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MCL coexpression mm9:441: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0042359;vitamin D metabolic process;0.00175313647071714;14473!GO:0005499;vitamin D binding;0.00175313647071714;14473!GO:0051183;vitamin transporter activity;0.00204532588250333;14473!GO:0006775;fat-soluble vitamin metabolic process;0.00482112529447214;14473!GO:0005496;steroid binding;0.00823974141237057;14473!GO:0006766;vitamin metabolic process;0.00905787176537191;14473!GO:0019842;vitamin binding;0.0131485235303786;14473!GO:0003779;actin binding;0.0265161891195968;14473!GO:0008092;cytoskeletal protein binding;0.0325304211788626;14473!}}
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D metabolic process;0.00175313647071714;14473!GO:0005499;vitamin D binding;0.00175313647071714;14473!GO:0051183;vitamin transporter activity;0.00204532588250333;14473!GO:0006775;fat-soluble vitamin metabolic process;0.00482112529447214;14473!GO:0005496;steroid binding;0.00823974141237057;14473!GO:0006766;vitamin metabolic process;0.00905787176537191;14473!GO:0019842;vitamin binding;0.0131485235303786;14473!GO:0003779;actin binding;0.0265161891195968;14473!GO:0008092;cytoskeletal protein binding;0.0325304211788626;14473!|ontology_enrichment_celltype=CL:0000066!5.79e-08!25;CL:0002563!1.26e-07!9;CL:0002251!1.26e-07!9;CL:0000838!1.61e-07!12;CL:0000084!6.40e-07!11;CL:0000827!6.40e-07!11;CL:0000542!6.65e-07!13;CL:0000051!6.65e-07!13;CL:0000791!7.94e-07!9;CL:0000789!7.94e-07!9;CL:0002420!7.94e-07!9;CL:0002419!7.94e-07!9;CL:0000790!7.94e-07!9;CL:0002242!8.41e-07!16|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000344!3.72e-09!15;UBERON:0001242!1.41e-08!13;UBERON:0000060!1.41e-08!13;UBERON:0001262!1.41e-08!13;UBERON:0004786!1.41e-08!13;UBERON:0000485!2.39e-08!11;UBERON:0003350!1.26e-07!9;UBERON:0004808!1.26e-07!9;UBERON:0001277!1.26e-07!9;UBERON:0000490!4.04e-07!66|tfbs_overrepresentation_for_novel_motifs=1.00028,1.45774,0.157426,0.205657,0.0882392,0.216369,0.286882,0.376224,0.398834,1.19267,0.252112,0.277243,1.47689,0.296787,0.0975425,0,0.46143,0.285124,0.341555,0.53564,0.133242,0.585659,0.296055,0.294623,0.16256,0.319311,0.322606,0.232181,0.366819,1.05093,0.630968,0.552579,0.590954,0.279585,0.66368,0.373683,0.268195,0.753507,0.237064,0.43804,0.0860512,0.640129,0.33101,0.0986861,0.616787,0.573949,0.391673,0.244272,0.138979,0.37148,1.13348,0.905152,1.00774,0.683824,0.700221,0.817643,0.121631,0.736893,0.302464,0.300938,0.534331,0.349585,0.192373,0.43605,0.838156,0.471894,0.829699,1.16897,0.530087,1.02503,0.873486,0.17272,0.898377,0.731855,0.120421,0.791451,0.279429,0.994033,0.518764,0.835355,0.174228,0.476893,0.348372,0.157538,0.623727,0.572181,0.0831859,0.439688,0.395899,1.32869,0.896685,0.62835,0.564287,0.0914951,0.499944,0.0567726,0.661557,1.39136,0.391893,0.614116,1.43314,0.552324,0.667487,0.446498,0.445567,1.19572,0.498793,0.241171,0.43037,0.418437,0.980265,0.669156,0.136675,0.256145,0.903482,0.288262,0.346208,0.208431,0.462587,0.262826,0.736964,0.4177,0.320815,0.381122,0.955823,0.522111,0.293459,1.37283,0.828246,0.310322,0.651613,0.200314,0.799981,0.313768,0.92434,0.0946587,0.181334,0.226479,0.876916,1.69384,1.29725,0.834212,0.330794,0.562149,0.439