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MCL coexpression mm9:906: Difference between revisions

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{{MCL_coexpression_mm9
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class II protein complex;0.0195077156806841;14999!GO:0051085;chaperone cofactor-dependent protein folding;0.0195077156806841;14999!GO:0006458;'de novo' protein folding;0.0195077156806841;14999!GO:0051084;'de novo' posttranslational protein folding;0.0195077156806841;14999!GO:0002495;antigen processing and presentation of peptide antigen via MHC class II;0.0195077156806841;14999!GO:0019886;antigen processing and presentation of exogenous peptide antigen via MHC class II;0.0195077156806841;14999!GO:0002478;antigen processing and presentation of exogenous peptide antigen;0.0195077156806841;14999!GO:0002504;antigen processing and presentation of peptide or polysaccharide antigen via MHC class II;0.0195077156806841;14999!GO:0019884;antigen processing and presentation of exogenous antigen;0.0209884571534992;14999!GO:0042611;MHC protein complex;0.0221723299436552;14999!GO:0048002;antigen processing and presentation of peptide antigen;0.0253775944494857;14999!GO:0019882;antigen processing and 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|coexpression_dpi_cluster_scores_median=0,0.374812541965839,0.221947893822551,0.939570011938875,0.793381594993783,0.220909281041545,0.333536012540613,0,0,0,0,0,0,0,0,0,0,0.084129859861042,0.0279020860741917,0,0.153106280842865,0,0,0.401169189647611,0.475149014432444,0.2645983963912,0.352461966204564,0.263833268597209,0.764585826935356,0.938631279606164,0.190434627270153,0,0,0,1.03177570342533,0.712075782947904,0.931066595746763,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.055272043172713,0,0,0,0,0,0.125346668336851,0,0,0,0,0,0,0,0,0,0,0.255100480297832,0.357941141880739,0.0300545597055,0,0,0,0,0,0,0,0.110319863569628,0,0,0,0,0.228480260119283,0,0,0.968224106238893,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0430998257964463,0,0,0,1.1770927768014,0.248891521923355,0,0,0,0,0,0.098043425305356,0.337141718919576,0.0662136857075299,0.0973736644748266,0.141036409786105,0.225192348419931,0.139241831090348,0.258577637711746,0.460961439647787,0,0,0,0.0805006992779881,0.0384935222863376,0.0294389011296462,0.0266298923127834,0.0298971899647678,0,0.0731640704872308,0.112756652096095,0,0,0,0,0,0,0,0,0.10536076625968,0,0,0,0,0.0358300855065507,0.085489078226422,0.421112830976558,0,0,0,0,0,0.0463679768904873,0,0.059507504784391,0.123062996466791,0.0642538110976656,0.353726674418046,0.155064609281699,0.336714826373178,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0288216590713588,0,0,0.0663147875126409,0,0,0,0,0,0,0,0,0,0.0596340098159245,0,0,0,0,0,0,0,0,0,0,0.0233256667533105,0,0,0,0,0,0,0,0.363059837905097,0,0.0638344686817875,0,0,0.0374755578790873,0.055643654597214,0.0447367441903353,0,0,0,0.231897331272141,0,0,0.0222709268946923,0,0,0,0.0923568851569585,0.100975358632432,0.360307167084185,0,0,0,0,0,0,0,0,0,0,0,0,0.290534061368087,0.073907766449828,0,0,0.066458422198436,0.0726545746805335,0,0.0299122093309719,0.0608271539290338,0.0308041899510522,0.0398894237220457,0.099980008127235,0.143896423759131,0.139388180619654,0,0,0,0,0.0383547285828163,0.134336252040636,0.162863016520274,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0375226752578547,0,0.0269518943326477,0,0,0.0238095886952444,0,0,0,0,0,0,0,0.0195303707501796,0.017637724668944,0,0,0,0,0,0,0,0,0,0,0.0430926821803413,0,0,0,0
|gostat_on_MCL_coexpression=GO:0042613;MHC class II protein complex;0.0195077156806841;14999!GO:0051085;chaperone cofactor-dependent protein folding;0.0195077156806841;14999!GO:0006458;'de novo' protein folding;0.0195077156806841;14999!GO:0051084;'de novo' posttranslational protein folding;0.0195077156806841;14999!GO:0002495;antigen processing and presentation of peptide antigen via MHC class II;0.0195077156806841;14999!GO:0019886;antigen processing and presentation of exogenous peptide antigen via MHC class II;0.0195077156806841;14999!GO:0002478;antigen processing and presentation of exogenous peptide antigen;0.0195077156806841;14999!GO:0002504;antigen processing and presentation of peptide or polysaccharide antigen via MHC class II;0.0195077156806841;14999!GO:0019884;antigen processing and presentation of exogenous antigen;0.0209884571534992;14999!GO:0042611;MHC protein complex;0.0221723299436552;14999!GO:0048002;antigen processing and presentation of peptide antigen;0.0253775944494857;14999!GO:0019882;antigen processing and presentation;0.0389747969703214;14999!
|ontology_enrichment_celltype=CL:0002563!2.97e-11!9;CL:0002251!2.97e-11!9;CL:0000239!1.03e-07!6;CL:0000677!1.03e-07!6;CL:0000212!1.03e-07!6;CL:0000584!1.03e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005409!3.42e-22!47;UBERON:0004119!8.26e-22!118;UBERON:0000925!8.26e-22!118;UBERON:0006595!8.26e-22!118;UBERON:0000160!9.17e-22!31;UBERON:0001007!1.13e-21!116;UBERON:0001555!1.13e-21!116;UBERON:0007026!1.13e-21!116;UBERON:0004921!7.02e-20!114;UBERON:0000344!5.39e-18!15;UBERON:0001242!1.01e-15!13;UBERON:0000060!1.01e-15!13;UBERON:0001262!1.01e-15!13;UBERON:0004786!1.01e-15!13;UBERON:0004923!1.15e-15!24;UBERON:0003350!2.97e-11!9;UBERON:0004808!2.97e-11!9;UBERON:0001277!2.97e-11!9;UBERON:0000485!1.07e-08!11;UBERON:0005911!3.25e-08!69
|tfbs_overrepresentation_for_novel_motifs=0.393008,0.121181,0.367606,0.434198,0.260188,1.13872,0.538088,0.173246,0.181564,0.687027,0.494602,0.526159,0.173454,0.550255,0.275867,0,0.742571,0.252772,0.160384,0.29826,0.332107,0.223663,0.549359,0.717658,0.374936,0.577606,0.466037,0.469052,0.303071,0.376624,0.455168,0.843667,0.250677,0.136998,0.276324,1.66153,0.242032,0.522578,1.1836,0.195877,0.256422,0.460258,0.784847,0.761266,0.403938,0.423266,0.662995,0.484612,0.170971,0.305876,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.314394,0.513517,0.145699,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.0665967,1.03623,0.140213,0.131016,0.136938,0.651651,0.806481,0.336166,1.01677,0.759925,0.612313,0.501608,0.920903,0.025519,0.0299392,0.757533,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,1.10739,0.1711,0.859272,0.663249,0.681235,0.679141,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,2.72355,0.254749,0.0359654,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,1.56744,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.766041,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.676555,0.524587,0.0131724
}}

