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MCL coexpression mm9:962: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0.0462963944026387,0.016250504047769,0.0203578457864595,0.0143457248414071,0.0440876305088735,0.0157159950891022,0.034192054073677,0.708227032989883,0.310064572062647,0.361548644216124,0.182727718776414,0.0886454988133248,0.351744724005984,0.381165286322475,0.031216477148738,0.0964498888731516,0.0287921226403624,0.422635908369479,0.312850842503464,0.462525110046063,0.00886176641219205,0.109978813034897,0.13753601242178,0.0524667868603999,0.0577699254416606,0,0,0.0105930855729004,0.00944443853967459,0,0.0108719274729244,0,0,0,0.0137753652090801,0,0.025937737058448,0.0330155140017492,0.0313432106352375,0.0457123067624895,0.0924473609747901,0.207033369813378,0.0429689207243575,0.012874647931423,0.0100220950299435,0,0,0,0,0,0,0,0.936068614425712,0.22855817231145,0.37016698897652,0,0.0273552697493265,0,0,0,0,0,0,0.0201691229955633,0.0373257003321355,0,0,0,0.0102304623341822,0,0,0,0,0.0237907330869729,0.00993732927257223,0,0,0,0,0,0.00950470588951562,0,0,0,0,0,0.00722592855984183,0,0.0303876847985543,0.0182932202741001,0.197204770109202,0,0.028162733897373,0,0,0,0.0214027967508719,0.00854319557738549,0,0,0.0587520957112941,0,0,0,0.0106386143583423,0,0.0379278285916221,0.0058696088364538,0.0890148299637119,0.0300545597055,0.00868470794502844,0,0,0.015242664488445,0,0,0,0.00733168719612996,0,0.00813987251056347,0.0216648225944688,0.0702094071085625,0,0,0,0.0123502327011177,0.277093236974373,0.186358664461123,0.33448440044145,0,0,0,0.00870038791460429,0,0,0,0.00526478546708814,0.0235829922085091,0,0,0.0066405913786389,0,0,0.00762049142827827,0.00714652363876167,0.0123835344675541,0.00972472422872995,0,0.0105974070212031,0.00940257497036715,0.0163681612892216,0,0,0,0.0101586056911953,0.00985394935498842,0.119289846251268,0.178436592616588,0.144541128535362,0.0102190652941123,0,0,0,0.00975107509399393,0.00778829025209214,0.0113498611067201,0,0.0173889856106142,0,0.0154134490544022,0.00423166718530719,0.00740754991964957,0.0197613803463854,0.019744091197682,0,0.00531724411976776,0,0.0127377319240807,0.0104954989897117,0,0,0,0.0109006925718742,0,0.0421633341243007,0,0,0,0,0.0348104577725871,0,0,0.0188564359547338,0.00587275787833987,0,0.0100625874097485,0.0177949665380359,0.00735972528241155,0.0149145216698919,0.00747429749119195,0.0158332203576922,0.0126333307852741,0.0393683246098001,0.00837665111476695,0,0,0,0.0330982247853135,0.012314279000749,0.013726674124346,0.00815708322120846,0,0,0,0,0,0.00895752137663766,0,0.0446809650354206,0,0.00819582947787884,0.00851140366878255,0,0.0168148042292738,0.0231839884452437,0.00967705921508934,0.0238393885706353,0.0108601146021445,0.0240951791616246,0.0153885832164641,0,0.0275883371097478,0.0499140548557321,0.0399614072357905,0,0,0.00808300958689154,0.00601693374873821,0,0.0122209567075048,0,0,0.0105909490697472,0.0116325461614489,0,0,0,0,0,0.0151260551711858,0.00720541476783971,0.00889618449371135,0.00819218754451894,0.00828934843908011,0,0,0.0143398620408535,0.0281390932409003,0.0251952514716046,0.0145525194975186,0,0,0.016552369