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MCL coexpression mm9:405: Difference between revisions

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{{MCL_coexpression_mm9
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ligand-gated calcium channel activity;0.0352514829974452;20191!GO:0014074;response to purine;0.0352514829974452;20191!GO:0005219;ryanodine-sensitive calcium-release channel activity;0.0352514829974452;20191!GO:0031000;response to caffeine;0.0352514829974452;20191!GO:0046873;metal ion transmembrane transporter activity;0.0352514829974452;16519,11938,20191!GO:0004691;cAMP-dependent protein kinase activity;0.0471455207305244;18747!GO:0030001;metal ion transport;0.0471455207305244;16519,11938,20191!GO:0015467;G-protein activated inward rectifier potassium channel activity;0.0471455207305244;16519!GO:0000209;protein polyubiquitination;0.0471455207305244;17237!GO:0006816;calcium ion transport;0.0471455207305244;11938,20191!GO:0004690;cyclic nucleotide-dependent protein kinase activity;0.0471455207305244;18747!GO:0015278;calcium-release channel activity;0.0471455207305244;20191!GO:0050811;GABA receptor binding;0.0471455207305244;70827!GO:0008324;cation transmembrane transporter activity;0.0471455207305244;16519,11938,20191!GO:0006812;cation transport;0.0471455207305244;16519,11938,20191!GO:0015674;di-, tri-valent inorganic cation 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|gostat_on_MCL_coexpression=GO:0005218;intracellular ligand-gated calcium channel activity;0.0352514829974452;20191!GO:0014074;response to purine;0.0352514829974452;20191!GO:0005219;ryanodine-sensitive calcium-release channel activity;0.0352514829974452;20191!GO:0031000;response to caffeine;0.0352514829974452;20191!GO:0046873;metal ion transmembrane transporter activity;0.0352514829974452;16519,11938,20191!GO:0004691;cAMP-dependent protein kinase activity;0.0471455207305244;18747!GO:0030001;metal ion transport;0.0471455207305244;16519,11938,20191!GO:0015467;G-protein activated inward rectifier potassium channel activity;0.0471455207305244;16519!GO:0000209;protein polyubiquitination;0.0471455207305244;17237!GO:0006816;calcium ion transport;0.0471455207305244;11938,20191!GO:0004690;cyclic nucleotide-dependent protein kinase activity;0.0471455207305244;18747!GO:0015278;calcium-release channel activity;0.0471455207305244;20191!GO:0050811;GABA receptor binding;0.0471455207305244;70827!GO:0008324;cation transmembrane transporter activity;0.0471455207305244;16519,11938,20191!GO:0006812;cation transport;0.0471455207305244;16519,11938,20191!GO:0015674;di-, tri-valent inorganic cation transport;0.0499393897011789;11938,20191!
|ontology_enrichment_celltype=CL:0000117!8.42e-10!23;CL:0000337!8.42e-10!23
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010314!5.26e-25!92;UBERON:0000073!1.86e-18!54;UBERON:0001049!3.19e-17!52;UBERON:0005068!3.19e-17!52;UBERON:0006241!3.19e-17!52;UBERON:0007135!3.19e-17!52;UBERON:0001017!5.52e-16!73;UBERON:0002020!1.75e-15!34;UBERON:0001016!3.23e-15!75;UBERON:0002346!4.41e-15!64;UBERON:0003075!4.41e-15!64;UBERON:0007284!4.41e-15!64;UBERON:0000955!1.93e-14!47;UBERON:0006238!1.93e-14!47;UBERON:0004111!4.39e-14!122;UBERON:0000025!6.83e-14!114;UBERON:0002616!8.38e-14!46;UBERON:0004121!6.03e-13!95;UBERON:0000924!6.03e-13!95;UBERON:0006601!6.03e-13!95