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MCL coexpression mm9:1167: Difference between revisions

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{{MCL_coexpression_mm9
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of calcium ion transport;0.0207684070054428;12293!GO:0030315;T-tubule;0.0207684070054428;12293!GO:0030865;cortical cytoskeleton organization and biogenesis;0.0207684070054428;104027!GO:0043197;dendritic spine;0.0207684070054428;104027!GO:0043269;regulation of ion transport;0.0207684070054428;12293!GO:0016529;sarcoplasmic reticulum;0.0302739810623657;12293!GO:0042383;sarcolemma;0.0302739810623657;12293!GO:0016528;sarcoplasm;0.0302739810623657;12293!GO:0030425;dendrite;0.0461064870399759;104027!GO:0044459;plasma membrane part;0.0465217281282534;12293,104027!GO:0005262;calcium channel activity;0.0465217281282534;12293!GO:0044463;cell projection part;0.0465217281282534;104027!GO:0005923;tight junction;0.0465217281282534;104027!GO:0051049;regulation of transport;0.0485719141194373;12293!GO:0043296;apical junction complex;0.0485719141194373;104027!GO:0016327;apicolateral plasma membrane;0.0485719141194373;104027!GO:0005886;plasma membrane;0.0493937890147435;12293,104027!GO:0006816;calcium ion transport;0.0493937890147435;12293!GO:0045211;postsynaptic membrane;0.0495118245516327;104027!GO:0043005;neuron projection;0.0497117321580318;104027!GO:0044456;synapse 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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010314!8.96e-19!92;UBERON:0004121!3.80e-13!95;UBERON:0000924!3.80e-13!95;UBERON:0006601!3.80e-13!95;UBERON:0001017!4.85e-13!73;UBERON:0001016!5.10e-13!75;UBERON:0000073!3.19e-12!54;UBERON:0002346!6.29e-12!64;UBERON:0003075!6.29e-12!64;UBERON:0007284!6.29e-12!64;UBERON:0010371!1.68e-11!73;UBERON:0001049!1.94e-11!52;UBERON:0005068!1.94e-11!52;UBERON:0006241!1.94e-11!52;UBERON:0007135!1.94e-11!52;UBERON:0000955!2.26e-11!47;UBERON:0006238!2.26e-11!47;UBERON:0002616!8.99e-11!46;UBERON:0003056!1.37e-09!49;UBERON:0003080!1.38e-09!40;UBERON:0004111!2.28e-09!122;UBERON:0000025!3.58e-09!114;UBERON:0002780!4.41e-09!39;UBERON:0001890!4.41e-09!39;UBERON:0006240!4.41e-09!39;UBERON:0000468!4.29e-08!333;UBERON:0002021!7.40e-08!10;UBERON:0000411!7.40e-08!10;UBERON:0001950!7.40e-08!10;UBERON:0002020!4.11e-07!34;UBERON:0003528!6.64e-07!29;UBERON:0002791!6.64e-07!29;UBERON:0001893!6.64e-07!29
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,1.05921,0.480627,0.299217,0.495263,0.587291,0.206208,1.15776,1.7494,1.34037,0.575086,1.12363,0.599731,0.847296,0,1.86712,0.291368,1.06769,0.112498,0.374752,0.08187,1.45867,0.29769,0.419327,0.62766,0.184473,0.516511,1.63164,0.446946,1.25421,0.897561,0.78719,0.166577,3.22048,0.248902,0.279977,0.57142,0.258564,1.21701,0.295233,0.507468,0.258106,0.317766,2.10004,0.469348,0.714592,1.31862,0.82704,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,4.13143,1.09164,10.6707,1.49715,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,10.5362,0.042613,0.877485,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.708155,0.237542,0.203879,0.913319,0.71485,0.79664,0.280055,0.897279,1.02279,0.778243,0.777175,1.26443,0.837607,0.528416,0.998363,0.982279,0.430942,1.02459,0.380122,2.31879,1.27206,0.293461,2.68499,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,2.00769,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,1.46009,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.886471,2.51473,1.04192,3.60413,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,9.08673
|tfbs_overrepresentation_jaspar=MA0003.1;7.93748,MA0004.1;0.481116,MA0006.1;0.837454,MA0007.1;1.17655,MA0009.1;0.92425,MA0014.1;6.7174,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;0.40238,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;0.232592,MA0061.1;0.724575,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;10.6906,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;0.598004,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;0.488671,MA0106.1;2.73793,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;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;1.74348,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.585936,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.631666,MA0146.1;1.57153,MA0147.1;1.38091,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;9.35346,MA0138.2;2.89475,MA0002.2;1.11916,MA0137.2;0.365364,MA0104.2;1.17226,MA0047.2;0.626803,MA0112.2;0.0910939,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;1.13804,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;4.62777,MA0163.1;8.1524,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;13.202,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.729797,MA0442.1;0
}}