845675,0.0149085024539811,0.0390799728941331,0.0384732399861714,0.0159059064227662,0,0,0.0105424050495677,0.00886274819537199,0.00891015519222358,0.00826972180945102,0.014429051766189,0.0114439370749989,0,0,0.00828544001235514,0.00812573909739565,0.00317925692149189,0,0,0,0.00923427408633047,0.055551834249127,0,0.00922370468248341,0.0267252591160682,0.0561923158859609,0.061359507289197,0.52667763211226,0.456972501736663,0.471012660438178,0,0.00797144500891131,0,0.0250614188417084,0.0103072521518129,0,0,0,0,0.00661630505169458,0.0262342391617639,0,0,0.00831210126076806,0,0,0,0.00602400585703865,0,0,0,0,0.0149074448990132,0.0200416040264456,0.00530771124917056,0.0258014981137175,0.0855379304134583,0.0461652560937515,0.0336348344574025,0.0215276611381901,0.0152067884822584,0.0221451737561472,0.0052148439365095,0.0139235115075441,0.0364283122986468,0.0354062178611987,0,0,0,0,0.00958868214570406,0,0,0.0105438062638504,0,0.0243056839551481,0,0,0,0,0,0,0,0,0,0.0053606764446993,0,0,0.0118135516438084,0,0.00916178713235262,0.010894860405555,0,0.0151095319991816,0,0.0122646457951885,0,0.0145781193176664,0,0.0146936107127796,0,0.0119047943476222,0.0177132920178519,0.0187326395956812,0,0.0160042162399776,0.00886899904417806,0.0232184086513983,0.0212199700003655,0.0097651853750898,0.00881886233447202,0.0273593631525657,0,0,0,0,0.00510022917129024,0.037245550361761,0,0.0272888932508063,0.0121055245070021,0.0114113861596931,0,0,0.0108212890621753,0.0226410289579719|coexpression_dpi_cluster_scores_median=0.032256856393288,0,0,0,0,0,0,0.6681701804925,0.405650992429202,0.381004399693277,0.177230224899924,0.0488097387351863,0.358391918090397,0.399896202325608,0,0.0800761525331175,0,0.411166798147301,0.274502502745681,0.430970888944806,0,0.0411126530948397,0.0503919447329045,0.0322275761868389,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.113047926555807,0,0,0,0,0,0,0,0,0,0,0.895180152955226,0.236880264493592,0.42821078821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|ontology_enrichment_celltype=CL:0000988!6.52e-34!32;CL:0002032!6.52e-34!32;CL:0000037!6.52e-34!32;CL:0000566!6.52e-34!32;CL:0000837!6.52e-34!32;CL:0000838!2.24e-31!12;CL:0000542!9.21e-29!13;CL:0000051!9.21e-29!13;CL:0000084!1.62e-28!11;CL:0000827!1.62e-28!11;CL:0002031!2.15e-25!25;CL:0002320!1.65e-24!46;CL:0000134!1.65e-24!46;CL:0000791!3.54e-24!9;CL:0000789!3.54e-24!9;CL:0002420!3.54e-24!9;CL:0002419!3.54e-24!9;CL:0000790!3.54e-24!9;CL:0002242!6.99e-23!16;CL:0000219!4.35e-22!54;CL:0000624!1.74e-21!8;CL:0000738!2.21e-21!17;CL:0002087!2.21e-21!17;CL:0000893!2.90e-16!6;CL:0002489!2.90e-16!6;CL:0000898!2.90e-16!6;CL:0000809!2.90e-16!6;CL:0000810!2.90e-16!6;CL:0000895!2.90e-16!6;CL:0000808!2.90e-16!6;CL:0000894!2.90e-16!6;CL:0000806!2.90e-16!6;CL:0000807!2.90e-16!6;CL:0000805!2.90e-16!6;CL:0002425!2.90e-16!6;CL:0002436!2.90e-16!6;CL:0002427!2.90e-16!6;CL:0002428!2.90e-16!6;CL:0002429!2.90e-16!6;CL:0002433!2.90e-16!6;CL:0002431!2.90e-16!6;CL:0002432!2.90e-16!6;CL:0000034!5.05e-14!97;CL:0000723!4.82e-11!91;CL:0000048!4.82e-11!91;CL:0000049!3.34e-10!19;CL:0000548!1.51e-08!115;CL:0000255!1.51e-08!115;CL:0002371!3.38e-08!118;CL:0000553!9.43e-08!6;CL:0000556!9.43e-08!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!1.65e-24!46;UBERON:0002193!7.64e-11!48;UBERON:0002405!7.64e-11!48;UBERON:0002390!6.97e-09!45;UBERON:0003061!6.97e-09!45
