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MCL coexpression mm9:386: Difference between revisions

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{{MCL_coexpression_mm9
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decarboxylase activator activity;0.0170902711785424;54375!GO:0030904;retromer complex;0.0170902711785424;13185!GO:0005672;transcription factor TFIIA complex;0.0170902711785424;83602!GO:0042979;ornithine decarboxylase regulator activity;0.0213593277225945;54375!GO:0006596;polyamine biosynthetic process;0.0239185150232815;54375!GO:0007034;vacuolar transport;0.0390217600260289;13185!GO:0006595;polyamine metabolic 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|coexpression_dpi_cluster_scores_median=0.058061279135179,0.663907692891998,0.658331678453009,0.931803308363196,1.01385575104817,0.341359789333773,0.403261124755707,0.320479107901854,0.250750767287275,0.296382675464508,0,0,0.268578825882798,0.217959435061983,0,0,0,0.0498645174073449,0,0.052811750176248,0.0518325320548473,0.0712741785830819,0.0328167850619146,0.0644551523736777,0.119445037115781,0.556676656017048,0.358663141135989,0.357229436323178,0.0755555083173967,0.0455745767693708,0.0991875855609932,0.247967805798467,0.180216597562281,0,0.536152455169372,0.281209516076665,0.574598245245182,0.702491010299453,0.616309725718225,0.410029642905161,1.09224303383595,0.651221505517025,0.502414761085689,0.030611549326279,0.0378470120613375,0.0211452145859256,0,0,0,0.00176638967982557,0,-0.0208870423994129,0.264561190163111,0.371284910541222,0.239583209011051,0,0.00634491331458923,0.0414837431332911,0,0,0,0,0,0.0438625485867266,0,0,0.0350990108181725,0,0,0,0,0,0,0,0,0,0,0,0,0,0,-0.0208870423994129,0,0,0,0,0,0,0,0.0137581998510735,0.820075447256833,0,0.0814977745811235,0.102246027707419,0.167488161830826,0,0.000450170561829389,0,0.0519266110680566,0,0.0679658026554914,0,0,0,0.0216674150339563,0.0857856518853037,0.0886053903169914,0.0716731801056126,0,0,0,-0.0208870423994129,0,0,0,0,0.0983851985245734,0.0604840258151488,0,0.0189112844883889,0.00651570179341125,0,0,0,0,0.0748984888248946,0.131595807759876,0.362166772647161,0.159371081002095,0,-0.00589075668668315,-0.00358624499401669,0,0,0,0,0,0.0356811402079827,0,0.0149768283460688,0,0,0,0,0,0.0388966350797377,0,0,0,0,0,0,0,0.0048786349565011,0,0,0.067902448560704,0.251158133487427,0.251916678405508,0,-0.00329422517558481,0,0,-0.0341512198029002,0,0,0,0.0112992932681333,0,0,0,0.0592603993571966,0,0.0421624213952017,0,0,0.172157763559108,0.101901855392646,-0.0102864818206164,0,0,0,0,0,0,0.011853040707422,0,0,0.0247589866138427,0,0.0113382773217589,0.0727974683912195,0,0,-0.00435209396517932,0,0,0,0,0,0.042445839031356,0.0390232367821778,0,0,0,0,0,0,0,0,0,0.0104860022855386,0,0.0123590564481309,0,0.0621923087914436,0,0.0486751348308956,0.0736278867910527,0,0,0,0,0,0.0223653221363023,0.0020261308615699,0,0,0.00881277113303247,0.0919555047233444,0.0413105596487485,0.064907987906009,0,0,0,0,0,0,0,0.0542792992782083,0,0,0,0.0930603692915911,0,0,0.00522230957032695,0.00340577699048521,0,0,0,0,0,0.0251021209078276,0,0,0,0,0,0,0.0415718247675936,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0555071295930174,0.0463433607307207,0.0835988423902335,0,0.0254340553719351,0.00360024396044575,0,0.0980122900961991,0,0,0,0,0,0,0,0.171012169074365,0.230386905221361,0.209629533516687,0,0,0,0,0,0,0,0.0295778519638216,0,0.0529304404135566,0,0,0,0,0,0,0,0,0,0,0,0.0054013146232641,0.0073613018165901,0,0,0,0,0,0,-0.0069017340645544,0,-0.00493917515476883,-0.0159545676494884,0,0,0,0.0528714126932928,0,0,0,0,0.0323706002183864,0,0,0,-0.0423297481782101,0,0,0,0,-0.0208870423994129,0,0,0,-0.0104032543580742,0,0,0,0,0,0,0,0,0,0,0,0,0.0061239664453835,0,0,0,0,0,0,0,0,0,0,0,0,0.0125071235367774,0,0,0,0,0,0,0,0,0,0,0,0.017987861361206,0,0,0
|gostat_on_MCL_coexpression=GO:0042978;ornithine decarboxylase activator activity;0.0170902711785424;54375!GO:0030904;retromer complex;0.0170902711785424;13185!GO:0005672;transcription factor TFIIA complex;0.0170902711785424;83602!GO:0042979;ornithine decarboxylase regulator activity;0.0213593277225945;54375!GO:0006596;polyamine biosynthetic process;0.0239185150232815;54375!GO:0007034;vacuolar transport;0.0390217600260289;13185!GO:0006595;polyamine metabolic process;0.0390217600260289;54375!
