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MCL coexpression mm9:1020: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0001017!6.74e-26!73;UBERON:0001016!9.01e-26!75;UBERON:0002020!5.39e-22!34;UBERON:0003528!1.78e-17!29;UBERON:0002791!1.78e-17!29;UBERON:0001893!1.78e-17!29;UBERON:0004121!8.17e-17!95;UBERON:0000924!8.17e-17!95;UBERON:0006601!8.17e-17!95;UBERON:0000073!1.40e-15!54;UBERON:0000956!4.05e-14!21;UBERON:0001869!4.05e-14!21;UBERON:0000203!4.05e-14!21;UBERON:0001049!4.74e-13!52;UBERON:0005068!4.74e-13!52;UBERON:0006241!4.74e-13!52;UBERON:0007135!4.74e-13!52;UBERON:0002619!1.25e-12!17;UBERON:0002384!4.75e-12!46;UBERON:0002346!3.13e-11!64;UBERON:0003075!3.13e-11!64;UBERON:0007284!3.13e-11!64;UBERON:0002780!6.94e-11!39;UBERON:0001890!6.94e-11!39;UBERON:0006240!6.94e-11!39;UBERON:0003080!2.03e-10!40;UBERON:0002021!2.70e-10!10;UBERON:0000411!2.70e-10!10;UBERON:0001950!2.70e-10!10;UBERON:0002616!5.44e-10!46;UBERON:0000955!1.33e-09!47;UBERON:0006238!1.33e-09!47;UBERON:0010371!1.44e-08!73;UBERON:0011216!3.13e-07!194;UBERON:0003056!3.78e-07!49;UBERON:0002410!4.87e-07!9;UBERON:0002371!6.75e-07!16
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.0418382,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.215218,0.0609112,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,0.19222,0.112498,1.73763,0.27937,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,0.344372,0.446946,0.50223,0.897561,0.289148,0.498917,0.316253,0.0235321,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.0742755,0.317766,0.0275764,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,1.09164,0.17012,0.482617,0.498755,0.703064,0.859987,0.378988,0.212973,0.812889,1.59309,0.200155,0.975495,0.0369809,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.708155,0.237542,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,1.10097,1.02459,0.380122,0.547992,1.27206,0.293461,0.0501572,0.484437,0.796633,0.276329,1.09707,1.76329,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.0206035
|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;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;1.519,MA0040.1;2.15736,MA0041.1;1.04397,MA0042.1;1.01509,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;0.362005,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;1.49567,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;4.19963e-05,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;0.0841779,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;1.0468,MA0103.1;0.348572,MA0105.1;0.162418,MA0106.1;0.677988,MA0107.1;0.906859,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;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;1.3943,MA0141.1;0.964041,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.0910975,MA0146.1;0.0256827,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.014361,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.304722,MA0065.2;0.0914071,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.792589,MA0155.1;0.102995,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.0312493,MA0163.1;0.0280055,MA0164.1;1.46244,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;6.36279e-07,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:16, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:30698559..30698561,-p@chr10:30698559..30698561
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Mm9::chr11:110813223..110813228,-p@chr11:110813223..110813228
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Mm9::chr11:11954302..11954310,-p1@ENSMUST00000082868
Mm9::chr12:55340225..55340232,+p1@ENSMUST00000082671
Mm9::chr13:96667070..96667075,-p1@ENSMUST00000083932
Mm9::chr3:65892179..65892181,-p1@ENSMUST00000082588
Mm9::chr5:34873297..34873300,+p1@ENSMUST00000157707


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>

Cell Type
Ontology termp-valuen
animal cell8.05e-39115
eukaryotic cell8.05e-39115
somatic cell3.07e-37118
stem cell4.24e-3697
somatic stem cell8.60e-3591
multi fate stem cell8.60e-3591
neural cell1.87e-3343
non-terminally differentiated cell5.54e-3349
ectodermal cell2.32e-3244
neurectodermal cell2.32e-3244
embryonic cell3.32e-2970
neuron8.82e-2733
neuronal stem cell8.82e-2733
neuroblast8.82e-2733
electrically signaling cell8.82e-2733
electrically responsive cell3.96e-2639
electrically active cell3.96e-2639
CNS neuron (sensu Vertebrata)4.91e-2223
neuroblast (sensu Vertebrata)4.91e-2223
motile cell3.28e-1654
connective tissue cell4.75e-1246
mesenchymal cell4.75e-1246
hematopoietic lineage restricted progenitor cell2.09e-0825
oligodendrocyte precursor cell3.89e-088
myeloid lineage restricted progenitor cell8.94e-0813
migratory neural crest cell2.62e-0710
neuron associated cell2.62e-0710
glial cell (sensu Vertebrata)2.62e-0710
neuron associated cell (sensu Vertebrata)2.62e-0710
glial cell2.62e-0710
glioblast2.62e-0710
glioblast (sensu Vertebrata)2.62e-0710
autonomic neuron4.87e-079
neuron of cerebral cortex6.41e-076

Uber Anatomy
Ontology termp-valuen
central nervous system6.74e-2673
nervous system9.01e-2675
gray matter5.39e-2234
brain grey matter1.78e-1729
regional part of telencephalon1.78e-1729
telencephalon1.78e-1729
ectoderm-derived structure8.17e-1795
ectoderm8.17e-1795
presumptive ectoderm8.17e-1795
regional part of nervous system1.40e-1554
cerebral cortex4.05e-1421
cerebral hemisphere4.05e-1421
pallium4.05e-1421
neural tube4.74e-1352
neural rod4.74e-1352
future spinal cord4.74e-1352
neural keel4.74e-1352
regional part of cerebral cortex1.25e-1217
connective tissue4.75e-1246
neurectoderm3.13e-1164
neural plate3.13e-1164
presumptive neural plate3.13e-1164
regional part of forebrain6.94e-1139
forebrain6.94e-1139
future forebrain6.94e-1139
anterior neural tube2.03e-1040
occipital lobe2.70e-1010
visual cortex2.70e-1010
neocortex2.70e-1010
regional part of brain5.44e-1046
brain1.33e-0947
future brain1.33e-0947
ecto-epithelium1.44e-0873
organ system subdivision3.13e-07194
pre-chordal neural plate3.78e-0749
autonomic nervous system4.87e-079
bone marrow6.75e-0716


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
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.11.519
MA0040.12.15736
MA0041.11.04397
MA0042.11.01509
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.11.49567
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.14.19963e-05
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.0468
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.906859
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
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
MA0140.11.3943
MA0141.10.964041
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.0910975
MA0146.10.0256827
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.014361
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.304722
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.792589
MA0155.10.102995
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.0312493
MA0163.10.0280055
MA0164.11.46244
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.26.36279e-07
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:1020&oldid=3073019"