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MCL coexpression mm9:1073: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!1.77e-13!73;UBERON:0000073!4.41e-13!54;UBERON:0001016!6.67e-13!75;UBERON:0001049!4.53e-12!52;UBERON:0005068!4.53e-12!52;UBERON:0006241!4.53e-12!52;UBERON:0007135!4.53e-12!52;UBERON:0002346!1.01e-11!64;UBERON:0003075!1.01e-11!64;UBERON:0007284!1.01e-11!64;UBERON:0000955!1.69e-10!47;UBERON:0006238!1.69e-10!47;UBERON:0002020!2.32e-10!34;UBERON:0010371!3.19e-10!73;UBERON:0004121!3.25e-10!95;UBERON:0000924!3.25e-10!95;UBERON:0006601!3.25e-10!95;UBERON:0002616!4.79e-10!46;UBERON:0003080!1.61e-09!40;UBERON:0002780!5.02e-09!39;UBERON:0001890!5.02e-09!39;UBERON:0006240!5.02e-09!39;UBERON:0003528!7.95e-09!29;UBERON:0002791!7.95e-09!29;UBERON:0001893!7.95e-09!29;UBERON:0003056!1.14e-08!49;UBERON:0002021!9.98e-08!10;UBERON:0000411!9.98e-08!10;UBERON:0001950!9.98e-08!10;UBERON:0010314!2.42e-07!92;UBERON:0002390!2.73e-07!45;UBERON:0003061!2.73e-07!45;UBERON:0002193!3.51e-07!48;UBERON:0002405!3.51e-07!48;UBERON:0004177!7.95e-07!29;UBERON:0005057!7.95e-07!29
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.161863,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.215218,1.7494,0.542749,0.575086,1.76146,0.599731,0.315771,0,0.795315,0.291368,1.06769,0.361892,0.374752,0.586604,0.598814,0.29769,0.419327,0.62766,0.542568,0.516511,1.63164,0.145661,0.50223,0.897561,0.289148,0.166577,1.53201,0.248902,0.279977,0.57142,0.717242,0.652422,0.295233,0.507468,0.54842,0.317766,0.822425,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,1.00328,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,0.611537,1.09164,0.97874,0.482617,0.166511,1.67636,0.859987,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.613286,0.374181,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.823238,0.254625,0.237542,0.589174,0.913319,0.71485,0.399703,0.280055,0.897279,2.33242,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,2.62202,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,1.12953,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.829907,1.00568,0.473246,1.16374,0.620831,1.29374,0.580299,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.927167,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.705627
|tfbs_overrepresentation_jaspar=MA0003.1;2.21402,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;1.17655,MA0009.1;0.92425,MA0014.1;3.41543,MA0017.1;0.89657,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;1.55156,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;4.04772,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;1.43589,MA0056.1;0,MA0057.1;0.756125,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;2.47843,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;1.06143,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;1.49527,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.879104,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;1.0468,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;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;1.04809,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;0.964041,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.631666,MA0146.1;0.493711,MA0147.1;0.753844,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;1.54019,MA0035.2;0.573016,MA0039.2;1.72008,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.624968,MA0047.2;0.626803,MA0112.2;1.05549,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;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;2.75316,MA0163.1;1.63182,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;3.46801,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.729797,MA0442.1;0
}}

Latest revision as of 16:21, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:46125785..46125840,-p1@Cyfip2
Mm9::chr12:88541150..88541234,-p1@Tmed8
Mm9::chr1:59030179..59030198,-p2@Trak2
Mm9::chr7:129432590..129432739,+p1@Prkcb
Mm9::chr7:129775816..129775821,+p@chr7:129775816..129775821
+
Mm9::chr8:26311821..26311931,-p3@Tacc1
Mm9::chrX:7367139..7367155,+p2@Gripap1


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:0050811GABA receptor binding0.0306723247151294



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
central nervous system1.77e-1373
regional part of nervous system4.41e-1354
nervous system6.67e-1375
neural tube4.53e-1252
neural rod4.53e-1252
future spinal cord4.53e-1252
neural keel4.53e-1252
neurectoderm1.01e-1164
neural plate1.01e-1164
presumptive neural plate1.01e-1164
brain1.69e-1047
future brain1.69e-1047
gray matter2.32e-1034
ecto-epithelium3.19e-1073
ectoderm-derived structure3.25e-1095
ectoderm3.25e-1095
presumptive ectoderm3.25e-1095
regional part of brain4.79e-1046
anterior neural tube1.61e-0940
regional part of forebrain5.02e-0939
forebrain5.02e-0939
future forebrain5.02e-0939
brain grey matter7.95e-0929
regional part of telencephalon7.95e-0929
telencephalon7.95e-0929
pre-chordal neural plate1.14e-0849
occipital lobe9.98e-0810
visual cortex9.98e-0810
neocortex9.98e-0810
structure with developmental contribution from neural crest2.42e-0792
hematopoietic system2.73e-0745
blood island2.73e-0745
hemolymphoid system3.51e-0748
immune system3.51e-0748
hemopoietic organ7.95e-0729
immune organ7.95e-0729


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)
MA0003.12.21402
MA0004.10.481116
MA0006.10.311391
MA0007.11.17655
MA0009.10.92425
MA0014.13.41543
MA0017.10.89657
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.11.55156
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
MA0048.14.04772
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.11.43589
MA0056.10
MA0057.10.756125
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.12.47843
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.11.06143
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.11.49527
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.879104
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.0468
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
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.11.04809
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
MA0141.10.964041
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.631666
MA0146.10.493711
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.21.54019
MA0035.20.573016
MA0039.21.72008
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.21.05549
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.102995
MA0156.10.936991
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.12.75316
MA0163.11.63182
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.23.46801
MA0102.21.65195
MA0258.10.246285
MA0259.10.729797
MA0442.10
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