;UBERON:0010371!6.40e-13!73;UBERON:0003528!1.34e-12!29;UBERON:0002791!1.34e-12!29;UBERON:0001893!1.34e-12!29;UBERON:0003080!4.32e-12!40;UBERON:0002780!1.73e-11!39;UBERON:0001890!1.73e-11!39;UBERON:0006240!1.73e-11!39;UBERON:0003056!2.22e-11!49;UBERON:0007100!8.41e-10!18;UBERON:0000948!8.41e-10!18;UBERON:0005498!8.41e-10!18;UBERON:0004140!8.41e-10!18;UBERON:0009881!8.41e-10!18;UBERON:0004141!8.41e-10!18;UBERON:0003084!8.41e-10!18;UBERON:0007005!8.41e-10!18;UBERON:0004139!8.41e-10!18;UBERON:0004291!8.41e-10!18;UBERON:0002021!5.93e-09!10;UBERON:0000411!5.93e-09!10;UBERON:0001950!5.93e-09!10;UBERON:0000956!1.27e-08!21;UBERON:0001869!1.27e-08!21;UBERON:0000203!1.27e-08!21;UBERON:0002619!1.21e-07!17;UBERON:0004535!1.82e-07!23;UBERON:0001009!1.82e-07!23
|tfbs_overrepresentation_for_novel_motifs=0.149902,1.80443,0.823928,0.178048,0.0709145,0.188081,0.708527,0.130554,0.936804,1.94794,1.18299,0.24561,1.2848,0.264234,0.968697,0,0.42315,0.0671461,0.277053,0.951721,0.358501,0.461365,0.263535,0.070175,0.138033,0.285776,1.14076,1.10998,2.82127,0.884629,0.562931,0.512187,0.868591,1.02289,0.0793793,1.47138,0.834323,0.242872,0.194199,0.652383,0.243076,0.571717,0.249206,0.0801495,1.34469,0.508392,0.355451,0.614044,0.0396353,0.317394,0.408111,0.828085,0.333099,0.641205,0.657376,0.269785,0.100694,0.664869,0.457729,2.08876,1.23731,0.314847,0.354886,0.398468,0.278491,0.433342,0.785371,1.12243,0.490165,0.979213,0.773285,0.919753,2.51872,0.6886,2.36678,1.77719,1.40751,0.346003,0.479091,0.113666,0.0344911,0.438213,0.31368,0.294676,0.582029,7.78812,0.00521875,0.35371,0.359539,1.2816,0.851763,0.586575,0.523661,0.0737837,0.421433,0.0436985,0.303029,0.526183,0.936209,1.07633,0.483457,0.511936,0.625103,0.408622,0.407717,0.570967,0.459578,0.607107,0.116526,0.730452,0.44617,3.75161,0.114328,1.19764,0.858505,0.068143,4.23202,0.180644,0.424276,0.474273,0.693645,0.380657,0.782806,0.345253,0.910454,0.482363,0.261058,1.28693,0.783932,0.0752496,0.609469,0.173056,0.75595,0.280468,0.879201,0.0658603,0.471259,0.197578,0.832159,1.64606,1.25025,0.789841,0.296788,0.521565,0.402166,0.196898,0.358053,1.60668,0.156941,0.912901,0.600737,2.23466,0.642658,1.0784,0.765783,0.718834,0.30804,0.085296,0.14831,0.470802,0.841238,0.581248,1.21258,0.442531,0.39934,0.273933,0.0613242,0.244407,1.08909
|tfbs_overrepresentation_jaspar=MA0003.1;5.00947,MA0004.1;0.527785,MA0006.1;0.561862,MA0007.1;0.168178,MA0009.1;0.535932,MA0014.1;2.56655,MA0017.1;0.0906268,MA0019.1;0.376509,MA0024.1;0.496718,MA0025.1;0.751694,MA0027.1;2.14278,MA0028.1;0.280241,MA0029.1;0.477444,MA0030.1;0.483253,MA0031.1;0.451927,MA0038.1;0.285714,MA0040.1;0.547233,MA0041.1;0.129017,MA0042.1;0.121046,MA0043.1;0.624178,MA0046.1;0.568473,MA0048.1;0.768218,MA0050.1;0.205672,MA0051.1;0.2928,MA0052.1;1.36531,MA0055.1;1.15409,MA0056.1;0,MA0057.1;0.262449,MA0058.1;0.373672,MA0059.1;0.124358,MA0060.1;2.48788,MA0061.1;0.438647,MA0063.1;0,MA0066.1;0.277072,MA0067.1;0.857286,MA0068.1;0.0481248,MA0069.1;0.554839,MA0070.1;0.54606,MA0071.1;0.20507,MA0072.1;0.538403,MA0073.1;3.14638,MA0074.1;0.249359,MA0076.1;0.101055,MA0077.1;0.518913,MA0078.1;0.319336,MA0081.1;0.138626,MA0083.1;0.623446,MA0084.1;1.1752,MA0087.1;0.583879,MA0088.1;1.29308,MA0089.1;0,MA0090.1;0.15538,MA0091.1;0.187483,MA0092.1;0.155586,MA0093.1;0.609251,MA0095.1;0,MA0098.1;0,MA0100.1;0.2406,MA0101.1;0.12981,MA0103