856,0.225756,0.394362,1.65442,0.183006,0.299565,0.236,0.523888,0.685297,0.215456,0.313008,0.762455,0.342508,0.694768,0.516355,1.0234,0.886073,0.622933,0.522515,0.168927,0.436947,0.306938,0.266569,0.275979,2.73141|tfbs_overrepresentation_jaspar=MA0003.1;0.88149,MA0004.1;0.206012,MA0006.1;0.650564,MA0007.1;0.56814,MA0009.1;0.576798,MA0014.1;2.32027,MA0017.1;0.356464,MA0019.1;0.413421,MA0024.1;0.536784,MA0025.1;0.795679,MA0027.1;2.19092,MA0028.1;1.12427,MA0029.1;0.51708,MA0030.1;0.523021,MA0031.1;0.490954,MA0038.1;0.855094,MA0040.1;0.588314,MA0041.1;0.152751,MA0042.1;0.144042,MA0043.1;0.666547,MA0046.1;0.609938,MA0048.1;0.373835,MA0050.1;0.235075,MA0051.1;0.326637,MA0052.1;0.595747,MA0055.1;0.0306466,MA0056.1;0,MA0057.1;1.19127,MA0058.1;0.139612,MA0059.1;0.451977,MA0060.1;4.09652,MA0061.1;1.33602,MA0063.1;0,MA0066.1;0.310219,MA0067.1;0.902253,MA0068.1;0.0143498,MA0069.1;0.59606,MA0070.1;0.587119,MA0071.1;0.234437,MA0072.1;0.579318,MA0073.1;0.00260795,MA0074.1;0.281183,MA0076.1;1.26377,MA0077.1;0.559443,MA0078.1;0.354249,MA0081.1;0.950346,MA0083.1;5.23727,MA0084.1;1.22195,MA0087.1;0.625609,MA0088.1;0.871568,MA0089.1;0,MA0090.1;0.181323,MA0091.1;0.215731,MA0092.1;0.181545,MA0093.1;0.105788,MA0095.1;0,MA0098.1;0,MA0100.1;0.271974,MA0101.1;0.910487,MA0103.1;0.116929,MA0105.1;2.585,MA0106.1;1.68921,MA0107.1;0.73481,MA0108.2;1.10626,MA0109.1;0,MA0111.1;1.67806,MA0113.1;0.337108,MA0114.1;1.32388,MA0115.1;0.669167,MA0116.1;1.08249,MA0117.1;0.639033,MA0119.1;0.154009,MA0122.1;0.657549,MA0124.1;0.851049,MA0125.1;0.780232,MA0130.1;0,MA0131.1;1.85698,MA0132.1;0,MA0133.1;0,MA0135.1;0.700734,MA0136.1;0.805431,MA0139.1;1.93849,MA0140.1;0.747831,MA0141.1;0.405018,MA0142.1;0.477975,MA0143.1;0.350815,MA0144.1;0.0688535,MA0145.1;0.938465,MA0146.1;1.02566,MA0147.1;0.552127,MA0148.1;0.218033,MA0149.1;0.157322,MA0062.2;1.6347,MA0035.2;0.756371,MA0039.2;4.95061,MA0138.2;0.402586,MA0002.2;0.164166,MA0137.2;0.127311,MA0104.2;0.720139,MA0047.2;0.318614,MA0112.2;0.654297,MA0065.2;2.06468,MA0150.1;0.195003,MA0151.1;0,MA0152.1;0.318703,MA0153.1;0.716409,MA0154.1;1.26673,MA0155.1;1.40943,MA0156.1;0.77202,MA0157.1;0.4495,MA0158.1;0,MA0159.1;1.45645,MA0160.1;0.220282,MA0161.1;0,MA0162.1;0.918106,MA0163.1;2.02401,MA0164.1;0.297489,MA0080.2;0.737223,MA0018.2;0.305372,MA0099.2;0.397135,MA0079.2;5.51712,MA0102.2;1.27355,MA0258.1;0.0609037,MA0259.1;0.524511,MA0442.1;0}}

Latest revision as of 15:18, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:98724343..98724360,-p@chr10:98724343..98724360
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Mm9::chr11:20531724..20531728,-p@chr11:20531724..20531728
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Mm9::chr11:69571790..69571798,+p@chr11:69571790..69571798
+
Mm9::chr11:87405214..87405225,-p@chr11:87405214..87405225
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Mm9::chr13:114584613..114584618,-p@chr13:114584613..114584618
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Mm9::chr15:89026611..89026618,+p@chr15:89026611..89026618
+
Mm9::chr17:26853167..26853205,-p@chr17:26853167..26853205
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Mm9::chr19:53603451..53603479,-p@chr19:53603451..53603479
-
Mm9::chr3:107949118..107949141,+p@chr3:107949118..107949141
