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MCL coexpression mm9:457: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000160!1.24e-26!31;UBERON:0000344!3.22e-26!15;UBERON:0001242!2.43e-19!13;UBERON:0000060!2.43e-19!13;UBERON:0001262!2.43e-19!13;UBERON:0004786!2.43e-19!13;UBERON:0005409!3.32e-19!47;UBERON:0002108!2.73e-16!4;UBERON:0004923!8.52e-16!24;UBERON:0000331!5.62e-13!3;UBERON:0002116!5.62e-13!3;UBERON:0001204!5.62e-13!3;UBERON:0001168!5.62e-13!3;UBERON:0003350!2.09e-11!9;UBERON:0004808!2.09e-11!9;UBERON:0001277!2.09e-11!9;UBERON:0001962!1.52e-09!2;UBERON:0001961!1.52e-09!2;UBERON:0001744!1.52e-09!2;UBERON:0000485!2.71e-09!11;UBERON:0001155!5.67e-09!2;UBERON:0000059!5.67e-09!2;UBERON:0001007!2.66e-08!116;UBERON:0001555!2.66e-08!116;UBERON:0007026!2.66e-08!116;UBERON:0004119!4.16e-08!118;UBERON:0000925!4.16e-08!118;UBERON:0006595!4.16e-08!118
|ontology_enrichment_uberon=UBERON:0000160!1.24e-26!31;UBERON:0000344!3.22e-26!15;UBERON:0001242!2.43e-19!13;UBERON:0000060!2.43e-19!13;UBERON:0001262!2.43e-19!13;UBERON:0004786!2.43e-19!13;UBERON:0005409!3.32e-19!47;UBERON:0002108!2.73e-16!4;UBERON:0004923!8.52e-16!24;UBERON:0000331!5.62e-13!3;UBERON:0002116!5.62e-13!3;UBERON:0001204!5.62e-13!3;UBERON:0001168!5.62e-13!3;UBERON:0003350!2.09e-11!9;UBERON:0004808!2.09e-11!9;UBERON:0001277!2.09e-11!9;UBERON:0001962!1.52e-09!2;UBERON:0001961!1.52e-09!2;UBERON:0001744!1.52e-09!2;UBERON:0000485!2.71e-09!11;UBERON:0001155!5.67e-09!2;UBERON:0000059!5.67e-09!2;UBERON:0001007!2.66e-08!116;UBERON:0001555!2.66e-08!116;UBERON:0007026!2.66e-08!116;UBERON:0004119!4.16e-08!118;UBERON:0000925!4.16e-08!118;UBERON:0006595!4.16e-08!118
|tfbs_overrepresentation_for_novel_motifs=0.19013,0.196655,0.171413,1.18186,1.10803,1.9025,0.305009,0.416085,0.439801,0.0744694,0.26934,0.295134,0.0498401,0.315149,0.713337,0,0.482714,0.645746,0.043517,0.359873,0.878946,0.115953,0.3144,0.322638,0.176763,0.338177,0.359615,0.248835,0.126301,0.490013,0.237846,0.574932,0.0927567,0.314034,0.108791,0.0966689,0.0875334,0.292182,0.55598,0.0613737,1.61024,0.241862,0.599247,0.109711,0.0210161,0.213039,0.41191,0.26128,0.166243,0.128181,0.467043,0.360991,0.100464,0.7073,0.723811,0.321095,0.133938,0.284741,0.611426,0.319396,0.556492,0.369066,0.215066,0.456979,0.330403,0.493315,0.854035,1.19441,0.552202,1.05011,0.158281,0.19416,0.126616,0.755651,0.0343898,0.297446,0.313869,0.401969,0.540754,0.148967,1.16178,0.498379,0.36783,1.5412,0.646739,0.00141663,0.0019315,0.262344,0.416206,1.35441,0.92132,0.6514,0.586758,0.683646,0.073664,0.85842,0.722691,0.589355,0.412133,0.681961,1.0304,0.574674,0.690844,0.467576,0.466632,0.241519,0.52055,1.32023,0.463457,0.147333,0.185018,0.692526,0.457145,0.273484,0.928143,0.0952498,0.0169638,0.224335,0.483885,1.01531,0.760792,0.438354,0.900811,0.40118,0.980682,0.544138,0.311744,0.580495,0.852575,1.14378,0.67485,0.617809,0.824167,0.332514,0.949083,0.0397143,0.196278,1.26361,0.901468,1.71991,1.32292,0.85857,0.923442,0.584599,0.46084,0.242215,1.06559,1.68046,0.198013,0.0996378,0.110319,0.00625462,0.708784,0.23951,0.331737,0.786435,0.361851,0.746682,0.188342,0.196072,0.910663,0.645939,1.34418,0.183389,0.457889,0.869172,0.293289,0.293837,0.0365208
