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MCL coexpression mm9:550: Difference between revisions

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{{MCL_coexpression_mm9
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deaminase activity;0.0398565399935037;21744!GO:0019239;deaminase activity;0.0398565399935037;21744!GO:0016814;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines;0.0398565399935037;21744!GO:0003725;double-stranded RNA binding;0.0398565399935037;21744!GO:0007286;spermatid development;0.0449441648598232;21744!GO:0048515;spermatid differentiation;0.0449441648598232;21744!|ontology_enrichment_celltype=CL:0000239!1.76e-28!6;CL:0000677!1.76e-28!6;CL:0000212!1.76e-28!6;CL:0000584!1.76e-28!6;CL:0000075!2.30e-24!7;CL:0002563!7.21e-19!9;CL:0002251!7.21e-19!9;CL:0000627!7.91e-15!3;CL:0000682!7.91e-15!3;CL:0000066!2.63e-14!25;CL:0002076!3.79e-11!15;CL:0000223!3.06e-08!20|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000344!3.68e-44!15;UBERON:0001242!4.16e-35!13;UBERON:0000060!4.16e-35!13;UBERON:0001262!4.16e-35!13;UBERON:0004786!4.16e-35!13;UBERON:0000160!2.72e-27!31;UBERON:0004923!5.92e-27!24;UBERON:0003350!7.21e-19!9;UBERON:0004808!7.21e-19!9;UBERON:0001277!7.21e-19!9;UBERON:0005409!2.74e-17!47;UBERON:0000485!2.30e-15!11;UBERON:0000331!9.81e-15!3;UBERON:0002116!9.81e-15!3;UBERON:0001204!9.81e-15!3;UBERON:0001168!9.81e-15!3;UBERON:0002108!3.45e-11!4;UBERON:0001962!5.33e-11!2;UBERON:0001961!5.33e-11!2;UBERON:0001744!5.33e-11!2;UBERON:0001007!5.85e-08!116;UBERON:0001555!5.85e-08!116;UBERON:0007026!5.85e-08!116;UBERON:0004119!8.82e-08!118;UBERON:0000925!8.82e-08!118;UBERON:0006595!8.82e-08!118;UBERON:0002465!1.32e-07!3|tfbs_overrepresentation_for_novel_motifs=0.244604,0.0867717,0.223558,0.765013,1.37055,0.291576,0.370193,0.268276,0.0833551,0.282547,0.331725,0.35958,0.0780266,0.381063,0.15081,0,0.557619,0.133477,0.524522,0.119642,0.194751,0.634211,0.38026,0.427399,0.229596,0.405649,0.0651848,0.309422,0.171781,0.384773,0.297405,0.653099,0.412165,0.447379,0.460714,0.195932,0.125578,0.356403,0.358188,0.0929685,0.836384,0.301802,0.347242,0.463442,0.0153958,0.270091,0.48361,0.322976,0.742531,0.517045,0.541299,0.429887,0.366754,0.788877,0.805733,0.387424,0.533349,0.348382,0.218496,0.385607,0.634076,0.438439,0.302747,0.5308,0.397364,0.568642,0.938213,1.28193,0.629645,1.13654,0.208654,0.583711,0.0186364,0.838198,0.0571922,0.427563,0.447182,0.473159,0.617814,0.575143,0.587166,0.573903,0.437131,0.0742829,0.72691,0.00415894,0.0297453,0.385151,1.22406,1.44275,1.0064,0.731688,0.665283,0.440626,0.108477,1.09934,0.948949,0.667958,0.483845,0.597503,0.790338,0.652833,0.772062,0.541854,0.54087,0.301427,0.596902,0.319507,0.201775,0.196131,0.238877,0.773781,0.19888,0.336214,1.01331,0.41985,0.037872,0.282562,0.558838,0.389429,0.843435,0.511336,0.407285,0.472327,1.06644,0.621313,0.377415,0.658832,0.936732,0.145259,0.755703,0.273302,0.907893,0.399614,1.03449,0.377676,0.251471,0.303003,0.986296,1.80931,1.41113,0.942814,0.418119,0.66306,0.53483,0.302189,0.486482,1.76978,0.253405,0.433248,0.0455135,0.0139939,0.790393,0.101059,0.398786,0.869538,1.10066,1.49437,0.242603,0.251242,0.995609,0.726089,0.621734,0.237049,0.531751,0.392164,0.12482,0.358185,0.