|ontology_enrichment_celltype=CL:0000066!5.37e-13!25;CL:0000223!1.15e-09!20;CL:0002563!2.47e-09!9;CL:0002251!2.47e-09!9;CL:0002371!6.31e-09!118;CL:0002076!9.27e-08!15;CL:0000548!1.84e-07!115;CL:0000255!1.84e-07!115;CL:0000075!2.79e-07!7;CL:0002320!3.73e-07!46;CL:0000134!3.73e-07!46;CL:0000988!4.55e-07!32;CL:0002032!4.55e-07!32;CL:0000037!4.55e-07!32;CL:0000566!4.55e-07!32;CL:0000837!4.55e-07!32;CL:0000239!7.57e-07!6;CL:0000677!7.57e-07!6;CL:0000212!7.57e-07!6;CL:0000584!7.57e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000344!1.88e-12!15;UBERON:0001242!2.23e-11!13;UBERON:0000060!2.23e-11!13;UBERON:0001262!2.23e-11!13;UBERON:0004786!2.23e-11!13;UBERON:0000485!3.65e-10!11;UBERON:0003350!2.47e-09!9;UBERON:0004808!2.47e-09!9;UBERON:0001277!2.47e-09!9;UBERON:0004923!4.03e-08!24;UBERON:0002384!3.73e-07!46
|tfbs_overrepresentation_for_novel_motifs=0.847691,0.426221,0.778176,0.165951,0.227727,0.175657,1.25441,0.027826,0.125781,0.873517,0.5998,0.231566,0.827439,0.249744,0.249925,0,0.405853,0.0601435,0.758457,0.601422,0.101766,0.86396,0.249061,0.0629783,0.798169,0.745368,0.721038,0.556066,1.016,0.535987,0.532548,0.493846,0.0591615,0.384407,0.911799,0.0740471,0.44687,0.228897,0.396493,0.142999,0.222477,0.541149,0.551639,0.25264,0.960448,0.931275,1.61331,1.1029,0.439989,0.293801,1.01403,0.793253,0.297906,0.621761,0.63782,0.255168,0.0917696,0.632526,0.416036,0.705824,0.476165,0.810165,0.323654,0.381514,0.26368,1.06834,0.765078,1.10104,0.472057,0.958179,1.75038,0.122106,0.917807,0.66884,1.33922,0.603659,0.634832,0.329879,0.461106,0.339733,0.293881,0.420719,0.807577,0.109746,0.563042,5.19473,0.174419,0.813009,0.908536,1.25993,0.831175,0.56755,0.505205,0.0663617,0.387366,1.39758,0.113637,0.507703,0.339375,0.69381,0.0552129,0.493598,1.47329,0.391523,1.01318,0.540415,1.12451,0.198293,0.705696,2.27401,0.134437,0.607409,0.34141,0.608615,0.837889,0.220154,1.54331,0.971953,0.406964,0.0536296,0.673855,0.363969,0.272218,0.329142,0.889642,0.464341,0.246642,0.499188,1.8018,0.239481,0.590261,0.485482,0.735806,0.265613,0.858504,1.82191,0.144091,0.184858,0.811653,1.62404,1.22863,0.769526,0.281588,0.50313,1.00119,1.0357,0.905286,1.58469,0.446755,0.497371,1.1597,2.47648,0.623204,1.0078,0.264901,0.698893,0.292614,0.0771958,0.425787,1.40075,0.820693,0.562267,0.464731,0.415022,0.995075,0.259222,0.201311,0.230394,0.754756
}}

Latest revision as of 15:12, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:93858548..93858552,-p@chr11:93858548..93858552
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Mm9::chr12:92828393..92828408,-p2@Gtf2a1
Mm9::chr14:76244742..76244755,-p3@Gm4285
Mm9::chr15:38448263..38448268,+p@chr15:38448263..38448268
+
Mm9::chr15:83295244..83295247,+p@chr15:83295244..83295247
+
Mm9::chr15:89260490..89260495,+p@chr15:89260490..89260495
+
Mm9::chr16:94748437..94748446,-p4@Dscr3
Mm9::chr17:15841756..15841774,-p@chr17:15841756..15841774
-
Mm9::chr17:87682111..87682126,-p1@ENSMUST00000161759
Mm9::chr19:6278195..6278220,-p@chr19:6278195..6278220
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Mm9::chr2:14976686..14976706,-p2@Nsun6
