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MCL coexpression mm9:1124: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0002031!2.37e-11!25;CL:0000791!8.58e-11!9;CL:0000789!8.58e-11!9;CL:0002420!8.58e-11!9;CL:0002419!8.58e-11!9;CL:0000790!8.58e-11!9;CL:0000838!3.83e-10!12;CL:0000542!3.14e-09!13;CL:0000051!3.14e-09!13;CL:0000624!5.40e-09!8;CL:0000553!1.26e-08!6;CL:0000556!1.26e-08!6;CL:0000084!1.40e-08!11;CL:0000827!1.40e-08!11;CL:0000988!3.88e-08!32;CL:0002032!3.88e-08!32;CL:0000037!3.88e-08!32;CL:0000566!3.88e-08!32;CL:0000837!3.88e-08!32;CL:0002242!3.50e-07!16
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000077!1.06e-20!35;UBERON:0002193!2.23e-19!48;UBERON:0002405!2.23e-19!48;UBERON:0004177!2.95e-19!29;UBERON:0005057!2.95e-19!29;UBERON:0002390!4.85e-19!45;UBERON:0003061!4.85e-19!45;UBERON:0002370!2.29e-15!23;UBERON:0000974!2.29e-15!23;UBERON:0004807!2.29e-15!23;UBERON:0005058!2.29e-15!23;UBERON:0003351!2.29e-15!23;UBERON:0009113!2.29e-15!23;UBERON:0003295!2.29e-15!23;UBERON:0009722!2.29e-15!23;UBERON:0005562!2.29e-15!23;UBERON:0007690!2.29e-15!23;UBERON:0000065!7.34e-15!41;UBERON:0006562!1.46e-14!24;UBERON:0003408!1.46e-14!24;UBERON:0001557!1.46e-14!24;UBERON:0001042!1.46e-14!24;UBERON:0008814!1.46e-14!24;UBERON:0009145!1.46e-14!24;UBERON:0001004!2.24e-14!42;UBERON:0000072!1.64e-12!27;UBERON:0001041!3.71e-11!80;UBERON:0003081!3.88e-10!87;UBERON:0000063!4.07e-10!35;UBERON:0005911!2.17e-09!69;UBERON:0007811!1.90e-08!36;UBERON:0000926!4.42e-08!120;UBERON:0004120!4.42e-08!120;UBERON:0006603!4.42e-08!120;UBERON:0004119!4.50e-08!118;UBERON:0000925!4.50e-08!118;UBERON:0006595!4.50e-08!118;UBERON:0004921!7.34e-08!114;UBERON:0001007!1.34e-07!116;UBERON:0001555!1.34e-07!116;UBERON:0007026!1.34e-07!116
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.0418382,0.411716,0.480627,0.810002,0.495263,0.587291,0.206208,0.215218,0.0609112,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,0.561256,0.361892,0.978328,0.08187,0.598814,0.29769,0.419327,0.62766,0.542568,0.516511,0.344372,0.145661,0.50223,0.897561,0.289148,0.166577,0.316253,0.101236,0.279977,0.57142,0.717242,0.230656,0.295233,0.507468,0.258106,3.23003,0.0275764,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,1.09164,0.17012,0.159969,0.166511,0.703064,0.859987,2.6336,0.212973,0.812889,1.59309,1.72681,0.975495,0.0369809,0.374181,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.990132,0.547992,1.27206,0.293461,0.0501572,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,2.29762,0.473246,1.16374,0.620831,1.29374,0.580299,0.446555,0.508896,2.78138,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,1.13988,0.300961,0.452587,0.0736236,1.04192,0.243291,0.619892,4.12533,0.655955,0.327731,1.11101,0.446272,1.25393,3.66612,0.864173,0.428662,3.02053,0.612377,0.278874,0.573477,0.0206035
|tfbs_overrepresentation_jaspar=MA0003.1;0.00513025,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.0200028,MA0017.1;2.43592,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.860672,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;1.93597,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;1.30252,MA0050.1;4.43208,MA0051.1;5.07834,MA0052.1;0.945011,MA0055.1;0.0406078,MA0056.1;0,MA0057.1;0.117936,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.121435,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;2.13722,MA0073.1;0.00782298,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;1.60783,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;3.49626,MA0087.1;0.977537,MA0088.1;0.285759,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;0.162418,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.259463,MA0115.1;2.3361,MA0116.1;0.311187,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;0.600242,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.72625,MA0145.1;0.0910975,MA0146.1;0.0256827,MA0147.1;0.274511,MA0148.1;1.24416,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.0478878,MA0138.2;0.727395,MA0002.2;1.11916,MA0137.2;0.957645,MA0104.2;0.218974,MA0047.2;1.51738,MA0112.2;0.631649,MA0065.2;0.0914071,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;0.102995,MA0156.1;0.936991,MA0157.1;1.83902,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.127623,MA0163.1;0.0280055,MA0164.1;0.600609,MA0080.2;0.908823,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;9.18389e-06,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:26, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:91624165..91624180,+p@chr13:91624165..91624180
+
Mm9::chr17:52288610..52288620,+p@chr17:52288610..52288620
+
Mm9::chr17:52288630..52288664,+p@chr17:52288630..52288664
+
Mm9::chr1:175529374..175529408,-p1@Pydc4
Mm9::chr1:175603782..175603817,+p1@Pydc3
Mm9::chr1:175603833..175603841,+p4@Pydc3
Mm9::chr1:175604032..175604047,+p2@Pydc3