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.367606,0.434198,0.720982,0.448401,0.538088,0.991481,0.181564,0.0447303,0.494602,0.526159,0.173454,0.550255,0.756943,0,0.742571,0.252772,0.160384,0.29826,1.58838,0.223663,0.549359,0.258745,0.374936,0.577606,0.153291,0.469052,0.818708,0.376624,0.455168,0.843667,0.699026,0.425071,0.276324,0.185086,0.242032,0.522578,1.1836,0.195877,1.31403,0.460258,0.204736,0.761266,0.0824666,0.423266,0.662995,0.484612,0.0447507,0.305876,0.725127,0.604356,0.362495,0.985264,1.00271,0.557354,1.52537,0.513517,0.447041,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.178433,0.236196,1.03623,0.140213,0.409836,0.136938,1.56933,0.806481,0.336166,0.530481,0.759925,1.48701,0.968721,0.920903,0.025519,0.0299392,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.585369,0.510015,0.859272,0.663249,0.101559,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,1.00333,0.96962,0.337254,0.499714,1.21576,0.708441,0.0359654,0.437894,0.743872,0.238599,1.04163,0.692953,0.579418,1.56744,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,1.03631,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.120154,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.782826,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.166768
|tfbs_overrepresentation_jaspar=MA0003.1;0.00271136,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.325341,MA0017.1;0.804572,MA0019.1;1.64517,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,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;0.102483,MA0050.1;1.19121,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.117901,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.90507,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.638933,MA0063.1;0,MA0066.1;1.39085,MA0067.1;1.21448,MA0068.1;0.319589,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.577203,MA0074.1;0.531046,MA0076.1;0.315013,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;0.950493,MA0103.1;0.307078,MA0105.1;0.133231,MA0106.1;0.626997,MA0107.1;1.47808,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.633896,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;0.937363,MA0119.1;0.362692,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;0.169849,MA0140.1;1.29098,MA0141.1;1.56635,MA0142.1;3.00123,MA0143.1;2.53683,MA0144.1;0.640537,MA0145.1;0.0701568,MA0146.1;0.0169049,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.426733,MA0035.2;0.524137,MA0039.2;0.027551,MA0138.2;0.675599,MA0002.2;0.988033,MA0137.2;0.32312,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;1.35357,MA0065.2;0.528619,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;0.0804339,MA0156.1;0.843735,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;1.14982,MA0161.1;0,MA0162.1;0.0211019,MA0163.1;0.212034,MA0164.1;0.551114,MA0080.2;0.816435,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.0468707,MA0102.2;1.59466,MA0258.1;1.13923,MA0259.1;0.227035,MA0442.1;0
}}