Latest revision as of 16:05, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:53670461..53670487,+p@chr11:53670461..53670487
+
Mm9::chr16:10489821..10489850,+p4@Ciita
Mm9::chr16:10489852..10489897,+p2@Ciita
Mm9::chr16:55816886..55816906,+p@chr16:55816886..55816906
+
Mm9::chr17:34290110..34290184,+p1@H2-DMb1
Mm9::chr17:84555738..84555750,-p@chr17:84555738..84555750
-
Mm9::chr5:73948518..73948529,+p@chr5:73948518..73948529
+
Mm9::chr5:73948543..73948565,+p@chr5:73948543..73948565
+


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:0042613MHC class II protein complex0.0195077156806841
GO:0051085chaperone cofactor-dependent protein folding0.0195077156806841
GO:0006458'de novo' protein folding0.0195077156806841
GO:0051084'de novo' posttranslational protein folding0.0195077156806841
GO:0002495antigen processing and presentation of peptide antigen via MHC class II0.0195077156806841
GO:0019886antigen processing and presentation of exogenous peptide antigen via MHC class II0.0195077156806841
GO:0002478antigen processing and presentation of exogenous peptide antigen0.0195077156806841
GO:0002504antigen processing and presentation of peptide or polysaccharide antigen via MHC class II0.0195077156806841
GO:0019884antigen processing and presentation of exogenous antigen0.0209884571534992
GO:0042611MHC protein complex0.0221723299436552
GO:0048002antigen processing and presentation of peptide antigen0.0253775944494857
GO:0019882antigen processing and presentation0.0389747969703214



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)
MA0003.10.0545917
MA0004.11.10905
MA0006.10.271714
MA0007.11.07722
MA0009.10.870101
MA0014.10.0611475
MA0017.10.296816
MA0019.10.688051
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
MA0042.10.919611
MA0043.10.966833
MA0046.10.906029
MA0048.10.102483
MA0050.13.06864
MA0051.13.57551
MA0052.10.890676
MA0055.10.0283571
MA0056.10
MA0057.10.31126
MA0058.12.45447
MA0059.12.51175
MA0060.10.197678
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.657844
MA0069.10.891016
MA0070.12.04375
MA0071.10.471969
MA0072.10.872842
MA0073.10.138438
MA0074.10.531046
MA0076.10.315013
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.064239
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.11.43515
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.133231
MA0106.10.626997
MA0107.10.814533
MA0108.21.69252
MA0109.10
MA0111.10.415012
MA0113.10.598933
MA0114.11.18683
MA0115.10.969632
MA0116.10.747001
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
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.246409
MA0146.10.0169049
MA0147.11.24068
MA0148.10.450593
MA0149.10.367458
MA0062.20.137653
MA0035.20.524137
MA0039.20.254826
MA0138.20.675599
MA0002.20.988033
MA0137.20.32312
MA0104.21.03907
MA0047.20.576767
MA0112.20.2464
MA0065.20.0704227
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.10.100744
MA0155.10.0804339
MA0156.10.314185
MA0157.10.729116
MA0158.10
MA0159.10.246253
MA0160.10.453546
MA0161.10
MA0162.10.0211019
MA0163.10.0186439
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.685525
MA0102.21.59466
MA0258.10.60477
MA0259.10.643936
MA0442.10
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