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MCL coexpression mm9:1160: Difference between revisions

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{{MCL_coexpression_mm9
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adaptor activity;0.0403155565721875;27371!GO:0042612;MHC class I protein complex;0.0403155565721875;15018!GO:0002474;antigen processing and presentation of peptide antigen via MHC class I;0.0403155565721875;15018!GO:0030674;protein binding, bridging;0.0403155565721875;27371!GO:0042611;MHC protein complex;0.0403155565721875;15018!GO:0004907;interleukin receptor activity;0.0403155565721875;60504!GO:0048002;antigen processing and presentation of peptide antigen;0.0403155565721875;15018!GO:0019965;interleukin binding;0.0403155565721875;60504!GO:0060090;molecular adaptor activity;0.0437708186230869;27371!GO:0004896;hematopoietin/interferon-class (D200-domain) cytokine receptor activity;0.0463438870390452;60504!GO:0019882;antigen processing and presentation;0.0463438870390452;15018!GO:0019955;cytokine 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|gostat_on_MCL_coexpression=GO:0005070;SH3/SH2 adaptor activity;0.0403155565721875;27371!GO:0042612;MHC class I protein complex;0.0403155565721875;15018!GO:0002474;antigen processing and presentation of peptide antigen via MHC class I;0.0403155565721875;15018!GO:0030674;protein binding, bridging;0.0403155565721875;27371!GO:0042611;MHC protein complex;0.0403155565721875;15018!GO:0004907;interleukin receptor activity;0.0403155565721875;60504!GO:0048002;antigen processing and presentation of peptide antigen;0.0403155565721875;15018!GO:0019965;interleukin binding;0.0403155565721875;60504!GO:0060090;molecular adaptor activity;0.0437708186230869;27371!GO:0004896;hematopoietin/interferon-class (D200-domain) cytokine receptor activity;0.0463438870390452;60504!GO:0019882;antigen processing and presentation;0.0463438870390452;15018!GO:0019955;cytokine binding;0.049893815526705;60504!
|ontology_enrichment_celltype=CL:0002031!5.22e-13!25;CL:0000838!1.08e-11!12;CL:0000084!6.31e-11!11;CL:0000827!6.31e-11!11;CL:0000738!1.73e-10!17;CL:0002087!1.73e-10!17;CL:0000542!2.13e-10!13;CL:0000051!2.13e-10!13;CL:0000988!4.05e-10!32;CL:0002032!4.05e-10!32;CL:0000037!4.05e-10!32;CL:0000566!4.05e-10!32;CL:0000837!4.05e-10!32;CL:0000791!6.93e-10!9;CL:0000789!6.93e-10!9;CL:0002420!6.93e-10!9;CL:0002419!6.93e-10!9;CL:0000790!6.93e-10!9;CL:0000624!6.39e-09!8;CL:0002242!1.54e-07!16;CL:0000893!4.60e-07!6;CL:0002489!4.60e-07!6;CL:0000898!4.60e-07!6;CL:0000809!4.60e-07!6;CL:0000810!4.60e-07!6;CL:0000895!4.60e-07!6;CL:0000808!4.60e-07!6;CL:0000894!4.60e-07!6;CL:0000806!4.60e-07!6;CL:0000807!4.60e-07!6;CL:0000805!4.60e-07!6;CL:0002425!4.60e-07!6;CL:0002436!4.60e-07!6;CL:0002427!4.60e-07!6;CL:0002428!4.60e-07!6;CL:0002429!4.60e-07!6;CL:0002433!4.60e-07!6;CL:0002431!4.60e-07!6;CL:0002432!4.60e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!3.86e-20!48;UBERON:0002405!3.86e-20!48;UBERON:0002390!6.46e-18!45;UBERON:0003061!6.46e-18!45;UBERON:0000077!6.15e-17!35;UBERON:0004177!2.39e-16!29;UBERON:0005057!2.39e-16!29;UBERON:0003408!1.80e-14!24;UBERON:0006562!4.81e-14!24;UBERON:0001557!4.81e-14!24;UBERON:0001042!4.81e-14!24;UBERON:0008814!4.81e-14!24;UBERON:0009145!4.81e-14!24;UBERON:0002370!9.20e-14!23;UBERON:0000974!9.20e-14!23;UBERON:0004807!9.20e-14!23;UBERON:0005058!9.20e-14!23;UBERON:0003351!9.20e-14!23;UBERON:0009113!9.20e-14!23;UBERON:0003295!9.20e-14!23;UBERON:0009722!9.20e-14!23;UBERON:0005562!9.20e-14!23;UBERON:0007690!9.20e-14!23;UBERON:0004119!1.24e-12!118;UBERON:0000925!1.24e-12!118;UBERON:0006595!1.24e-12!118;UBERON:0001041!1.41e-12!80;UBERON:0001007!4.24e-12!116;UBERON:0001555!4.24e-12!116;UBERON:0007026!4.24e-12!116;UBERON:0000072!1.65e-11!27;UBERON:0001004!3.59e-11!42;UBERON:0004921!3.87e-11!114;UBERON:0000065!1.45e-10!41;UBERON:0002530!5.04e-09!65;UBERON:0007811!8.43e-09!36;UBERON:0005911!1.54e-08!69;UBERON:0003081!3.90e-08!87;UBERON:0003929!4.35e-08!55;UBERON:0000063!5.54e-08!35;UBERON:0002368!4.26e-07!60
