;0.0935008,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.224905,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.657844,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;1.1212e-05,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.49616,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;1.03695,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.827743,MA0105.1;0.133231,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;0.937363,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.169849,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.225588,MA0145.1;0.527241,MA0146.1;0.198184,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;9.29472,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;0.0706842,MA0138.2;1.61926,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.2464,MA0065.2;0.528619,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.330759,MA0155.1;0.0804339,MA0156.1;0.843735,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.230918,MA0163.1;0.0186439,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.685525,MA0102.2;1.59466,MA0258.1;0.60477,MA0259.1;0.227035,MA0442.1;0
}}

Latest revision as of 16:04, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:34108085..34108092,-p1@Foxi1
Mm9::chr11:96156719..96156721,-p@chr11:96156719..96156721
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Mm9::chr2:74975548..74975563,-p1@ENSMUST00000143898
Mm9::chr7:81210431..81210442,-p@chr7:81210431..81210442
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Mm9::chr7:86741445..86741455,-p@chr7:86741445..86741455
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Mm9::chr7:86741570..86741584,-p@chr7:86741570..86741584
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Mm9::chr7:86741766..86741778,-p@chr7:86741766..86741778
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Mm9::chr7:86762435..86762451,-p1@Rhcg


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:0015696ammonium transport0.0140239391447833
GO:0008519ammonium transmembrane transporter activity0.0140239391447833
GO:0015695organic cation transport0.0140239391447833
GO:0015101organic cation transmembrane transporter activity0.0157760670721659



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
kidney1.54e-1914
kidney mesenchyme1.54e-1914
upper urinary tract1.54e-1914
kidney rudiment1.54e-1914
kidney field1.54e-1914
urinary system structure1.83e-1418
renal system1.57e-1319
cavitated compound organ6.17e-1221
male reproductive organ1.71e-1015
male organism1.07e-0916
male reproductive system1.07e-0916
testis6.14e-0914
gonad3.10e-0818
gonad primordium3.10e-0818
reproductive organ4.13e-0724
external genitalia4.82e-0717
indifferent external genitalia4.82e-0717
indifferent gonad4.82e-0717
epididymis9.96e-073
excretory tube9.96e-073
mesonephric epithelium9.96e-073
mesonephric tubule9.96e-073
nephric duct9.96e-073
kidney epithelium9.96e-073
renal duct9.96e-073
mesonephric duct9.96e-073
pronephric duct9.96e-073


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)
MA0003.10.241599
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.162935
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.335404
MA0050.10.472794
MA0051.11.43259
MA0052.10.890676
MA0055.11.2091
MA0056.10
MA0057.10.0935008
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.657844
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.11.1212e-05
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.49616
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.11.03695
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.827743
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.527241
MA0146.10.198184
MA0147.10.236889
MA0148.10.450593
MA0149.19.29472
MA0062.20.137653
MA0035.20.524137
MA0039.20.0706842
MA0138.21.61926
MA0002.20.172399
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.20.2464
MA0065.20.528619
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.330759
MA0155.10.0804339
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.230918
MA0163.10.0186439
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.685525
MA0102.21.59466
MA0258.10.60477
MA0259.10.227035
MA0442.10
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