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MCL coexpression mm9:1890: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002193!1.94e-21!48;UBERON:0002405!1.94e-21!48;UBERON:0002390!5.64e-20!45;UBERON:0003061!5.64e-20!45;UBERON:0001007!1.63e-11!116;UBERON:0001555!1.63e-11!116;UBERON:0007026!1.63e-11!116;UBERON:0004119!2.70e-11!118;UBERON:0000925!2.70e-11!118;UBERON:0006595!2.70e-11!118;UBERON:0004921!7.12e-11!114;UBERON:0004177!1.46e-10!29;UBERON:0005057!1.46e-10!29;UBERON:0002371!1.70e-10!16;UBERON:0001474!5.28e-09!22;UBERON:0004765!5.28e-09!22;UBERON:0001434!5.28e-09!22;UBERON:0001041!7.73e-09!80;UBERON:0000077!8.41e-09!35;UBERON:0002384!1.70e-08!46;UBERON:0003408!4.00e-08!24;UBERON:0003081!5.26e-08!87;UBERON:0002370!1.02e-07!23;UBERON:0000974!1.02e-07!23;UBERON:0004807!1.02e-07!23;UBERON:0005058!1.02e-07!23;UBERON:0003351!1.02e-07!23;UBERON:0009113!1.02e-07!23;UBERON:0003295!1.02e-07!23;UBERON:0009722!1.02e-07!23;UBERON:0005562!1.02e-07!23;UBERON:0007690!1.02e-07!23;UBERON:0006562!1.29e-07!24;UBERON:0001557!1.29e-07!24;UBERON:0001042!1.29e-07!24;UBERON:0008814!1.29e-07!24;UBERON:0009145!1.29e-07!24;UBERON:0002204!7.42e-07!32
|ontology_enrichment_uberon=UBERON:0002193!1.94e-21!48;UBERON:0002405!1.94e-21!48;UBERON:0002390!5.64e-20!45;UBERON:0003061!5.64e-20!45;UBERON:0001007!1.63e-11!116;UBERON:0001555!1.63e-11!116;UBERON:0007026!1.63e-11!116;UBERON:0004119!2.70e-11!118;UBERON:0000925!2.70e-11!118;UBERON:0006595!2.70e-11!118;UBERON:0004921!7.12e-11!114;UBERON:0004177!1.46e-10!29;UBERON:0005057!1.46e-10!29;UBERON:0002371!1.70e-10!16;UBERON:0001474!5.28e-09!22;UBERON:0004765!5.28e-09!22;UBERON:0001434!5.28e-09!22;UBERON:0001041!7.73e-09!80;UBERON:0000077!8.41e-09!35;UBERON:0002384!1.70e-08!46;UBERON:0003408!4.00e-08!24;UBERON:0003081!5.26e-08!87;UBERON:0002370!1.02e-07!23;UBERON:0000974!1.02e-07!23;UBERON:0004807!1.02e-07!23;UBERON:0005058!1.02e-07!23;UBERON:0003351!1.02e-07!23;UBERON:0009113!1.02e-07!23;UBERON:0003295!1.02e-07!23;UBERON:0009722!1.02e-07!23;UBERON:0005562!1.02e-07!23;UBERON:0007690!1.02e-07!23;UBERON:0006562!1.29e-07!24;UBERON:0001557!1.29e-07!24;UBERON:0001042!1.29e-07!24;UBERON:0008814!1.29e-07!24;UBERON:0009145!1.29e-07!24;UBERON:0002204!7.42e-07!32
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,1.21364,0.704257,0.803568,0.96814,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.906602,0.727368,1.32554,0.790816,0.711848,1.12823,0.471365,0.318879,0.503207,0.623685,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,0.504971,0.325217,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.593145,1.32691,0.323563,0.834514,0.318792,0.926147,1.08947,0.575233,0.986898,1.04072,0.884013,0.951203,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,1.09896,1.05366,0.367176,1.14445,0.938512,1.34553,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,4.04103,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,1.069,0.838313,1.35996,0.87653,1.28473,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.280875
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.402508,0.612053,0.688265,1.21364,0.704257,0.803568,0.96814,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.352304,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.906602,0.727368,1.32554,0.790816,0.711848,1.12823,0.471365,0.318879,0.503207,0.623685,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,0.504971,0.325217,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.593145,1.32691,0.323563,0.834514,0.318792,0.926147,1.08947,0.575233,0.986898,1.04072,0.884013,0.951203,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,1.09896,1.05366,0.367176,1.14445,0.938512,1.34553,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,4.04103,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,1.069,0.838313,1.35996,0.87653,1.28473,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.280875
|tfbs_overrepresentation_jaspar=MA0003.1;0.0356887,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.0809287,MA0017.1;1.30949,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;2.90785,MA0051.1;1.99205,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;0.251896,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;1.04037,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.00221226,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.201215,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;1.11164,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.21199,MA0146.1;0.313734,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;0.0220513,MA0138.2;0.951653,MA0002.2;0.965577,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.609584,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.263609,MA0155.1;0.650923,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.10667,MA0163.1;0.0996272,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.000201415,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}
}}

Revision as of 14:01, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:33847761..33847786,-p1@Fam26f
Mm9::chr12:109873953..109874049,+p3@Evl
Mm9::chr6:125021344..125021363,+p2@Lpar5
Mm9::chr9:108959809..108959823,+p@chr9:108959809..108959823
+