.1;0.319254,MA0105.1;1.37354,MA0106.1;0.325663,MA0107.1;0.310214,MA0108.2;0.395878,MA0109.1;0,MA0111.1;0.164756,MA0113.1;0.302851,MA0114.1;0.195359,MA0115.1;0.626759,MA0116.1;0.951399,MA0117.1;0.597086,MA0119.1;0.130171,MA0122.1;0.615314,MA0124.1;0.80652,MA0125.1;0.736412,MA0130.1;0,MA0131.1;0.372683,MA0132.1;0,MA0133.1;0,MA0135.1;0.657882,MA0136.1;0.264624,MA0139.1;1.70292,MA0140.1;0.675435,MA0141.1;0.10748,MA0142.1;0.439269,MA0143.1;0.31603,MA0144.1;0.19926,MA0145.1;1.75613,MA0146.1;3.76784,MA0147.1;0.813958,MA0148.1;0.189643,MA0149.1;0.133214,MA0062.2;0.0201154,MA0035.2;0.244063,MA0039.2;1.93701,MA0138.2;0.959075,MA0002.2;0.0318175,MA0137.2;0.3443,MA0104.2;0.609994,MA0047.2;0.285109,MA0112.2;1.05475,MA0065.2;0.768768,MA0150.1;0.502665,MA0151.1;0,MA0152.1;0.285194,MA0153.1;0.67335,MA0154.1;0.755185,MA0155.1;1.54192,MA0156.1;0.330301,MA0157.1;0.411541,MA0158.1;0,MA0159.1;0.851047,MA0160.1;0.191754,MA0161.1;0,MA0162.1;6.70163,MA0163.1;3.49923,MA0164.1;0.73183,MA0080.2;0.0935932,MA0018.2;0.749098,MA0099.2;0.360735,MA0079.2;3.66261,MA0102.2;1.22663,MA0258.1;0.0472094,MA0259.1;0.774997,MA0442.1;0
}}

Latest revision as of 15:14, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:12199124..12199135,-p3@Ryr2
Mm9::chr13:12199136..12199148,-p4@Ryr2
Mm9::chr13:12199242..12199251,-p5@Ryr2
Mm9::chr15:99079365..99079378,-p5@Mcrs1
Mm9::chr15:99079383..99079403,-p2@Mcrs1
Mm9::chr16:4886302..4886320,+p3@Mgrn1
Mm9::chr17:43938737..43938766,+p4@Rcan2
Mm9::chr18:24867811..24867826,+p4@Fhod3
Mm9::chr19:34736884..34736923,-p1@Gm14446
Mm9::chr19:7061950..7062007,-p2@Vegfb
Mm9::chr1:59030230..59030241,-p7@Trak2
Mm9::chr2:55288199..55288212,+p4@Kcnj3
Mm9::chr3:32716442..32716498,+p4@Usp13
Mm9::chr5:122952145..122952154,-p3@Atp2a2
Mm9::chr5:122952171..122952185,-p2@Atp2a2
Mm9::chr5:122952636..122952663,-p5@Atp2a2
Mm9::chr6:136499682..136499700,+p@chr6:136499682..136499700
+
Mm9::chr7:36340444..36340532,-p2@Nudt19
Mm9::chr8:86496850..86496927,+p1@Prkaca


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:0005218intracellular ligand-gated calcium channel activity0.0352514829974452
GO:0014074response to purine0.0352514829974452
GO:0005219ryanodine-sensitive calcium-release channel activity0.0352514829974452
GO:0031000response to caffeine0.0352514829974452
GO:0046873metal ion transmembrane transporter activity0.0352514829974452
GO:0004691cAMP-dependent protein kinase activity0.0471455207305244
GO:0030001metal ion transport0.0471455207305244
GO:0015467G-protein activated inward rectifier potassium channel activity0.0471455207305244
GO:0000209protein polyubiquitination0.0471455207305244
GO:0006816calcium ion transport0.0471455207305244
GO:0004690cyclic nucleotide-dependent protein kinase activity0.0471455207305244
GO:0015278calcium-release channel activity0.0471455207305244
GO:0050811GABA receptor binding0.0471455207305244
GO:0008324cation transmembrane transporter activity0.0471455207305244
GO:0006812cation transport0.0471455207305244
GO:0015674di-, tri-valent inorganic cation transport0.0499393897011789



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
CNS neuron (sensu Vertebrata)8.42e-1023
neuroblast (sensu Vertebrata)8.42e-1023

Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest5.26e-2592
regional part of nervous system1.86e-1854
neural tube3.19e-1752
neural rod3.19e-1752