Latest revision as of 16:10, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:72970599..72970609,-p@chr15:72970599..72970609
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Mm9::chr15:72985061..72985073,-p@chr15:72985061..72985073
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Mm9::chr5:32001104..32001125,+p@chr5:32001104..32001125
+
Mm9::chr6:125418343..125418350,-p@chr6:125418343..125418350
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Mm9::chr6:48650528..48650539,+p@chr6:48650528..48650539
+
Mm9::chr7:80684146..80684159,-p@chr7:80684146..80684159
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Mm9::chr7:80684250..80684264,+p@chr7:80684250..80684264
+
Mm9::chr9:7872584..7872603,-p@chr9:7872584..7872603
-


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

no results for this coexpression

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>

Cell Type
Ontology termp-valuen
hematopoietic cell6.52e-3432
hematopoietic oligopotent progenitor cell6.52e-3432
hematopoietic stem cell6.52e-3432
angioblastic mesenchymal cell6.52e-3432
hematopoietic multipotent progenitor cell6.52e-3432
lymphoid lineage restricted progenitor cell2.24e-3112
lymphocyte9.21e-2913
common lymphoid progenitor9.21e-2913
T cell1.62e-2811
pro-T cell1.62e-2811
hematopoietic lineage restricted progenitor cell2.15e-2525
connective tissue cell1.65e-2446
mesenchymal cell1.65e-2446
mature alpha-beta T cell3.54e-249
alpha-beta T cell3.54e-249
immature T cell3.54e-249
mature T cell3.54e-249
immature alpha-beta T cell3.54e-249
nucleate cell6.99e-2316
motile cell4.35e-2254
CD4-positive, alpha-beta T cell1.74e-218
leukocyte2.21e-2117
nongranular leukocyte2.21e-2117
thymocyte2.90e-166
double negative thymocyte2.90e-166
naive T cell2.90e-166
double-positive, alpha-beta thymocyte2.90e-166
CD4-positive, alpha-beta thymocyte2.90e-166
naive thymus-derived CD4-positive, alpha-beta T cell2.90e-166
DN4 thymocyte2.90e-166
DN1 thymic pro-T cell2.90e-166
DN2 thymocyte2.90e-166
DN3 thymocyte2.90e-166
immature single positive thymocyte2.90e-166
early T lineage precursor2.90e-166
mature CD4 single-positive thymocyte2.90e-166
resting double-positive thymocyte2.90e-166
double-positive blast2.90e-166
CD69-positive double-positive thymocyte2.90e-166
CD69-positive, CD4-positive single-positive thymocyte2.90e-166
CD4-positive, CD8-intermediate double-positive thymocyte2.90e-166
CD24-positive, CD4 single-positive thymocyte2.90e-166
stem cell5.05e-1497
somatic stem cell4.82e-1191
multi fate stem cell4.82e-1191
common myeloid progenitor3.34e-1019
animal cell1.51e-08115
eukaryotic cell1.51e-08115
somatic cell3.38e-08118
megakaryocyte progenitor cell9.43e-086
megakaryocyte9.43e-086

Uber Anatomy
Ontology termp-valuen
connective tissue1.65e-2446
hemolymphoid system7.64e-1148
immune system7.64e-1148
hematopoietic system6.97e-0945
blood island6.97e-0945


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)
MA0003.10.00271136
MA0004.10.434673
MA0006.10.271714
MA0007.10.419994
MA0009.10.870101
MA0014.10.325341
MA0017.10.804572
MA0019.11.64517
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.10.281528
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
MA0048.10.102483
MA0050.11.19121
MA0051.10.586414
MA0052.10.890676
MA0055.10.117901
MA0056.10
MA0057.10.31126
MA0058.10.90507
MA0059.10.353484
MA0060.10.197678
MA0061.10.638933
MA0063.10
MA0066.11.39085
MA0067.11.21448
MA0068.10.319589
MA0069.10.891016
MA0070.10.881319
MA0071.10.471969
MA0072.10.872842
MA0073.10.577203
MA0074.10.531046
MA0076.10.315013
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
MA0101.10.950493
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.11.47808
MA0108.20.710846
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.10.633896
MA0115.10.969632
MA0116.10.27152
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.10.683521
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.169849
MA0140.11.29098
MA0141.11.56635
MA0142.13.00123
MA0143.12.53683
MA0144.10.640537
MA0145.10.0701568
MA0146.10.0169049
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.20.426733
MA0035.20.524137
MA0039.20.027551
MA0138.20.675599
MA0002.20.988033
MA0137.20.32312
MA0104.20.54394
MA0047.20.576767
MA0112.21.35357
MA0065.20.528619
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.677425
MA0155.10.0804339
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.11.14982
MA0161.10
MA0162.10.0211019
MA0163.10.212034
MA0164.10.551114
MA0080.20.816435
MA0018.20.560731
MA0099.20.669311
MA0079.20.0468707
MA0102.21.59466
MA0258.11.13923
MA0259.10.227035
MA0442.10
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