Latest revision as of 16:30, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr18:60783855..60783901,-p1@Synpo
Mm9::chr18:60783958..60784005,-p3@Synpo
Mm9::chr5:15440374..15440442,+p2@Cacna2d1
Mm9::chr5:15440524..15440537,+p4@Cacna2d1
Mm9::chr5:15440580..15440605,+p3@Cacna2d1
Mm9::chr5:15440731..15440744,+p6@Cacna2d1
Mm9::chr5:15440771..15440780,+p11@Cacna2d1


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:0051924regulation of calcium ion transport0.0207684070054428
GO:0030315T-tubule0.0207684070054428
GO:0030865cortical cytoskeleton organization and biogenesis0.0207684070054428
GO:0043197dendritic spine0.0207684070054428
GO:0043269regulation of ion transport0.0207684070054428
GO:0016529sarcoplasmic reticulum0.0302739810623657
GO:0042383sarcolemma0.0302739810623657
GO:0016528sarcoplasm0.0302739810623657
GO:0030425dendrite0.0461064870399759
GO:0044459plasma membrane part0.0465217281282534
GO:0005262calcium channel activity0.0465217281282534
GO:0044463cell projection part0.0465217281282534
GO:0005923tight junction0.0465217281282534
GO:0051049regulation of transport0.0485719141194373
GO:0043296apical junction complex0.0485719141194373
GO:0016327apicolateral plasma membrane0.0485719141194373
GO:0005886plasma membrane0.0493937890147435
GO:0006816calcium ion transport0.0493937890147435
GO:0045211postsynaptic membrane0.0495118245516327
GO:0043005neuron projection0.0497117321580318
GO:0044456synapse part0.0497117321580318



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
structure with developmental contribution from neural crest8.96e-1992
ectoderm-derived structure3.80e-1395
ectoderm3.80e-1395
presumptive ectoderm3.80e-1395
central nervous system4.85e-1373
nervous system5.10e-1375
regional part of nervous system3.19e-1254
neurectoderm6.29e-1264
neural plate6.29e-1264
presumptive neural plate6.29e-1264
ecto-epithelium1.68e-1173
neural tube1.94e-1152
neural rod1.94e-1152
future spinal cord1.94e-1152
neural keel1.94e-1152
brain2.26e-1147
future brain2.26e-1147
regional part of brain8.99e-1146
pre-chordal neural plate1.37e-0949
anterior neural tube1.38e-0940
anatomical conduit2.28e-09122
tube3.58e-09114
regional part of forebrain4.41e-0939
forebrain4.41e-0939
future forebrain4.41e-0939
multi-cellular organism4.29e-08333
occipital lobe7.40e-0810
visual cortex7.40e-0810
neocortex7.40e-0810
gray matter4.11e-0734
brain grey matter6.64e-0729
regional part of telencephalon6.64e-0729
telencephalon6.64e-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)
MA0003.17.93748
MA0004.10.481116
MA0006.10.837454
MA0007.11.17655
MA0009.10.92425
MA0014.16.7174
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
MA0048.10.40238
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.648475
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.724575
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.110.6906
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.598004
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
MA0105.10.488671
MA0106.12.73793
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
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.11.74348
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.585936
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.631666
MA0146.11.57153
MA0147.11.38091
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.29.35346
MA0138.22.89475
MA0002.21.11916
MA0137.20.365364
MA0104.21.17226
MA0047.20.626803
MA0112.20.0910939
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.792589
MA0155.11.13804
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.14.62777
MA0163.18.1524
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.213.202
MA0102.21.65195
MA0258.10.246285
MA0259.10.729797
MA0442.10
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