|tfbs_overrepresentation_for_novel_motifs=0.19013,0.196655,0.171413,1.18186,1.10803,1.9025,0.305009,0.416085,0.439801,0.0744694,0.26934,0.295134,0.0498401,0.315149,0.713337,0,0.482714,0.645746,0.043517,0.359873,0.878946,0.115953,0.3144,0.322638,0.176763,0.338177,0.359615,0.248835,0.126301,0.490013,0.237846,0.574932,0.0927567,0.314034,0.108791,0.0966689,0.0875334,0.292182,0.55598,0.0613737,1.61024,0.241862,0.599247,0.109711,0.0210161,0.213039,0.41191,0.26128,0.166243,0.128181,0.467043,0.360991,0.100464,0.7073,0.723811,0.321095,0.133938,0.284741,0.611426,0.319396,0.556492,0.369066,0.215066,0.456979,0.330403,0.493315,0.854035,1.19441,0.552202,1.05011,0.158281,0.19416,0.126616,0.755651,0.0343898,0.297446,0.313869,0.401969,0.540754,0.148967,1.16178,0.498379,0.36783,1.5412,0.646739,0.00141663,0.0019315,0.262344,0.416206,1.35441,0.92132,0.6514,0.586758,0.683646,0.073664,0.85842,0.722691,0.589355,0.412133,0.681961,1.0304,0.574674,0.690844,0.467576,0.466632,0.241519,0.52055,1.32023,0.463457,0.147333,0.185018,0.692526,0.457145,0.273484,0.928143,0.0952498,0.0169638,0.224335,0.483885,1.01531,0.760792,0.438354,0.900811,0.40118,0.980682,0.544138,0.311744,0.580495,0.852575,1.14378,0.67485,0.617809,0.824167,0.332514,0.949083,0.0397143,0.196278,1.26361,0.901468,1.71991,1.32292,0.85857,0.923442,0.584599,0.46084,0.242215,1.06559,1.68046,0.198013,0.0996378,0.110319,0.00625462,0.708784,0.23951,0.331737,0.786435,0.361851,0.746682,0.188342,0.196072,0.910663,0.645939,1.34418,0.183389,0.457889,0.869172,0.293289,0.293837,0.0365208
|tfbs_overrepresentation_jaspar=MA0003.1;0.000187754,MA0004.1;0.221835,MA0006.1;0.105852,MA0007.1;0.210531,MA0009.1;2.48581,MA0014.1;0.0349468,MA0017.1;0.774877,MA0019.1;0.434009,MA0024.1;0.558971,MA0025.1;0.819843,MA0027.1;2.21717,MA0028.1;0.112137,MA0029.1;0.53905,MA0030.1;0.545058,MA0031.1;0.512616,MA0038.1;0.33811,MA0040.1;0.611015,MA0041.1;0.498821,MA0042.1;0.15744,MA0043.1;0.689898,MA0046.1;0.632833,MA0048.1;0.0196258,MA0050.1;0.251816,MA0051.1;0.345658,MA0052.1;0.618515,MA0055.1;0.0395234,MA0056.1;0,MA0057.1;0.0760759,MA0058.1;0.152805,MA0059.1;0.161227,MA0060.1;0.0623353,MA0061.1;3.93887,MA0063.1;0,MA0066.1;0.876672,MA0067.1;0.92691,MA0068.1;0.0176199,MA0069.1;0.618831,MA0070.1;0.609808,MA0071.1;0.251158,MA0072.1;0.601934,MA0073.1;7.10148e-08,MA0074.1;0.299171,MA0076.1;0.134359,MA0077.1;2.42907,MA0078.1;0.976277,MA0081.1;0.525479,MA0083.1;0.68915,MA0084.1;1.24749,MA0087.1;1.56303,MA0088.1;0.120779,MA0089.1;0,MA0090.1;0.196267,MA0091.1;0.231874,MA0092.1;0.196497,MA0093.1;0.11723,MA0095.1;0,MA0098.1;0,MA0100.1;0.788514,MA0101.1;2.93628,MA0103.1;0.404646,MA0105.1;1.71592,MA0106.1;0.380511,MA0107.1;4.00331,MA0108.2;0.454274,MA0109.1;0,MA0111.1;0.206727,MA0113.1;0.356344,MA0114.1;0.263654,MA0115.1;0.692537,MA0116.1;0.105729,MA0117.1;0.662171,