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MCL coexpression mm9:1085: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000221!9.49e-17!44;CL:0000133!9.49e-17!44;CL:0002319!2.39e-16!43;CL:0000117!6.49e-15!23;CL:0000337!6.49e-15!23;CL:0000540!3.79e-14!33;CL:0000047!3.79e-14!33;CL:0000031!3.79e-14!33;CL:0000404!3.79e-14!33;CL:0000055!3.26e-13!49;CL:0000393!7.53e-11!39;CL:0000211!7.53e-11!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.24e-30!73;UBERON:0001016!2.06e-29!75;UBERON:0004121!5.11e-28!95;UBERON:0000924!5.11e-28!95;UBERON:0006601!5.11e-28!95;UBERON:0000073!7.21e-25!54;UBERON:0002346!4.76e-24!64;UBERON:0003075!4.76e-24!64;UBERON:0007284!4.76e-24!64;UBERON:0001049!1.26e-23!52;UBERON:0005068!1.26e-23!52;UBERON:0006241!1.26e-23!52;UBERON:0007135!1.26e-23!52;UBERON:0010371!3.60e-23!73;UBERON:0002020!7.04e-21!34;UBERON:0000955!3.59e-20!47;UBERON:0006238!3.59e-20!47;UBERON:0002616!1.34e-19!46;UBERON:0003056!2.28e-18!49;UBERON:0003080!1.50e-17!40;UBERON:0003528!2.49e-17!29;UBERON:0002791!2.49e-17!29;UBERON:0001893!2.49e-17!29;UBERON:0002780!4.20e-17!39;UBERON:0001890!4.20e-17!39;UBERON:0006240!4.20e-17!39;UBERON:0010314!1.09e-14!92;UBERON:0000956!5.40e-13!21;UBERON:0001869!5.40e-13!21;UBERON:0000203!5.40e-13!21;UBERON:0002619!1.61e-10!17;UBERON:0000468!4.62e-07!333;UBERON:0002021!6.16e-07!10;UBERON:0000411!6.16e-07!10;UBERON:0001950!6.16e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.660133,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.616096,0.826837,1.34037,0.575086,1.12363,0.599731,0.315771,0,0.795315,0.291368,0.561256,0.361892,0.978328,0.586604,1.45867,0.29769,1.89054,0.62766,0.184473,0.516511,3.39612,0.145661,0.50223,0.897561,0.78719,0.498917,0.316253,0.248902,0.279977,0.57142,0.258564,0.652422,0.295233,0.507468,0.0742755,0.317766,1.19315,0.469348,0.714592,0.532496,0.0609361,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,1.59614,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.611537,1.09164,4.62315,0.159969,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,2.93639,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.708155,0.237542,0.589174,0.913319,0.71485,0.79664,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,3.97128,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,1.47713,0.886471,1.92168,1.04192,1.26486,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.763807,0.573477,5.353
|tfbs_overrepresentation_jaspar=MA0003.1;4.19152,MA0004.1;2.09829,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;7.46153,MA0017.1;0.337808,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;1.30252,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.362005,MA0056.1;0,MA0057.1;4.70208,MA0058.1;3.642,MA0059.1;3.71611,MA0060.1;0.232592,MA0061.1;2.86794,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;0.927016,MA0073.1;4.00719,MA0074.1;1.41926,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;1.07783,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;2.05511,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;3.30666,MA0095.1;0,MA0098.1;0,MA0100.1;1.39455,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;6.35526,MA0106.1;0.677988,MA0107.1;2.45837,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;1.32534,MA0115.1;1.0246,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;2.05933,MA0145.1;4.21283,MA0146.1;3.71137,MA0147.1;2.12106,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;8.00829,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.957645,MA0104.2;1.17226,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;1.56466,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.397336,MA0155.1;0.687925,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;6.8052,MA0163.1;2.64114,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;21.2804,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.729797,MA0442.1;0
}}

Latest revision as of 16:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:69650582..69650623,-p@chr11:69650582..69650623
-
Mm9::chr19:46575657..46575687,+p7@Trim8
Mm9::chr2:102291917..102291931,-p2@Fjx1
Mm9::chr2:102291954..102291972,-p1@Fjx1
Mm9::chr2:102291983..102292000,-p3@Fjx1
Mm9::chr5:141124892..141124903,-p4@Ttyh3
Mm9::chr5:141124934..141124968,-p2@Ttyh3


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
central nervous system3.24e-3073
nervous system2.06e-2975
ectoderm-derived structure5.11e-2895
ectoderm5.11e-2895
presumptive ectoderm5.11e-2895
regional part of nervous system7.21e-2554
neurectoderm4.76e-2464
neural plate4.76e-2464
presumptive neural plate4.76e-2464
neural tube1.26e-2352
neural rod1.26e-2352
future spinal cord1.26e-2352
neural keel1.26e-2352
ecto-epithelium3.60e-2373
gray matter7.04e-2134
brain3.59e-2047
future brain3.59e-2047
regional part of brain1.34e-1946
pre-chordal neural plate2.28e-1849
anterior neural tube1.50e-1740
brain grey matter2.49e-1729
regional part of telencephalon2.49e-1729
telencephalon2.49e-1729
regional part of forebrain4.20e-1739
forebrain4.20e-1739
future forebrain4.20e-1739
structure with developmental contribution from neural crest1.09e-1492
cerebral cortex5.40e-1321
cerebral hemisphere5.40e-1321
pallium5.40e-1321
regional part of cerebral cortex1.61e-1017
multi-cellular organism4.62e-07333
occipital lobe6.16e-0710
visual cortex6.16e-0710
neocortex6.16e-0710


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)
MA0003.14.19152
MA0004.12.09829
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.17.46153
MA0017.10.337808
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
MA0048.11.30252
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.14.70208
MA0058.13.642
MA0059.13.71611
MA0060.10.232592
MA0061.12.86794
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.14.00719
MA0074.11.41926
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.11.07783
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.12.05511
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.13.30666
MA0095.10
MA0098.10
MA0100.11.39455
MA0101.10.406019
MA0103.10.348572
MA0105.16.35526
MA0106.10.677988
MA0107.12.45837
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.11.32534
MA0115.11.0246
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
MA0144.12.05933
MA0145.14.21283
MA0146.13.71137
MA0147.12.12106
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.28.00829
MA0138.20.727395
MA0002.20.205289
MA0137.20.957645
MA0104.21.17226
MA0047.20.626803
MA0112.20.0910939
MA0065.21.56466
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.687925
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.16.8052
MA0163.12.64114
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.221.2804
MA0102.21.65195
MA0258.10.246285
MA0259.10.729797
MA0442.10
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