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MCL coexpression mm9:869: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!1.56e-18!31;UBERON:0002113!4.82e-13!14;UBERON:0003918!4.82e-13!14;UBERON:0011143!4.82e-13!14;UBERON:0005095!4.82e-13!14;UBERON:0007687!4.82e-13!14;UBERON:0005409!2.27e-11!47;UBERON:0000344!5.39e-11!15;UBERON:0006554!1.64e-09!18;UBERON:0000489!3.89e-09!21;UBERON:0001008!7.26e-09!19;UBERON:0001242!1.42e-08!13;UBERON:0000060!1.42e-08!13;UBERON:0001262!1.42e-08!13;UBERON:0004786!1.42e-08!13;UBERON:0003350!6.11e-08!9;UBERON:0004808!6.11e-08!9;UBERON:0001277!6.11e-08!9
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,0.448401,0.538088,0.991481,0.535519,0.170907,0.494602,0.526159,0.992329,0.550255,0.756943,0,0.742571,2.00903,0.483643,0.0887261,0.332107,0.0622758,0.549359,0.258745,0.374936,0.577606,0.153291,0.469052,0.818708,0.118137,0.455168,0.843667,0.250677,0.136998,0.276324,0.903852,0.242032,0.522578,0.631914,0.195877,0.712303,1.16427,0.204736,0.27776,0.0824666,0.423266,0.662995,0.484612,0.386968,0.305876,0.725127,0.604356,0.732634,0.985264,1.00271,0.557354,0.844204,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.236196,1.03623,0.853709,0.131016,0.136938,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.968721,0.920903,0.025519,1.24076,0.376919,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.510015,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.895335,0.499714,1.21576,0.254749,0.946242,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,1.04134,0.261837,0.381863,0.0553085,0.986833,0.598134,0.569994,1.06851,0.605358,1.42739,1.01313,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,1.2562,0.524587,0.0628627
}}

Latest revision as of 16:01, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:69709163..69709181,+p@chr10:69709163..69709181
+
Mm9::chr10:76494975..76495000,+p5@Slc19a1
Mm9::chr10:76495003..76495022,+p7@Slc19a1
Mm9::chr10:76495456..76495492,+p2@Slc19a1
Mm9::chr19:29003616..29003621,-p8@4430402I18Rik
Mm9::chr6:120192714..120192748,-p3@B4galnt3
Mm9::chr6:142762864..142762905,+p1@ENSMUST00000159599
Mm9::chr6:24054140..24054156,-p@chr6:24054140..24054156
-


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:0008518reduced folate carrier activity0.010846937592383
GO:0005542folic acid binding0.0180747624529258
GO:0008376acetylgalactosaminyltransferase activity0.0216849603820765



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
intestine1.56e-1831
kidney4.82e-1314
kidney mesenchyme4.82e-1314
upper urinary tract4.82e-1314
kidney rudiment4.82e-1314
kidney field4.82e-1314
gastrointestinal system2.27e-1147
mucosa5.39e-1115
urinary system structure1.64e-0918
cavitated compound organ3.89e-0921
renal system7.26e-0919
intestinal mucosa1.42e-0813
anatomical wall1.42e-0813
wall of intestine1.42e-0813
gastrointestinal system mucosa1.42e-0813
epithelium of mucosa6.11e-089
gastrointestinal system epithelium6.11e-089
intestinal epithelium6.11e-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)
MA0003.10.016751
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.0611475
MA0017.11.46217
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
MA0046.12.09432
MA0048.10.102483
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.282934
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
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.744556
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.980744
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
MA0089.10
MA0090.11.03628
MA0091.10.447561
MA0092.10.401504
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
MA0114.11.18683
MA0115.10.969632
MA0116.10.747001
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
MA0139.13.76138
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.527241
MA0146.10.385068
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.21.30087
MA0039.21.07211
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.20.0701537
MA0065.20.247168
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.275377
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.0211019
MA0163.10.408151
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.0137335
MA0102.21.59466
MA0258.10.210437
MA0259.10.227035
MA0442.10
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