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MCL coexpression mm9:281: Difference between revisions

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{{MCL_coexpression_mm9
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membrane;0.00470690023203389;20355,14806,14802!GO:0005234;extracellular-glutamate-gated ion channel activity;0.00470690023203389;14806,14802!GO:0004970;ionotropic glutamate receptor activity;0.00470690023203389;14806,14802!GO:0044456;synapse part;0.00470690023203389;20355,14806,14802!GO:0030054;cell junction;0.00620867731463551;14806,230959,14802,13527!GO:0005231;excitatory extracellular ligand-gated ion channel activity;0.0139163769570832;14806,14802!GO:0008066;glutamate receptor activity;0.0139163769570832;14806,14802!GO:0016014;dystrobrevin complex;0.01840793294253;13527!GO:0005230;extracellular ligand-gated ion channel activity;0.0235807865386546;14806,14802!GO:0015277;kainate selective glutamate receptor activity;0.026499165811143;14806!GO:0007411;axon guidance;0.026499165811143;20355,14009!GO:0015276;ligand-gated ion channel activity;0.026499165811143;14806,14802!GO:0022834;ligand-gated channel activity;0.026499165811143;14806,14802!GO:0007638;mechanosensory behavior;0.0392283199289765;14009!GO:0015016;[heparan sulfate]-glucosamine N-sulfotransferase 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|gostat_on_MCL_coexpression=GO:0045211;postsynaptic membrane;0.00470690023203389;20355,14806,14802!GO:0005234;extracellular-glutamate-gated ion channel activity;0.00470690023203389;14806,14802!GO:0004970;ionotropic glutamate receptor activity;0.00470690023203389;14806,14802!GO:0044456;synapse part;0.00470690023203389;20355,14806,14802!GO:0030054;cell junction;0.00620867731463551;14806,230959,14802,13527!GO:0005231;excitatory extracellular ligand-gated ion channel activity;0.0139163769570832;14806,14802!GO:0008066;glutamate receptor activity;0.0139163769570832;14806,14802!GO:0016014;dystrobrevin complex;0.01840793294253;13527!GO:0005230;extracellular ligand-gated ion channel activity;0.0235807865386546;14806,14802!GO:0015277;kainate selective glutamate receptor activity;0.026499165811143;14806!GO:0007411;axon guidance;0.026499165811143;20355,14009!GO:0015276;ligand-gated ion channel activity;0.026499165811143;14806,14802!GO:0022834;ligand-gated channel activity;0.026499165811143;14806,14802!GO:0007638;mechanosensory behavior;0.0392283199289765;14009!GO:0015016;[heparan sulfate]-glucosamine N-sulfotransferase activity;0.0392283199289765;83398!
|ontology_enrichment_celltype=CL:0000540!1.33e-15!33;CL:0000047!1.33e-15!33;CL:0000031!1.33e-15!33;CL:0000404!1.33e-15!33;CL:0000393!7.73e-13!39;CL:0000211!7.73e-13!39;CL:0000221!1.78e-12!44;CL:0000133!1.78e-12!44;CL:0002319!4.51e-12!43;CL:0000055!2.70e-10!49;CL:0000117!1.83e-09!23;CL:0000337!1.83e-09!23;CL:0000107!1.64e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!7.36e-29!73;UBERON:0001016!2.05e-28!75;UBERON:0004121!9.93e-28!95;UBERON:0000924!9.93e-28!95;UBERON:0006601!9.93e-28!95;UBERON:0002346!2.86e-24!64;UBERON:0003075!2.86e-24!64;UBERON:0007284!2.86e-24!64;UBERON:0010371!4.86e-22!73;UBERON:0000073!1.07e-20!54;UBERON:0010314!1.15e-19!92;UBERON:0001049!1.49e-19!52;UBERON:0005068!1.49e-19!52;UBERON:0006241!1.49e-19!52;UBERON:0007135!1.49e-19!52;UBERON:0003056!5.68e-17!49;UBERON:0000955!6.11e-17!47;UBERON:0006238!6.11e-17!47;UBERON:0002616!2.68e-16!46;UBERON:0003080!1.20e-14!40;UBERON:0002020!4.62e-14!34;UBERON:0002780!4.71e-14!39;UBERON:0001890!4.71e-14!39;UBERON:0006240!4.71e-14!39;UBERON:0003528!1.62e-11!29;UBERON:0002791!1.62e-11!29;UBERON:0001893!1.62e-11!29;UBERON:0000468!2.54e-09!333;UBERON:0000956!7.12e-08!21;UBERON:0001869!7.12e-08!21;UBERON:0000203!7.12e-08!21;UBERON:0002619!1.63e-07!17;UBERON:0002410!1.64e-07!9;UBERON:0002021!2.82e-07!10;UBERON:0000411!2.82e-07!10;UBERON:0001950!2.82e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.23755,4.58799,0.207166,0.289799