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MCL coexpression mm9:1609: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0.0129027425573152,0.0459850211671674,0.0900497279534876,0,0.0352701044070988,0.044622164134639,0.0672143877046658,0,0,0,0,0,0.049728616350379,0,0,0,0,0.0336519439444168,0.0633032346574929,0.0533770141462728,0.279666759954591,0,0,0.0930738655305754,0.109394906730749,0.117568220301562,0.0997671046484152,0.0720742724604996,0.0660884578138182,0,0.131558135597132,0,0,0,0,0,0,0.0980663836014592,0,0,0.0675502567495246,0.0968353720671288,0.106996804502769,0.0278303298346352,0.00838719515376848,0.0146370835987414,0,0,0,0,0.04183511284258,0,0.035411894325991,0,0,0,0,0,0,0,0,0.0253460298483294,0,0.0557461356241752,0,0.0932472118774464,0.0455238958421948,0,0,0,0,0,0,0.0100365579766666,0.00794986341805778,0,0.0644917757070346,0,0,0,0,0,0,0,0.0355124566760334,0,0.0115614856957469,0,0.0300307501009016,0.0299745769749034,0.188575974198403,0.0869408482704168,0,0.0374874020040052,0,0,0.0544194016857283,0,0.0701120235883702,0,0,0,0,0,0.906505549810204,0.915757348426758,0.857078802522988,0.0420675160477021,0.0362472455126258,0.0319931881281674,0.0138955327120455,0.023086518062959,0,0.024388263181512,0.00965640094523602,0.010281955369983,0.0191868699727828,0.0117306995138079,0.0550443236814614,0,0,0,0,0.0223049784921262,0,0.0197603723217884,0,0,0.0103901955038261,0,0.056433810345152,0.0102810109601085,0.0139206206633669,0,0.0420831893022544,0,0.0476823527412791,0.0763318828766922,0.270092241589605,0.0165887865499927,0,0.0179741089226215,0.0143809746682251,0,0.0161331963839923,0,0,0,0.016955851233925,0,0,0,0,0,0.0162537691059124,0,0.0462027901480346,0,0.0217240643049498,0,0,0,0,0,0.0124612644033474,0,0,0,0,0.0264061830170419,0,0.0222793881788988,0.0172399303185785,0.0109384201478028,0.0165778852990865,0.0162557204018725,0.0247976735334282,0.0368758805175546,0,0,0,0,0,0,0.0579649580914,0.0348757508495214,0.0389494657899306,0.0157606832760691,0.0399999489715342,0,0.016996575332051,0.0582379747129756,0,0.0272712344417687,0,0.0296775014430774,0.0896775880333733,0.0611594954347652,0.023863234671827,0.0318430594843442,0.0461888854779462,0.048128965671688,0,0.0268052835672542,0,0,0,0,0.0197028464011984,0,0,0.021072153251936,0,0,0.0421212347461146,0,0,0.0341956312905688,0.111079583504116,0,0,0,0,0.0269036867668381,0,0,0,0,0.0128507622195331,0.04791028522828,0.0540623793245008,0.0590038912608925,0.0798624877691714,0,0.0347400403625538,0.0735520501733996,0,0.0192541879959623,0,0.035503944132517,0,0,0,0,0,0.0216505122427232,0,0,0,0.0242016882738972,0.342053162547864,0.0817677763102558,0.0721605493483617,0.441408824497234,0,0,0.0229437792653656,0.0150075163951468,0.0551039936431978,0.0232840311960298,0.0897102876104234,0.100518259653603,0.0888866254168996,0.0425479434838494,0.0985066024345344,0.141945921162923,0.025449450276426,0,0,0,0.0512333238321666,0.0840032676280198,0.0945020274484158,0.0826148488452132,0.15792029527122,0.0712431371295704,0.202248033241266,0,0.0260023651116661,0.010173622148774,0.0293847436318303,0.0132011095126881,0.0444351865474724,0.0147748385381288,0.027403602145496,0.0162973202140673,0.0147579274919735,0,0,0,0,0.0113772712432778,0.0413704401793351,0,0,0,0.0169874779739385,0,0.0171553092198588,0.0219775808627792,0.0068978932917068,0,0.101123713227393,0.0419747826588222,0.0388302949969878,0,0,0,0.0105510834322885,0,0,0,0,0,0,0.0238519118384212,0,0,0.010609602440298,0,0.0157407500055755,0.00985876082734042,0,0,0.0127582937957152,0,0,0.00797889783062888,0,0.04507173861125,0,0.0217967603198622,0,0.0437182974826889,0.22667292164744,1.0188832439311,0.264404153077156,0.155925822257103,0,0.0328899181007414,0,0,0,0,0,0,0,0,0,0,0,0.0475750804396942,0,0,0.0997708127037211,0.0580733356193652,0,0.0746685048976322,0.0687475752164774,0.0450272103094257,0.0276331213675158,0.0349038189971895,0.054851493265943,0.0338345527732368,0.0492234517292185,0.0396614436893096,0.0699043698863202,0.0343413018317401,0.0256067459839642,0.0263847572150414,0,0.0633823041848476,0.0538630706902678,0.0464862471770233,0.0861975160801743,0.036718842217826,0.0585560349660766,0,0.033731315910315,0.0566562375272402,0.0297964402894088,0.012511647014566,0.0396610129804362,0.0679482392401617,0.018258217855509,0.0338120738117178,0.0152033776317981,0,0.0458648612217138|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.267273341778078,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0570741246689917,0,0,0,0,0,0,0,1.06475968199697,0.908167290436919,1.00429729386248,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0421182837367051,0.096497738357694,0.303388537662931,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0769870445726752,0.0294389011296462,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.299633798006623,0,0.0655375003561515,0.3334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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000474!1.07e-14!9;UBERON:0004175!1.84e-14!9;UBERON:0003126!1.25e-12!3;UBERON:0001005!1.25e-12!3;UBERON:0007196!1.25e-12!3;UBERON:0001558!1.25e-12!3;UBERON:0003100!6.40e-12!11;UBERON:0003134!1.24e-11!8;UBERON:0001301!1.71e-11!3;UBERON:0006555!1.71e-11!3;UBERON:0005103!1.71e-11!3;UBERON:0000083!1.71e-11!3;UBERON:0009201!1.71e-11!3;UBERON:0004819!1.71e-11!3;UBERON:0006553!1.71e-11!3;UBERON:0003074!1.71e-11!3;UBERON:0003060!1.71e-11!3;UBERON:0005156!3.19e-10!26;UBERON:0000990!3.19e-10!26;UBERON:0003133!8.87e-09!24;UBERON:0000080!9.80e-09!4;UBERON:0005904!9.80e-09!4;UBERON:0006947!9.80e-09!4;UBERON:0002120!9.80e-09!4;UBERON:0004054!9.80e-09!4;UBERON:0004875!9.80e-09!4;UBERON:0004876!9.80e-09!4;UBERON:0005721!9.80e-09!4;UBERON:0005754!9.80e-09!4;UBERON:0007297!9.80e-09!4;UBERON:0001343!5.70e-08!2;UBERON:0004910!5.70e-08!2;UBERON:0004909!5.70e-08!2;UBERON:0005154!5.70e-08!2;UBERON:0005295!5.70e-08!2;UBERON:0005297!5.70e-08!2;UBERON:0005294!5.70e-08!2;UBERON:0010141!5.70e-08!2;UBERON:0005891!5.70e-08!2;UBERON:0003975!1.97e-07!5;UBERON:0004122!4.98e-07!5
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.836099,0.115752,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.775038,0.545768,0.489529,0.874994,0.727684,0.404661,0.537749,0.757752,1.38127,0.641282,0.456327,0.227599,1.51608,1.03545,0.395107,0.253145,0.425309,0.20704,0.384813,0.699032,0.360612,0.876199,0.401916,0.631725,0.134724,0.426986,0.227872,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,2.05899,0.689304,0.731291,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.257421,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.0793594,0.0882907,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.89388,0.297538,1.05152,0.848095,1.11561,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,1.03353,0.0998646,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,1.06895,1.14546,0.595426,1.3055,0.750642,1.43666,0.867604,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,2.38006,0.905521,0.632211,0.851091,2.18247,0.569503,1.05179,1.21592,0.133815,1.18223,0.908552,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.425122
}}