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:0045010actin nucleation0.0102266294125167
GO:0005522profilin binding0.0102266294125167
GO:0017124SH3 domain binding0.0102266294125167
GO:0030168platelet activation0.0102266294125167
GO:0030048actin filament-based movement0.0102266294125167
GO:0051016barbed-end actin filament capping0.0102266294125167
GO:0051693actin filament capping0.0102266294125167
GO:0030835negative regulation of actin filament depolymerization0.0102266294125167
GO:0030834regulation of actin filament depolymerization0.0102266294125167
GO:0030042actin filament depolymerization0.0102266294125167
GO:0005925focal adhesion0.0102266294125167
GO:0008064regulation of actin polymerization and/or depolymerization0.0102266294125167
GO:0005924cell-substrate adherens junction0.0102266294125167
GO:0051261protein depolymerization0.0102266294125167
GO:0032535regulation of cellular component size0.0102266294125167
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0102266294125167
GO:0030832regulation of actin filament length0.0102266294125167
GO:0051493regulation of cytoskeleton organization and biogenesis0.0102266294125167
GO:0033043regulation of organelle organization and biogenesis0.0102266294125167
GO:0051129negative regulation of cellular component organization and biogenesis0.0102266294125167
GO:0030055cell-matrix junction0.0102266294125167
GO:0008154actin polymerization and/or depolymerization0.0111563229954727
GO:0030027lamellipodium0.0118336711773407
GO:0007596blood coagulation0.0118336711773407
GO:0019904protein domain specific binding0.0118336711773407
GO:0051128regulation of cellular component organization and biogenesis0.0118336711773407
GO:0007599hemostasis0.0118336711773407
GO:0050817coagulation0.0118336711773407
GO:0005912adherens junction0.0129067116033831
GO:0051248negative regulation of protein metabolic process0.0134224511039281
GO:0016323basolateral plasma membrane0.0134224511039281
GO:0050878regulation of body fluid levels0.0134224511039281
GO:0031252leading edge0.0138497781186654
GO:0007411axon guidance0.0138497781186654
GO:0042060wound healing0.0138497781186654
GO:0030705cytoskeleton-dependent intracellular transport0.0167034947071106
GO:0007409axonogenesis0.0246935685814427
GO:0030036actin cytoskeleton organization and biogenesis0.0246935685814427
GO:0048667neuron morphogenesis during differentiation0.0246935685814427
GO:0048812neurite morphogenesis0.0246935685814427
GO:0030029actin filament-based process0.0246935685814427
GO:0000904cellular morphogenesis during differentiation0.0270275205902226
GO:0031175neurite development0.0278259451456849
GO:0048666neuron development0.0301344680022158
GO:0001775cell activation0.0301344680022158
GO:0051246regulation of protein metabolic process0.03067988823755
GO:0003779actin binding0.0315937572488813
GO:0032990cell part morphogenesis0.0326858809300052
GO:0030030cell projection organization and biogenesis0.0326858809300052
GO:0048858cell projection morphogenesis0.0326858809300052
GO:0016477cell migration0.0326858809300052
GO:0030182neuron differentiation0.0326858809300052
GO:0009611response to wounding0.033342670990243
GO:0048699generation of neurons0.0351518719467522
GO:0051674localization of cell0.0351518719467522
GO:0006928cell motility0.0351518719467522
GO:0009892negative regulation of metabolic process0.0351518719467522
GO:0008092cytoskeletal protein binding0.0351518719467522
GO:0022008neurogenesis0.0351518719467522
GO:0042995cell projection0.0372249310615607
GO:0030054cell junction0.0385258924425628
GO:0009605response to external stimulus0.0433477130582158
GO:0007010cytoskeleton organization and biogenesis0.0434238418131477
GO:0000902cell morphogenesis0.0434238418131477
GO:0032989cellular structure morphogenesis0.0434238418131477



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
hemolymphoid system1.94e-2148
immune system1.94e-2148
hematopoietic system5.64e-2045
blood island5.64e-2045
digestive system1.63e-11116
digestive tract1.63e-11116
primitive gut1.63e-11116
endoderm-derived structure2.70e-11118
endoderm2.70e-11118
presumptive endoderm2.70e-11118
subdivision of digestive tract7.12e-11114
hemopoietic organ1.46e-1029
immune organ1.46e-1029
bone marrow1.70e-1016
bone element5.28e-0922
skeletal element5.28e-0922
skeletal system5.28e-0922
foregut7.73e-0980
mixed endoderm/mesoderm-derived structure8.41e-0935
connective tissue1.70e-0846
gland of gut4.00e-0824
lateral plate mesoderm5.26e-0887
thymus1.02e-0723
neck1.02e-0723
respiratory system epithelium1.02e-0723
hemolymphoid system gland1.02e-0723
pharyngeal epithelium1.02e-0723
thymic region1.02e-0723
pharyngeal gland1.02e-0723
entire pharyngeal arch endoderm1.02e-0723
thymus primordium1.02e-0723
early pharyngeal endoderm1.02e-0723
pharynx1.29e-0724
upper respiratory tract1.29e-0724
chordate pharynx1.29e-0724
pharyngeal arch system1.29e-0724
pharyngeal region of foregut1.29e-0724
musculoskeletal system7.42e-0732


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)
MA0003.10.0356887
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.0809287
MA0017.11.30949
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.266382
MA0050.12.90785
MA0051.11.99205
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.11.04037
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.00221226
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.11.11164
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.21199
MA0146.10.313734
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.0220513
MA0138.20.951653
MA0002.20.965577
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.20.609584
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.10667
MA0163.10.0996272
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.000201415
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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