295984|tfbs_overrepresentation_jaspar=MA0003.1;0.000113023,MA0004.1;0.279808,MA0006.1;0.14766,MA0007.1;0.267314,MA0009.1;0.678286,MA0014.1;0.00137258,MA0017.1;0.166909,MA0019.1;0.506787,MA0024.1;0.636635,MA0025.1;0.9035,MA0027.1;2.3071,MA0028.1;0.155127,MA0029.1;0.616052,MA0030.1;0.622264,MA0031.1;0.588678,MA0038.1;0.405578,MA0040.1;0.690239,MA0041.1;1.82474,MA0042.1;1.12856,MA0043.1;0.771094,MA0046.1;0.712646,MA0048.1;0.0358824,MA0050.1;0.840337,MA0051.1;0.413609,MA0052.1;0.697946,MA0055.1;0.530364,MA0056.1;0,MA0057.1;0.127633,MA0058.1;0.202403,MA0059.1;0.212009,MA0060.1;0.0941959,MA0061.1;0.113212,MA0063.1;0,MA0066.1;0.395746,MA0067.1;1.01206,MA0068.1;0.571204,MA0069.1;0.698271,MA0070.1;0.688999,MA0071.1;0.311956,MA0072.1;0.680902,MA0073.1;1.35097,MA0074.1;0.363923,MA0076.1;0.181159,MA0077.1;0.660245,MA0078.1;0.443468,MA0081.1;0.230351,MA0083.1;0.77033,MA0084.1;1.33532,MA0087.1;0.728855,MA0088.1;0.204026,MA0089.1;0,MA0090.1;0.700834,MA0091.1;0.290854,MA0092.1;1.29646,MA0093.1;0.485518,MA0095.1;0,MA0098.1;0,MA0100.1;0.931999,MA0101.1;0.219061,MA0103.1;0.174916,MA0105.1;0.0530438,MA0106.1;0.450539,MA0107.1;0.170338,MA0108.2;0.527977,MA0109.1;0,MA0111.1;0.727672,MA0113.1;0.424958,MA0114.1;1.19632,MA0115.1;0.773793,MA0116.1;0.147513,MA0117.1;0.742722,MA0119.1;0.219527,MA0122.1;0.761823,MA0124.1;0.959967,MA0125.1;0.887718,MA0130.1;0,MA0131.1;0.502588,MA0132.1;0,MA0133.1;0,MA0135.1;0.806261,MA0136.1;0.38151,MA0139.1;0.262087,MA0140.1;0.931776,MA0141.1;0.18979,MA0142.1;0.575041,MA0143.1;0.439766,MA0144.1;0.1137,MA0145.1;0.0201868,MA0146.1;0.11048,MA0147.1;0.121834,MA0148.1;0.293462,MA0149.1;0.223436,MA0062.2;0.0556611,MA0035.2;0.357786,MA0039.2;0.0345046,MA0138.2;0.495254,MA0002.2;0.563955,MA0137.2;0.187581,MA0104.2;0.0856657,MA0047.2;0.404891,MA0112.2;0.0892873,MA0065.2;0.700231,MA0150.1;0.267221,MA0151.1;0,MA0152.1;1.04455,MA0153.1;0.822355,MA0154.1;0.139881,MA0155.1;0.105935,MA0156.1;0.180505,MA0157.1;0.545026,MA0158.1;0,MA0159.1;0.803691,MA0160.1;0.296006,MA0161.1;0,MA0162.1;0.0186388,MA0163.1;0.0518456,MA0164.1;0.381832,MA0080.2;0.170995,MA0018.2;0.390455,MA0099.2;0.489441,MA0079.2;0.000263132,MA0102.2;1.38728,MA0258.1;0.103004,MA0259.1;0.114734,MA0442.1;0}}
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|coexpression_dpi_cluster_scores_median=0,0.229925105835837,0.162862766291676,0.96220513967641,0.954933533740599,0.0673979504369913,0.380514389891372,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.859720839478819,0.944478504693811,0.197068726315728,0.269868638010351,0.15562217221269,0.563519988889442,0.177265236423641,0.0869754197833955,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.123988367667141,0.101901855392646,0,0,0,0,0,0,0,0.0662136857075299,0,0,0,0,0.0849828766602549,0.0788703512227347,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0004000;adenosine deaminase activity;0.0398565399935037;21744!GO:0019239;deaminase activity;0.0398565399935037;21744!GO:0016814;hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines;0.0398565399935037;21744!GO:0003725;double-stranded RNA binding;0.0398565399935037;21744!GO:0007286;spermatid development;0.0449441648598232;21744!GO:0048515;spermatid differentiation;0.0449441648598232;21744!