future spinal cord3.19e-1752
neural keel3.19e-1752
central nervous system5.52e-1673
gray matter1.75e-1534
nervous system3.23e-1575
neurectoderm4.41e-1564
neural plate4.41e-1564
presumptive neural plate4.41e-1564
brain1.93e-1447
future brain1.93e-1447
anatomical conduit4.39e-14122
tube6.83e-14114
regional part of brain8.38e-1446
ectoderm-derived structure6.03e-1395
ectoderm6.03e-1395
presumptive ectoderm6.03e-1395
ecto-epithelium6.40e-1373
brain grey matter1.34e-1229
regional part of telencephalon1.34e-1229
telencephalon1.34e-1229
anterior neural tube4.32e-1240
regional part of forebrain1.73e-1139
forebrain1.73e-1139
future forebrain1.73e-1139
pre-chordal neural plate2.22e-1149
primary circulatory organ8.41e-1018
heart8.41e-1018
primitive heart tube8.41e-1018
primary heart field8.41e-1018
anterior lateral plate mesoderm8.41e-1018
heart tube8.41e-1018
heart primordium8.41e-1018
cardiac mesoderm8.41e-1018
cardiogenic plate8.41e-1018
heart rudiment8.41e-1018
occipital lobe5.93e-0910
visual cortex5.93e-0910
neocortex5.93e-0910
cerebral cortex1.27e-0821
cerebral hemisphere1.27e-0821
pallium1.27e-0821
regional part of cerebral cortex1.21e-0717
cardiovascular system1.82e-0723
circulatory system1.82e-0723


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)
MA0003.15.00947
MA0004.10.527785
MA0006.10.561862
MA0007.10.168178
MA0009.10.535932
MA0014.12.56655
MA0017.10.0906268
MA0019.10.376509
MA0024.10.496718
MA0025.10.751694
MA0027.12.14278
MA0028.10.280241
MA0029.10.477444
MA0030.10.483253
MA0031.10.451927
MA0038.10.285714
MA0040.10.547233
MA0041.10.129017
MA0042.10.121046
MA0043.10.624178
MA0046.10.568473
MA0048.10.768218
MA0050.10.205672
MA0051.10.2928
MA0052.11.36531
MA0055.11.15409
MA0056.10
MA0057.10.262449
MA0058.10.373672
MA0059.10.124358
MA0060.12.48788
MA0061.10.438647
MA0063.10
MA0066.10.277072
MA0067.10.857286
MA0068.10.0481248
MA0069.10.554839
MA0070.10.54606
MA0071.10.20507
MA0072.10.538403
MA0073.13.14638
MA0074.10.249359
MA0076.10.101055
MA0077.10.518913
MA0078.10.319336
MA0081.10.138626
MA0083.10.623446
MA0084.11.1752
MA0087.10.583879
MA0088.11.29308
MA0089.10
MA0090.10.15538
MA0091.10.187483
MA0092.10.155586
MA0093.10.609251
MA0095.10
MA0098.10
MA0100.10.2406
MA0101.10.12981
MA0103.10.319254
MA0105.11.37354
MA0106.10.325663
MA0107.10.310214
MA0108.20.395878
MA0109.10
MA0111.10.164756
MA0113.10.302851
MA0114.10.195359
MA0115.10.626759
MA0116.10.951399
MA0117.10.597086
MA0119.10.130171
MA0122.10.615314
MA0124.10.80652
MA0125.10.736412
MA0130.10
MA0131.10.372683
MA0132.10
MA0133.10
MA0135.10.657882
MA0136.10.264624
MA0139.11.70292
MA0140.10.675435
MA0141.10.10748
MA0142.10.439269
MA0143.10.31603
MA0144.10.19926
MA0145.11.75613
MA0146.13.76784
MA0147.10.813958
MA0148.10.189643
MA0149.10.133214
MA0062.20.0201154
MA0035.20.244063
MA0039.21.93701
MA0138.20.959075
MA0002.20.0318175
MA0137.20.3443
MA0104.20.609994
MA0047.20.285109
MA0112.21.05475
MA0065.20.768768
MA0150.10.502665
MA0151.10
MA0152.10.285194
MA0153.10.67335
MA0154.10.755185
MA0155.11.54192
MA0156.10.330301
MA0157.10.411541
MA0158.10
MA0159.10.851047
MA0160.10.191754
MA0161.10
MA0162.16.70163
MA0163.13.49923
MA0164.10.73183
MA0080.20.0935932
MA0018.20.749098
MA0099.20.360735
MA0079.23.66261
MA0102.21.22663
MA0258.10.0472094
MA0259.10.774997
MA0442.10
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