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>

Uber Anatomy
Ontology termp-valuen
mixed endoderm/mesoderm-derived structure1.06e-2035
hemolymphoid system2.23e-1948
immune system2.23e-1948
hemopoietic organ2.95e-1929
immune organ2.95e-1929
hematopoietic system4.85e-1945
blood island4.85e-1945
thymus2.29e-1523
neck2.29e-1523
respiratory system epithelium2.29e-1523
hemolymphoid system gland2.29e-1523
pharyngeal epithelium2.29e-1523
thymic region2.29e-1523
pharyngeal gland2.29e-1523
entire pharyngeal arch endoderm2.29e-1523
thymus primordium2.29e-1523
early pharyngeal endoderm2.29e-1523
respiratory tract7.34e-1541
pharynx1.46e-1424
gland of gut1.46e-1424
upper respiratory tract1.46e-1424
chordate pharynx1.46e-1424
pharyngeal arch system1.46e-1424
pharyngeal region of foregut1.46e-1424
respiratory system2.24e-1442
segment of respiratory tract1.64e-1227
foregut3.71e-1180
lateral plate mesoderm3.88e-1087
organ segment4.07e-1035
endo-epithelium2.17e-0969
craniocervical region1.90e-0836
mesoderm4.42e-08120
mesoderm-derived structure4.42e-08120
presumptive mesoderm4.42e-08120
endoderm-derived structure4.50e-08118
endoderm4.50e-08118
presumptive endoderm4.50e-08118
subdivision of digestive tract7.34e-08114
digestive system1.34e-07116
digestive tract1.34e-07116
primitive gut1.34e-07116


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)
MA0003.10.00513025
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.0200028
MA0017.12.43592
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.860672
MA0029.10.858105
MA0030.10.864739
MA0031.11.93597
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.11.30252
MA0050.14.43208
MA0051.15.07834
MA0052.10.945011
MA0055.10.0406078
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.12.13722
MA0073.10.00782298
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.11.60783
MA0081.10.420276
MA0083.11.02098
MA0084.13.49626
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.12.3361
MA0116.10.311187
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
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.72625
MA0145.10.0910975
MA0146.10.0256827
MA0147.10.274511
MA0148.11.24416
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.0478878
MA0138.20.727395
MA0002.21.11916
MA0137.20.957645
MA0104.20.218974
MA0047.21.51738
MA0112.20.631649
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.102995
MA0156.10.936991
MA0157.11.83902
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.127623
MA0163.10.0280055
MA0164.10.600609
MA0080.20.908823
MA0018.20.610433
MA0099.20.721008
MA0079.29.18389e-06
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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