}}

Latest revision as of 15:29, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:34618028..34618035,+p@chr10:34618028..34618035
+
Mm9::chr11:27827040..27827043,+p@chr11:27827040..27827043
+
Mm9::chr14:11955268..11955270,+p@chr14:11955268..11955270
+
Mm9::chr19:6058235..6058246,+p6@Fau
Mm9::chr19:6263605..6263632,+p@chr19:6263605..6263632
+
Mm9::chr3:29631752..29631756,+p@chr3:29631752..29631756
+
Mm9::chr3:36961964..36961971,+p6@Adad1
Mm9::chr7:106312893..106312899,+p@chr7:106312893..106312899
+
Mm9::chr8:102187819..102187863,+p1@ENSMUST00000118240
Mm9::chr8:102187902..102187909,+p2@ENSMUST00000118240
Mm9::chr8:14998614..14998618,-p@chr8:14998614..14998618
-
Mm9::chr8:83335499..83335501,+p@chr8:83335499..83335501
+
Mm9::chr9:78104927..78104933,+p1@Gm3776


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:0004000adenosine deaminase activity0.0398565399935037
GO:0019239deaminase activity0.0398565399935037
GO:0016814hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines0.0398565399935037
GO:0003725double-stranded RNA binding0.0398565399935037
GO:0007286spermatid development0.0449441648598232
GO:0048515spermatid differentiation0.0449441648598232



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
mucosa3.68e-4415
intestinal mucosa4.16e-3513
anatomical wall4.16e-3513
wall of intestine4.16e-3513
gastrointestinal system mucosa4.16e-3513
intestine2.72e-2731
organ component layer5.92e-2724
epithelium of mucosa7.21e-199
gastrointestinal system epithelium7.21e-199
intestinal epithelium7.21e-199
gastrointestinal system2.74e-1747
simple columnar epithelium2.30e-1511
ileal mucosa9.81e-153
ileum9.81e-153
mucosa of small intestine9.81e-153
wall of small intestine9.81e-153
small intestine3.45e-114
gut-associated lymphoid tissue5.33e-112
mucosa-associated lymphoid tissue5.33e-112
lymphoid tissue5.33e-112
digestive system5.85e-08116
digestive tract5.85e-08116
primitive gut5.85e-08116
endoderm-derived structure8.82e-08118
endoderm8.82e-08118
presumptive endoderm8.82e-08118
lymphoid system1.32e-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)
MA0003.10.000113023
MA0004.10.279808
MA0006.10.14766
MA0007.10.267314
MA0009.10.678286
MA0014.10.00137258
MA0017.10.166909
MA0019.10.506787
MA0024.10.636635
MA0025.10.9035
MA0027.12.3071
MA0028.10.155127
MA0029.10.616052
MA0030.10.622264
MA0031.10.588678
MA0038.10.405578
MA0040.10.690239
MA0041.11.82474
MA0042.11.12856
MA0043.10.771094
MA0046.10.712646
MA0048.10.0358824
MA0050.10.840337
MA0051.10.413609
MA0052.10.697946
MA0055.10.530364
MA0056.10
MA0057.10.127633
MA0058.10.202403
MA0059.10.212009
MA0060.10.0941959
MA0061.10.113212
MA0063.10
MA0066.10.395746
MA0067.11.01206
MA0068.10.571204
MA0069.10.698271
MA0070.10.688999
MA0071.10.311956
MA0072.10.680902
MA0073.11.35097
MA0074.10.363923
MA0076.10.181159
MA0077.10.660245
MA0078.10.443468
MA0081.10.230351
MA0083.10.77033
MA0084.11.33532
MA0087.10.728855
MA0088.10.204026
MA0089.10
MA0090.10.700834
MA0091.10.290854
MA0092.11.29646
MA0093.10.485518
MA0095.10
MA0098.10
MA0100.10.931999
MA0101.10.219061
MA0103.10.174916
MA0105.10.0530438
MA0106.10.450539
MA0107.10.170338
MA0108.20.527977
MA0109.10
MA0111.10.727672
MA0113.10.424958
MA0114.11.19632
MA0115.10.773793
MA0116.10.147513
MA0117.10.742722
MA0119.10.219527
MA0122.10.761823
MA0124.10.959967
MA0125.10.887718
MA0130.10
MA0131.10.502588
MA0132.10
MA0133.10
MA0135.10.806261
MA0136.10.38151
MA0139.10.262087
MA0140.10.931776
MA0141.10.18979
MA0142.10.575041
MA0143.10.439766
MA0144.10.1137
MA0145.10.0201868
MA0146.10.11048
MA0147.10.121834
MA0148.10.293462
MA0149.10.223436
MA0062.20.0556611
MA0035.20.357786
MA0039.20.0345046
MA0138.20.495254
MA0002.20.563955
MA0137.20.187581
MA0104.20.0856657
MA0047.20.404891
MA0112.20.0892873
MA0065.20.700231
MA0150.10.267221
MA0151.10
MA0152.11.04455
MA0153.10.822355
MA0154.10.139881
MA0155.10.105935
MA0156.10.180505
MA0157.10.545026
MA0158.10
MA0159.10.803691
MA0160.10.296006
MA0161.10
MA0162.10.0186388
MA0163.10.0518456
MA0164.10.381832
MA0080.20.170995
MA0018.20.390455
MA0099.20.489441
MA0079.20.000263132
MA0102.21.38728
MA0258.10.103004
MA0259.10.114734
MA0442.10
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