+
Mm9::chr4:115726172..115726197,+p@chr4:115726172..115726197
+
Mm9::chr4:33335638..33335658,+p@chr4:33335638..33335658
+
Mm9::chr5:122287292..122287303,+p@chr5:122287292..122287303
+
Mm9::chr5:130732674..130732679,-p@chr5:130732674..130732679
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Mm9::chr5:31189981..31189985,+p@chr5:31189981..31189985
+
Mm9::chr6:113027175..113027197,-p1@ENSMUST00000167415
Mm9::chr7:52962498..52962512,+p12@Dbp
Mm9::chr9:61970795..61970798,+p@chr9:61970795..61970798
+


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:0042359vitamin D metabolic process0.00175313647071714
GO:0005499vitamin D binding0.00175313647071714
GO:0051183vitamin transporter activity0.00204532588250333
GO:0006775fat-soluble vitamin metabolic process0.00482112529447214
GO:0005496steroid binding0.00823974141237057
GO:0006766vitamin metabolic process0.00905787176537191
GO:0019842vitamin binding0.0131485235303786
GO:0003779actin binding0.0265161891195968
GO:0008092cytoskeletal protein binding0.0325304211788626



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>


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)
MA0003.10.88149
MA0004.10.206012
MA0006.10.650564
MA0007.10.56814
MA0009.10.576798
MA0014.12.32027
MA0017.10.356464
MA0019.10.413421
MA0024.10.536784
MA0025.10.795679
MA0027.12.19092
MA0028.11.12427
MA0029.10.51708
MA0030.10.523021
MA0031.10.490954
MA0038.10.855094
MA0040.10.588314
MA0041.10.152751
MA0042.10.144042
MA0043.10.666547
MA0046.10.609938
MA0048.10.373835
MA0050.10.235075
MA0051.10.326637
MA0052.10.595747
MA0055.10.0306466
MA0056.10
MA0057.11.19127
MA0058.10.139612
MA0059.10.451977
MA0060.14.09652
MA0061.11.33602
MA0063.10
MA0066.10.310219
MA0067.10.902253
MA0068.10.0143498
MA0069.10.59606
MA0070.10.587119
MA0071.10.234437
MA0072.10.579318
MA0073.10.00260795
MA0074.10.281183
MA0076.11.26377
MA0077.10.559443
MA0078.10.354249
MA0081.10.950346
MA0083.15.23727
MA0084.11.22195
MA0087.10.625609
MA0088.10.871568
MA0089.10
MA0090.10.181323
MA0091.10.215731
MA0092.10.181545
MA0093.10.105788
MA0095.10
MA0098.10
MA0100.10.271974
MA0101.10.910487
MA0103.10.116929
MA0105.12.585
MA0106.11.68921
MA0107.10.73481
MA0108.21.10626
MA0109.10
MA0111.11.67806
MA0113.10.337108
MA0114.11.32388
MA0115.10.669167
MA0116.11.08249
MA0117.10.639033
MA0119.10.154009
MA0122.10.657549
MA0124.10.851049
MA0125.10.780232
MA0130.10
MA0131.11.85698
MA0132.10
MA0133.10
MA0135.10.700734
MA0136.10.805431
MA0139.11.93849
MA0140.10.747831
MA0141.10.405018
MA0142.10.477975
MA0143.10.350815
MA0144.10.0688535
MA0145.10.938465
MA0146.11.02566
MA0147.10.552127
MA0148.10.218033
MA0149.10.157322
MA0062.21.6347
MA0035.20.756371
MA0039.24.95061
MA0138.20.402586
MA0002.20.164166
MA0137.20.127311
MA0104.20.720139
MA0047.20.318614
MA0112.20.654297
MA0065.22.06468
MA0150.10.195003
MA0151.10
MA0152.10.318703
MA0153.10.716409
MA0154.11.26673
MA0155.11.40943
MA0156.10.77202
MA0157.10.4495
MA0158.10
MA0159.11.45645
MA0160.10.220282
MA0161.10
MA0162.10.918106
MA0163.12.02401
MA0164.10.297489
MA0080.20.737223
MA0018.20.305372
MA0099.20.397135
MA0079.25.51712
MA0102.21.27355
MA0258.10.0609037
MA0259.10.524511
MA0442.10
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