Mm9::chr2:154429699..154429704,+p@chr2:154429699..154429704
+
Mm9::chr4:43059163..43059187,+p@chr4:43059163..43059187
+
Mm9::chr5:122581952..122581957,+p@chr5:122581952..122581957
+
Mm9::chr5:125873800..125873824,+p@chr5:125873800..125873824
+
Mm9::chr6:86619601..86619640,+p@chr6:86619601..86619640
+
Mm9::chr7:130513816..130513835,+p@chr7:130513816..130513835
+
Mm9::chr7:16899383..16899398,-p@chr7:16899383..16899398
-
Mm9::chr7:16899402..16899412,-p@chr7:16899402..16899412
-
Mm9::chr7:29163499..29163533,-p@chr7:29163499..29163533
-


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:0042978ornithine decarboxylase activator activity0.0170902711785424
GO:0030904retromer complex0.0170902711785424
GO:0005672transcription factor TFIIA complex0.0170902711785424
GO:0042979ornithine decarboxylase regulator activity0.0213593277225945
GO:0006596polyamine biosynthetic process0.0239185150232815
GO:0007034vacuolar transport0.0390217600260289
GO:0006595polyamine metabolic process0.0390217600260289



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)
MA0003.11.95551
MA0004.10.49817
MA0006.10.243994
MA0007.10.473814
MA0009.11.28645
MA0014.13.44412
MA0017.10.991585
MA0019.10.359884
MA0024.10.47854
MA0025.10.731571
MA0027.12.12059
MA0028.10.548349
MA0029.10.459477
MA0030.10.465221
MA0031.10.434261
MA0038.11.36706
MA0040.10.528552
MA0041.10.118772
MA0042.10.11115
MA0043.11.47136
MA0046.10.549602
MA0048.11.34333
MA0050.10.19271
MA0051.10.277682
MA0052.12.27883
MA0055.11.61015
MA0056.10
MA0057.10.231719
MA0058.10.348173
MA0059.10.366652
MA0060.14.87421
MA0061.11.09874
MA0063.10
MA0066.10.262291
MA0067.10.836675
MA0068.10.423376
MA0069.10.536088
MA0070.10.52739
MA0071.10.561031
MA0072.10.519805
MA0073.10.920492
MA0074.10.235223
MA0076.10.636542
MA0077.10.500504
MA0078.10.303693
MA0081.10.800667
MA0083.10.604132
MA0084.11.15371
MA0087.10.564877
MA0088.11.1835
MA0089.10
MA0090.10.870232
MA0091.10.519739
MA0092.10.443474
MA0093.10.269439
MA0095.10
MA0098.10
MA0100.10.643107
MA0101.11.24765
MA0103.10.295593
MA0105.11.68494
MA0106.10.309901
MA0107.11.00878
MA0108.21.7522
MA0109.10
MA0111.10.465601
MA0113.10.287528
MA0114.11.08747
MA0115.11.47674
MA0116.11.34371
MA0117.10.577975
MA0119.10.119877
MA0122.10.596061
MA0124.10.786128
MA0125.10.716372
MA0130.10
MA0131.10.356119
MA0132.10
MA0133.10
MA0135.10.638323
MA0136.10.697748
MA0139.11.17479
MA0140.10.642909
MA0141.10.665563
MA0142.10.421761
MA0143.10.300449
MA0144.10.180765
MA0145.11.62274
MA0146.10.906195
MA0147.10.759328
MA0148.10.524837
MA0149.10.12279
MA0062.20.199205
MA0035.20.230058
MA0039.27.16702
MA0138.20.349554
MA0002.20.277315
MA0137.21.09444
MA0104.20.888584
MA0047.20.270154
MA0112.20.466674
MA0065.20.468632
MA0150.10.921891
MA0151.10
MA0152.10.270237
MA0153.10.653688
MA0154.10.68796
MA0155.10.5414
MA0156.10.306246
MA0157.10.394402
MA0158.10
MA0159.10.208462
MA0160.11.01566
MA0161.10
MA0162.14.78518
MA0163.12.47009
MA0164.10.698382
MA0080.20.288132
MA0018.22.03493
MA0099.20.911151
MA0079.25.8021
MA0102.21.20505
MA0258.10.368189
MA0259.11.10996
MA0442.10
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