MA0119.1;0.502046,MA0122.1;0.680832,MA0124.1;2.0318,MA0125.1;0.804312,MA0130.1;0,MA0131.1;0.43,MA0132.1;0,MA0133.1;0,MA0135.1;0.724328,MA0136.1;2.32699,MA0139.1;0.181201,MA0140.1;0.788302,MA0141.1;0.141822,MA0142.1;0.499475,MA0143.1;0.37032,MA0144.1;0.566612,MA0145.1;0.277688,MA0146.1;0.0504792,MA0147.1;0.0844713,MA0148.1;0.23425,MA0149.1;0.171305,MA0062.2;0.315856,MA0035.2;0.796986,MA0039.2;0.000979253,MA0138.2;0.423003,MA0002.2;0.728364,MA0137.2;0.139909,MA0104.2;0.0556953,MA0047.2;0.337465,MA0112.2;0.135501,MA0065.2;0.479069,MA0150.1;0.210447,MA0151.1;0,MA0152.1;0.896007,MA0153.1;0.740107,MA0154.1;1.38057,MA0155.1;0.16166,MA0156.1;3.34068,MA0157.1;0.47062,MA0158.1;0,MA0159.1;0.0900717,MA0160.1;0.23657,MA0161.1;0,MA0162.1;0.000977979,MA0163.1;0.000767531,MA0164.1;0.847515,MA0080.2;0.790324,MA0018.2;0.323932,MA0099.2;0.417463,MA0079.2;2.87812e-08,MA0102.2;1.29919,MA0258.1;0.24394,MA0259.1;0.0787033,MA0442.1;0
}}
}}

Revision as of 11:47, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:88202891..88202898,+p@chr10:88202891..88202898
+
Mm9::chr10:89055671..89055697,-p@chr10:89055671..89055697
-
Mm9::chr11:101797987..101797999,+p@chr11:101797987..101797999
+
Mm9::chr15:74647718..74647727,-p2@Gml
Mm9::chr16:57199200..57199210,-p@chr16:57199200..57199210
-
Mm9::chr17:24112500..24112507,-p3@Prss30
Mm9::chr17:24835294..24835316,+p4@Noxo1
Mm9::chr17:31579883..31579898,+p5@Pde9a
Mm9::chr18:15561204..15561233,-p4@Aqp4
Mm9::chr5:29550488..29550489,+p@chr5:29550488..29550489
+
Mm9::chr6:134193540..134193545,-p1@ENSMUST00000171098
Mm9::chrX:130646305..130646327,-p1@Nox1
Mm9::chrX:130646345..130646353,-p4@Nox1
Mm9::chrX:130646365..130646375,-p3@Nox1
Mm9::chrX:130646391..130646412,-p2@Nox1
Mm9::chrX:136330909..136330938,-p@chrX:136330909..136330938
-


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:0006801superoxide metabolic process0.000219149897867761
GO:0006800oxygen and reactive oxygen species metabolic process0.000423256398957932
GO:0016176superoxide-generating NADPH oxidase activator activity0.00847140396894049
GO:0042554superoxide release0.00847140396894049
GO:0050664oxidoreductase activity, acting on NADH or NADPH, with oxygen as acceptor0.00847140396894049
GO:0016175superoxide-generating NADPH oxidase activity0.00847140396894049
GO:0030104water homeostasis0.010745982262163
GO:00475553',5'-cyclic-GMP phosphodiesterase activity0.010745982262163
GO:0018987osmoregulation0.010745982262163
GO:0015250water channel activity0.010745982262163
GO:0005372water transporter activity0.010745982262163
GO:0006833water transport0.010745982262163
GO:0042044fluid transport0.010745982262163
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.021747829321369
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0219858569324737
GO:0008081phosphoric diester hydrolase activity0.0490826525886069
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.0490826525886069
GO:0050878regulation of body fluid levels0.0491491133962644