Latest revision as of 17:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:98568959..98568970,-p2@Med24
Mm9::chr11:98569050..98569057,-p7@Med24
Mm9::chr11:98569071..98569091,-p@chr11:98569071..98569091
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Mm9::chr15:75069502..75069519,-p1@ENSMUST00000089689
Mm9::chr15:76444647..76444681,-p@chr15:76444647..76444681
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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:0006882cellular zinc ion homeostasis0.0312234660803284
GO:0055069zinc ion homeostasis0.0312234660803284
GO:0005385zinc ion transmembrane transporter activity0.0346889380409686
GO:0000119mediator complex0.041610757046365
GO:0006829zinc ion transport0.041610757046365
GO:0046915transition metal ion transmembrane transporter activity0.041610757046365
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.0475447224348353



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
female reproductive system1.07e-149
internal genitalia1.84e-149
trachea1.25e-123
respiratory airway1.25e-123
tracheobronchial tree1.25e-123
lower respiratory tract1.25e-123
female organism6.40e-1211
female reproductive organ1.24e-118
epididymis1.71e-113
excretory tube1.71e-113
mesonephric epithelium1.71e-113
mesonephric tubule1.71e-113
nephric duct1.71e-113
kidney epithelium1.71e-113
renal duct1.71e-113
mesonephric duct1.71e-113
pronephric duct1.71e-113
reproductive structure3.19e-1026
reproductive system3.19e-1026
reproductive organ8.87e-0924
mesonephros9.80e-094
duct of male reproductive system9.80e-094
male genital duct9.80e-094
pronephros9.80e-094
internal male genitalia9.80e-094
nephrogenic cord9.80e-094
urogenital ridge9.80e-094
pronephric mesoderm9.80e-094
rostral part of nephrogenic cord9.80e-094
presumptive pronephric mesoderm9.80e-094
seminiferous tubule of testis5.70e-082
epithelium of male gonad5.70e-082
epithelium of gonad5.70e-082
epithelial cord5.70e-082
sex cord5.70e-082
testis sex cord5.70e-082
genital ridge5.70e-082
primitive sex cord of indifferent gonad5.70e-082
coelomic epithelium5.70e-082
internal female genitalia1.97e-075
genitourinary system4.98e-075


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)
MA0003.10.0185483
MA0004.10.603793
MA0006.11.07705
MA0007.11.43525
MA0009.11.06266
MA0014.10.0502051
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.12.99031
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.12.4883
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.28842
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.11.76548
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.12.43684
MA0071.10.644448
MA0072.11.06547
MA0073.10.0176764
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.888325
MA0089.10
MA0090.11.39153
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.693075
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.11.4237
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.11.89177
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.13.33982
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.0604336
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.0511423
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.927461
MA0065.20.477991
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.14.12188
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.245828
MA0163.10.230013
MA0164.10.729558
MA0080.21.15331
MA0018.20.739807
MA0099.20.854449
MA0079.20.0167818
MA0102.21.79669
MA0258.10.91616
MA0259.11.71005
MA0442.10
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