|tfbs_overrepresentation_for_novel_motifs=0.438063,1.02534,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.215218,0.0609112,0.542749,0.575086,0.206435,1.46059,0.847296,0,0.795315,0.291368,0.19222,0.112498,0.374752,0.08187,0.598814,0.29769,0.419327,0.62766,1.0368,0.516511,0.344372,0.145661,1.25421,0.897561,0.289148,0.166577,0.316253,0.101236,0.279977,0.57142,0.258564,0.230656,0.295233,1.26538,0.54842,0.317766,0.0275764,0.469348,0.714592,0.532496,0.478447,0.917701,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,1.59144,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.0869413,1.09164,0.17012,0.936963,0.166511,0.703064,2.00003,0.378988,1.14907,0.812889,0.663039,0.200155,0.975495,0.0369809,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.203879,0.913319,0.71485,0.127063,0.7665,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,1.92994,1.02459,0.380122,1.35148,1.27206,0.796976,0.187586,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,1.26843,1.24438,2.07659,1.67603,1.19971,1.54859,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.227149
|tfbs_overrepresentation_jaspar=MA0003.1;0.0861444,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.0886247,MA0017.1;1.60852,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.321735,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.648475,MA0056.1;0,MA0057.1;0.117936,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;1.22438,MA0061.1;1.33382,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;1.25994,MA0069.1;0.945354,MA0070.1;2.15469,MA0071.1;1.29103,MA0072.1;2.13722,MA0073.1;0.0890846,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.285759,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;1.13539,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;1.0468,MA0103.1;0.348572,MA0105.1;0.9471,MA0106.1;0.677988,MA0107.1;1.62481,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.719313,MA0115.1;1.0246,MA0116.1;1.51389,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;1.46167,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;0.964041,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.0910975,MA0146.1;0.108739,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.219063,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.631649,MA0065.2;0.305574,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;1.87278,MA0155.1;0.102995,MA0156.1;0.936991,MA0157.1;1.83902,MA0158.1;0,MA0159.1;0.284457,MA0160.1;1.25065,MA0161.1;0,MA0162.1;0.0312493,MA0163.1;0.0280055,MA0164.1;0.600609,MA0080.2;1.62792,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.0369305,MA0102.2;1.65195,MA0258.1;0.688848,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:29, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:35576137..35576140,+p1@H2-Q7
p1@H2-Q8
p1@H2-Q9
p1@LOC100044019
p1@LOC100044020
Mm9::chr18:80895129..80895141,-p@chr18:80895129..80895141
-
Mm9::chr1:61034742..61034781,+p1@Icos
Mm9::chr3:87650762..87650776,+p3@Sh2d2a
Mm9::chr5:122682269..122682291,+p@chr5:122682269..122682291
+
Mm9::chr7:132746957..132746988,+p1@Il21r
Mm9::chr7:132746995..132747010,+p3@Il21r