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
intestine1.24e-2631
mucosa3.22e-2615
intestinal mucosa2.43e-1913
anatomical wall2.43e-1913
wall of intestine2.43e-1913
gastrointestinal system mucosa2.43e-1913
gastrointestinal system3.32e-1947
small intestine2.73e-164
organ component layer8.52e-1624
ileal mucosa5.62e-133
ileum5.62e-133
mucosa of small intestine5.62e-133
wall of small intestine5.62e-133
epithelium of mucosa2.09e-119
gastrointestinal system epithelium2.09e-119
intestinal epithelium2.09e-119
gut-associated lymphoid tissue1.52e-092
mucosa-associated lymphoid tissue1.52e-092
lymphoid tissue1.52e-092
simple columnar epithelium2.71e-0911
colon5.67e-092
large intestine5.67e-092
digestive system2.66e-08116
digestive tract2.66e-08116
primitive gut2.66e-08116
endoderm-derived structure4.16e-08118
endoderm4.16e-08118
presumptive endoderm4.16e-08118


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)
MA0003.10.000187754
MA0004.10.221835
MA0006.10.105852
MA0007.10.210531
MA0009.12.48581
MA0014.10.0349468
MA0017.10.774877
MA0019.10.434009
MA0024.10.558971
MA0025.10.819843
MA0027.12.21717
MA0028.10.112137
MA0029.10.53905
MA0030.10.545058
MA0031.10.512616
MA0038.10.33811
MA0040.10.611015
MA0041.10.498821
MA0042.10.15744
MA0043.10.689898
MA0046.10.632833
MA0048.10.0196258
MA0050.10.251816
MA0051.10.345658
MA0052.10.618515
MA0055.10.0395234
MA0056.10
MA0057.10.0760759
MA0058.10.152805
MA0059.10.161227
MA0060.10.0623353
MA0061.13.93887
MA0063.10
MA0066.10.876672
MA0067.10.92691
MA0068.10.0176199
MA0069.10.618831
MA0070.10.609808
MA0071.10.251158
MA0072.10.601934
MA0073.17.10148e-08
MA0074.10.299171
MA0076.10.134359
MA0077.12.42907
MA0078.10.976277
MA0081.10.525479
MA0083.10.68915
MA0084.11.24749
MA0087.11.56303
MA0088.10.120779
MA0089.10
MA0090.10.196267
MA0091.10.231874
MA0092.10.196497
MA0093.10.11723
MA0095.10
MA0098.10
MA0100.10.788514
MA0101.12.93628
MA0103.10.404646
MA0105.11.71592
MA0106.10.380511
MA0107.14.00331
MA0108.20.454274
MA0109.10
MA0111.10.206727
MA0113.10.356344
MA0114.10.263654
MA0115.10.692537
MA0116.10.105729
MA0117.10.662171
MA0119.10.502046
MA0122.10.680832
MA0124.12.0318
MA0125.10.804312
MA0130.10
MA0131.10.43
MA0132.10
MA0133.10
MA0135.10.724328
MA0136.12.32699
MA0139.10.181201
MA0140.10.788302
MA0141.10.141822
MA0142.10.499475
MA0143.10.37032
MA0144.10.566612
MA0145.10.277688
MA0146.10.0504792
MA0147.10.0844713
MA0148.10.23425
MA0149.10.171305
MA0062.20.315856
MA0035.20.796986
MA0039.20.000979253
MA0138.20.423003
MA0002.20.728364
MA0137.20.139909
MA0104.20.0556953
MA0047.20.337465
MA0112.20.135501
MA0065.20.479069
MA0150.10.210447
MA0151.10
MA0152.10.896007
MA0153.10.740107
MA0154.11.38057
MA0155.10.16166
MA0156.13.34068
MA0157.10.47062
MA0158.10
MA0159.10.0900717
MA0160.10.23657
MA0161.10
MA0162.10.000977979
MA0163.10.000767531
MA0164.10.847515
MA0080.20.790324
MA0018.20.323932
MA0099.20.417463
MA0079.22.87812e-08
MA0102.21.29919
MA0258.10.24394
MA0259.10.0787033
MA0442.10
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