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MCL coexpression mm9:993: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!9.33e-17!118;UBERON:0000925!9.33e-17!118;UBERON:0006595!9.33e-17!118;UBERON:0001007!3.65e-16!116;UBERON:0001555!3.65e-16!116;UBERON:0007026!3.65e-16!116;UBERON:0004921!3.85e-15!114;UBERON:0005409!2.79e-10!47;UBERON:0000160!2.03e-09!31;UBERON:0002193!2.90e-08!48;UBERON:0002405!2.90e-08!48;UBERON:0000077!3.14e-08!35;UBERON:0004923!1.55e-07!24;UBERON:0002390!6.07e-07!45;UBERON:0003061!6.07e-07!45;UBERON:0004177!8.75e-07!29;UBERON:0005057!8.75e-07!29;UBERON:0000344!9.13e-07!15
|tfbs_overrepresentation_for_novel_motifs=1.01838,0.121181,0.96259,0.434198,0.260188,0.448401,0.538088,0.173246,0.535519,1.0625,1.23792,0.526159,0.515774,0.550255,0.756943,0,0.742571,0.252772,2.1477,0.620214,0.332107,0.223663,0.549359,0.258745,0.374936,0.577606,0.153291,1.18318,0.303071,0.757024,0.455168,0.843667,0.250677,0.425071,2.13031,0.185086,0.242032,0.522578,0.631914,3.19654,0.256422,0.460258,0.0558565,0.27776,0.209497,0.423266,1.593,0.484612,0.0447507,0.825035,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.140213,1.32088,0.136938,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,2.12473,3.10739,0.293679,0.376919,1.60318,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.585369,0.1711,0.859272,0.663249,0.681235,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,1.20804,0.903338,2.41655,0.386136,0.96962,0.337254,0.499714,1.21576,0.708441,2.33941,1.11602,0.743872,0.238599,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,2.6678,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.724779,1.82213,3.43703,0.986833,1.12835,0.569994,1.06851,0.605358,0.287226,0.39061,2.73712,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,1.56615
|tfbs_overrepresentation_jaspar=MA0003.1;3.57432,MA0004.1;1.10905,MA0006.1;1.37063,MA0007.1;1.07722,MA0009.1;0.870101,MA0014.1;4.67229,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.769859,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;1.13456,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;2.65362,MA0056.1;0,MA0057.1;1.58436,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.224905,MA0063.1;0,MA0066.1;1.39085,MA0067.1;1.21448,MA0068.1;0.0965831,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.312272,MA0074.1;0.531046,MA0076.1;0.845594,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;0.229377,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.787675,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.133231,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;1.06639,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;1.36991,MA0117.1;0.937363,MA0119.1;0.951747,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;0.977634,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;0.615203,MA0144.1;0.640537,MA0145.1;1.87609,MA0146.1;0.946874,MA0147.1;2.70055,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;2.64619,MA0035.2;0.524137,MA0039.2;2.84599,MA0138.2;1.61926,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;3.099,MA0047.2;0.576767,MA0112.2;1.87605,MA0065.2;0.528619,MA0150.1;1.07698,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;1.45843,MA0156.1;0.843735,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.688775,MA0160.1;0.453546,MA0161.1;0,MA0162.1;11.6633,MA0163.1;1.79588,MA0164.1;0.551114,MA0080.2;0.816435,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;12.7454,MA0102.2;1.59466,MA0258.1;0.60477,MA0259.1;2.63282,MA0442.1;0
}}

Latest revision as of 16:13, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr3:30993616..30993634,+p3@Skil
Mm9::chr3:87329494..87329565,+p1@Etv3
Mm9::chr3:87329568..87329589,+p2@Etv3
Mm9::chr4:155186603..155186638,+p1@Ccnl2
Mm9::chr4:59202074..59202085,+p3@Ugcg
Mm9::chr4:59202112..59202126,+p2@Ugcg
Mm9::chr5:109058705..109058726,-p2@Gak
Mm9::chr7:125386876..125386926,-p2@Smg1


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:0006679glucosylceramide biosynthetic process0.0183511363443851
GO:0046476glycosylceramide biosynthetic process0.0183511363443851
GO:0008120ceramide glucosyltransferase activity0.0183511363443851
GO:0006678glucosylceramide metabolic process0.0183511363443851
GO:0046513ceramide biosynthetic process0.0244574589523605
GO:0006688glycosphingolipid biosynthetic process0.0244574589523605
GO:0006677glycosylceramide metabolic process0.0244574589523605
GO:0035251UDP-glucosyltransferase activity0.0244574589523605
GO:0046520sphingoid biosynthetic process0.0244574589523605
GO:0046527glucosyltransferase activity0.0256775179255801
GO:0009247glycolipid biosynthetic process0.0266750174125593
GO:0017053transcriptional repressor complex0.0282077778601329
GO:0006687glycosphingolipid metabolic process0.0282077778601329
GO:0030148sphingolipid biosynthetic process0.0359484775696386
GO:0006664glycolipid metabolic process0.0359484775696386
GO:0043231intracellular membrane-bound organelle0.0359484775696386
GO:0043227membrane-bound organelle0.0359484775696386
GO:0006672ceramide metabolic process0.0467895503180661
GO:0046519sphingoid metabolic process0.0481709005625808



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
endoderm-derived structure9.33e-17118
endoderm9.33e-17118
presumptive endoderm9.33e-17118
digestive system3.65e-16116
digestive tract3.65e-16116
primitive gut3.65e-16116
subdivision of digestive tract3.85e-15114
gastrointestinal system2.79e-1047
intestine2.03e-0931
hemolymphoid system2.90e-0848
immune system2.90e-0848
mixed endoderm/mesoderm-derived structure3.14e-0835
organ component layer1.55e-0724
hematopoietic system6.07e-0745
blood island6.07e-0745
hemopoietic organ8.75e-0729
immune organ8.75e-0729
mucosa9.13e-0715


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)
MA0003.13.57432
MA0004.11.10905
MA0006.11.37063
MA0007.11.07722
MA0009.10.870101
MA0014.14.67229
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.769859
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
MA0048.11.13456
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.12.65362
MA0056.10
MA0057.11.58436
MA0058.10.341628
MA0059.10.353484
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.11.39085
MA0067.11.21448
MA0068.10.0965831
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.312272
MA0074.10.531046
MA0076.10.845594
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.229377
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.787675
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.11.06639
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.11.36991
MA0117.10.937363
MA0119.10.951747
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.977634
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.640537
MA0145.11.87609
MA0146.10.946874
MA0147.12.70055
MA0148.10.450593
MA0149.10.367458
MA0062.22.64619
MA0035.20.524137
MA0039.22.84599
MA0138.21.61926
MA0002.20.172399
MA0137.20.32312
MA0104.23.099
MA0047.20.576767
MA0112.21.87605
MA0065.20.528619
MA0150.11.07698
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.11.45843
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.688775
MA0160.10.453546
MA0161.10
MA0162.111.6633
MA0163.11.79588
MA0164.10.551114
MA0080.20.816435
MA0018.20.560731
MA0099.20.669311
MA0079.212.7454
MA0102.21.59466
MA0258.10.60477
MA0259.12.63282
MA0442.10
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