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MCL coexpression mm9:3094: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0019883;antigen processing and presentation of endogenous antigen;0.00379815018504548;14972!GO:0002483;antigen processing and presentation of endogenous peptide antigen;0.00379815018504548;14972!GO:0019885;antigen processing and presentation of endogenous peptide antigen via MHC class I;0.00379815018504548;14972!GO:0042612;MHC class I protein complex;0.0108202796308861;14972!GO:0002474;antigen processing and presentation of peptide antigen via MHC class I;0.0108202796308861;14972!GO:0042611;MHC protein complex;0.0128106795230008;14972!GO:0048002;antigen processing and presentation of peptide antigen;0.013824746690577;14972!GO:0019882;antigen processing and presentation;0.0202668944245671;14972!GO:0009897;external side of plasma membrane;0.0428900342339228;14972!
|ontology_enrichment_celltype=CL:0000988!1.24e-11!32;CL:0002032!1.24e-11!32;CL:0000037!1.24e-11!32;CL:0000566!1.24e-11!32;CL:0000837!1.24e-11!32;CL:0002320!3.25e-11!46;CL:0000134!3.25e-11!46;CL:0002031!1.23e-09!25;CL:0000738!2.13e-09!17;CL:0002087!2.13e-09!17;CL:0000838!6.01e-09!12;CL:0000084!2.43e-08!11;CL:0000827!2.43e-08!11;CL:0000219!3.37e-08!54;CL:0000542!1.41e-07!13;CL:0000051!1.41e-07!13;CL:0000791!4.66e-07!9;CL:0000789!4.66e-07!9;CL:0002420!4.66e-07!9;CL:0002419!4.66e-07!9;CL:0000790!4.66e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!5.51e-18!48;UBERON:0002405!5.51e-18!48;UBERON:0002390!1.26e-16!45;UBERON:0003061!1.26e-16!45;UBERON:0003081!2.93e-12!87;UBERON:0002384!3.25e-11!46;UBERON:0000077!4.27e-09!35;UBERON:0002371!6.16e-09!16;UBERON:0004177!7.10e-09!29;UBERON:0005057!7.10e-09!29;UBERON:0002204!7.63e-09!32;UBERON:0000926!9.00e-09!120;UBERON:0004120!9.00e-09!120;UBERON:0006603!9.00e-09!120;UBERON:0001041!5.53e-08!80;UBERON:0001474!6.54e-08!22;UBERON:0004765!6.54e-08!22;UBERON:0001434!6.54e-08!22;UBERON:0000072!1.73e-07!27;UBERON:0003408!2.15e-07!24;UBERON:0002370!2.78e-07!23;UBERON:0000974!2.78e-07!23;UBERON:0004807!2.78e-07!23;UBERON:0005058!2.78e-07!23;UBERON:0003351!2.78e-07!23;UBERON:0009113!2.78e-07!23;UBERON:0003295!2.78e-07!23;UBERON:0009722!2.78e-07!23;UBERON:0005562!2.78e-07!23;UBERON:0007690!2.78e-07!23
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.876292,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.663409,0.646474,1.12346,0.99279,0.971403,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,1.63704,0.476502,1.16055,1.00151,1.16164,1.32978,0.535545,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,2.53577,0.830796,1.18646,0.854628,0.689894,1.63106,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
|tfbs_overrepresentation_jaspar=MA0003.1;0.0699972,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.416365,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;1.49373,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;0.353763,MA0050.1;1.97065,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;1.06076,MA0056.1;0,MA0057.1;0.337566,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;0.502699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;3.3888,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.0430758,MA0074.1;0.911576,MA0076.1;1.58243,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;0.462282,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.292366,MA0146.1;0.151124,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;1.86813,MA0035.2;0.903829,MA0039.2;0.181475,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;0.312898,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.499274,MA0163.1;0.477233,MA0164.1;0.933981,MA0080.2;1.54848,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.0332569,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 19:34, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:34136411..34136432,-p2@H2-K1
Mm9::chr7:150813746..150813751,-p1@Tnfrsf26
Mm9::chr7:150813813..150813868,-p2@Tnfrsf26


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:0019883antigen processing and presentation of endogenous antigen0.00379815018504548
GO:0002483antigen processing and presentation of endogenous peptide antigen0.00379815018504548
GO:0019885antigen processing and presentation of endogenous peptide antigen via MHC class I0.00379815018504548
GO:0042612MHC class I protein complex0.0108202796308861
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0108202796308861
GO:0042611MHC protein complex0.0128106795230008
GO:0048002antigen processing and presentation of peptide antigen0.013824746690577
GO:0019882antigen processing and presentation0.0202668944245671
GO:0009897external side of plasma membrane0.0428900342339228



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 system5.51e-1848
immune system5.51e-1848
hematopoietic system1.26e-1645
blood island1.26e-1645
lateral plate mesoderm2.93e-1287
connective tissue3.25e-1146
mixed endoderm/mesoderm-derived structure4.27e-0935
bone marrow6.16e-0916
hemopoietic organ7.10e-0929
immune organ7.10e-0929
musculoskeletal system7.63e-0932
mesoderm9.00e-09120
mesoderm-derived structure9.00e-09120
presumptive mesoderm9.00e-09120
foregut5.53e-0880
bone element6.54e-0822
skeletal element6.54e-0822
skeletal system6.54e-0822
segment of respiratory tract1.73e-0727
gland of gut2.15e-0724
thymus2.78e-0723
neck2.78e-0723
respiratory system epithelium2.78e-0723
hemolymphoid system gland2.78e-0723
pharyngeal epithelium2.78e-0723
thymic region2.78e-0723
pharyngeal gland2.78e-0723
entire pharyngeal arch endoderm2.78e-0723
thymus primordium2.78e-0723
early pharyngeal endoderm2.78e-0723


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)
MA0003.10.0699972
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.416365
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.11.49373
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.11.97065
MA0051.10.973068
MA0052.11.29825
MA0055.11.06076
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.13.3888
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.0430758
MA0074.10.911576
MA0076.11.58243
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.21.86813
MA0035.20.903829
MA0039.20.181475
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.499274
MA0163.10.477233
MA0164.10.933981
MA0080.21.54848
MA0018.20.944669
MA0099.21.06348
MA0079.20.0332569
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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