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:0005070SH3/SH2 adaptor activity0.0403155565721875
GO:0042612MHC class I protein complex0.0403155565721875
GO:0002474antigen processing and presentation of peptide antigen via MHC class I0.0403155565721875
GO:0030674protein binding, bridging0.0403155565721875
GO:0042611MHC protein complex0.0403155565721875
GO:0004907interleukin receptor activity0.0403155565721875
GO:0048002antigen processing and presentation of peptide antigen0.0403155565721875
GO:0019965interleukin binding0.0403155565721875
GO:0060090molecular adaptor activity0.0437708186230869
GO:0004896hematopoietin/interferon-class (D200-domain) cytokine receptor activity0.0463438870390452
GO:0019882antigen processing and presentation0.0463438870390452
GO:0019955cytokine binding0.049893815526705



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 lineage restricted progenitor cell5.22e-1325
lymphoid lineage restricted progenitor cell1.08e-1112
T cell6.31e-1111
pro-T cell6.31e-1111
leukocyte1.73e-1017
nongranular leukocyte1.73e-1017
lymphocyte2.13e-1013
common lymphoid progenitor2.13e-1013
hematopoietic cell4.05e-1032
hematopoietic oligopotent progenitor cell4.05e-1032
hematopoietic stem cell4.05e-1032
angioblastic mesenchymal cell4.05e-1032
hematopoietic multipotent progenitor cell4.05e-1032
mature alpha-beta T cell6.93e-109
alpha-beta T cell6.93e-109
immature T cell6.93e-109
mature T cell6.93e-109
immature alpha-beta T cell6.93e-109
CD4-positive, alpha-beta T cell6.39e-098
nucleate cell1.54e-0716
thymocyte4.60e-076
double negative thymocyte4.60e-076
naive T cell4.60e-076
double-positive, alpha-beta thymocyte4.60e-076
CD4-positive, alpha-beta thymocyte4.60e-076
naive thymus-derived CD4-positive, alpha-beta T cell4.60e-076
DN4 thymocyte4.60e-076
DN1 thymic pro-T cell4.60e-076
DN2 thymocyte4.60e-076
DN3 thymocyte4.60e-076
immature single positive thymocyte4.60e-076
early T lineage precursor4.60e-076
mature CD4 single-positive thymocyte4.60e-076
resting double-positive thymocyte4.60e-076
double-positive blast4.60e-076
CD69-positive double-positive thymocyte4.60e-076
CD69-positive, CD4-positive single-positive thymocyte4.60e-076
CD4-positive, CD8-intermediate double-positive thymocyte4.60e-076
CD24-positive, CD4 single-positive thymocyte4.60e-076

Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.86e-2048
immune system3.86e-2048
hematopoietic system6.46e-1845
blood island6.46e-1845
mixed endoderm/mesoderm-derived structure6.15e-1735
hemopoietic organ2.39e-1629
immune organ2.39e-1629
gland of gut1.80e-1424
pharynx4.81e-1424
upper respiratory tract4.81e-1424
chordate pharynx4.81e-1424
pharyngeal arch system4.81e-1424
pharyngeal region of foregut4.81e-1424
thymus9.20e-1423
neck9.20e-1423
respiratory system epithelium9.20e-1423
hemolymphoid system gland9.20e-1423
pharyngeal epithelium9.20e-1423
thymic region9.20e-1423
pharyngeal gland9.20e-1423
entire pharyngeal arch endoderm9.20e-1423
thymus primordium9.20e-1423
early pharyngeal endoderm9.20e-1423
endoderm-derived structure1.24e-12118
endoderm1.24e-12118
presumptive endoderm1.24e-12118
foregut1.41e-1280
digestive system4.24e-12116
digestive tract4.24e-12116
primitive gut4.24e-12116
segment of respiratory tract1.65e-1127
respiratory system3.59e-1142
subdivision of digestive tract3.87e-11114
respiratory tract1.45e-1041
gland5.04e-0965
craniocervical region8.43e-0936
endo-epithelium1.54e-0869
lateral plate mesoderm3.90e-0887
gut epithelium4.35e-0855
organ segment5.54e-0835
endocrine gland4.26e-0760


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)
MA0003.10.0861444
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.0886247
MA0017.11.60852
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.648475
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.11.22438
MA0061.11.33382
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.11.25994
MA0069.10.945354
MA0070.12.15469
MA0071.11.29103
MA0072.12.13722
MA0073.10.0890846
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.11.13539
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.0468
MA0103.10.348572
MA0105.10.9471
MA0106.10.677988
MA0107.11.62481
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
MA0115.11.0246
MA0116.11.51389
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.11.46167
MA0139.10.202522
MA0140.10.568252
MA0141.10.964041
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.0910975
MA0146.10.108739
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.219063
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.631649
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.11.87278
MA0155.10.102995
MA0156.10.936991
MA0157.11.83902
MA0158.10
MA0159.10.284457
MA0160.11.25065
MA0161.10
MA0162.10.0312493
MA0163.10.0280055
MA0164.10.600609
MA0080.21.62792
MA0018.20.610433
MA0099.20.721008
MA0079.20.0369305
MA0102.21.65195
MA0258.10.688848
MA0259.10.26402
MA0442.10
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