,0.240898,0.0925204,1.99526,0.616403,0.94497,0.425781,0.372262,0.134115,1.5732,0.148257,0.111275,0,0.278333,0.0206826,0.346686,1.87821,0.379987,0.316516,0.147721,0.23832,1.73056,0.164963,1.73944,0.336599,0.584966,0.529733,0.31769,0.356376,0.698352,0.435403,0.111692,0.306761,5.17229,0.412507,0.0669699,0.7342,0.44469,0.0984395,0.0475639,0.273021,0.273535,0.579851,0.630144,0.111088,0.0625846,0.32702,1.34753,0.536423,0.964385,1.19301,0.488593,0.152527,0.343961,1.29502,0.706927,0.461079,0.340494,1.6591,0.130512,0.257242,0.480896,0.782577,0.608645,0.933761,0.336817,0.794446,0.416038,0.412597,11.4916,0.517629,0.450987,0.130009,0.265609,1.15063,0.327041,0.171714,0.93103,0.792145,0.548924,0.372969,0.419339,0.200368,0.00401566,0.0439553,0.638115,1.0899,0.671836,0.423481,0.366627,0.102201,13.0913,0.145477,0.217537,0.96541,0.630558,0.271897,0.403583,0.356153,0.458781,0.265886,0.265114,0.665575,0.309919,0.108981,3.21344,0.681917,0.853247,0.460295,0.172898,0.119253,0.678281,0.439834,0.606264,1.52657,1.39847,2.21863,0.522338,0.67935,1.53315,0.212759,0.728107,0.878992,0.877643,0.361192,0.607282,1.5401,0.444416,0.588578,0.580825,0.160813,0.698098,0.113323,0.0705995,0.099143,0.653122,1.45055,1.05907,0.612882,0.173636,0.364752,0.721437,0.0986655,0.635216,1.41144,0.534737,0.0988,0.355625,15.2315,0.474971,0.796557,0.483303,0.545909,1.02923,0.536326,0.06605,0.0704805,0.661783,0.418628,0.330273,0.8459,0.257983,0.472114,0.20739,0.133212,0.466179
|tfbs_overrepresentation_jaspar=MA0003.1;2.63589,MA0004.1;0.0858689,MA0006.1;0.786458,MA0007.1;0.271387,MA0009.1;0.98466,MA0014.1;2.28807,MA0017.1;0.0322854,MA0019.1;0.671243,MA0024.1;0.342622,MA0025.1;0.57681,MA0027.1;1.94532,MA0028.1;0.116488,MA0029.1;0.325591,MA0030.1;0.330711,MA0031.1;0.303242,MA0038.1;0.494825,MA0040.1;0.387805,MA0041.1;0.0540602,MA0042.1;0.0492946,MA0043.1;0.457929,MA0046.1;0.407017,MA0048.1;0.0310795,MA0050.1;0.104869,MA0051.1;0.170484,MA0052.1;0.394392,MA0055.1;0.614002,MA0056.1;0,MA0057.1;1.02207,MA0058.1;0.0469235,MA0059.1;0.0512607,MA0060.1;0.485647,MA0061.1;0.180685,MA0063.1;0,MA0066.1;0.158169,MA0067.1;0.677115,MA0068.1;0.00730072,MA0069.1;0.39467,MA0070.1;0.386747,MA0071.1;0.340616,MA0072.1;0.379853,MA0073.1;0.000728854,MA0074.1;0.136938,MA0076.1;0.149319,MA0077.1;0.36238,MA0078.1;0.191654,MA0081.1;1.73582,MA0083.1;0.457256,MA0084.1;0.985399,MA0087.1;0.421024,MA0088.1;0.123781,MA0089.1;0,MA0090.1;0.070593,MA0091.1;0.092107,MA0092.1;0.530193,MA0093.1;0.0301253,MA0095.1;0,MA0098.1;0,MA0100.1;0.408164,MA0101.1;0.443304,MA0103.1;0.141239,MA0105.1;0.625989,MA0106.1;0.572177,MA0107.1;0.135394,MA0108.2;0.709125,MA0109.1;0,MA0111.1;0.265025,MA0113.1;0.178447,MA0114.1;0.0143817,MA0115.1;0.460306,MA0116.1;0.107342,MA0117.1;0.433078,MA0119.1;0.444528,MA0122.1;0.449781,MA0124.1;0.628716,MA0125.1;0.562419,MA0130.1;0,MA0131.1;0.235509,MA0132.1;0,MA0133.1;0,MA0135.1;0.489063,MA0136.1;0.889206,MA0139.1;0.866511,MA0140.1;0.130298,MA0141.1;0.0414652,MA0142.1;0.292245,MA0143.1;0.188991,MA0144.1;0.0149196,MA0145.1;0.53959,MA0146.1;0.344756,MA0147.1;0.0782471,MA0148.1;0.311535,MA0149.1;2.22987,MA0062.2;0.0197237,MA0035.2;0.132954,MA0039.2;0.00949757,MA0138.2;0.229939,MA0002.2;0.103645,MA0137.2;0.040538,MA0104.2;0.120647,MA0047.2;0.16444,MA0112.2;1.51234,MA0065.2;0.145939,MA0150.1;0.0789524,MA0151.1;0,MA0152.1;0.493821,MA0153.1;0.503426,MA0154.1;2.10704,MA0155.1;0.100044,MA0156.1;0.619633,MA0157.1;0.26838,MA0158.1;0,MA0159.1;0.0857096,MA0160.1;0.095069,MA0161.1;0,MA0162.1;0.584704,MA0163.1;2.88524,MA0164.1;0.454747,MA0080.2;2.83852,MA0018.2;0.154575,MA0099.2;0.22555,MA0079.2;0.353785,MA0102.2;1.03585,MA0258.1;1.14049,MA0259.1;0.0707314,MA0442.1;0
}}

Latest revision as of 15:01, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:4707315..4707330,-p1@Vip
Mm9::chr10:48938780..48938784,-p@chr10:48938780..48938784
-
Mm9::chr10:49503296..49503388,-p3@Grik2
Mm9::chr10:49508549..49508575,-p1@Grik2
Mm9::chr12:39507404..39507441,+p4@Etv1
Mm9::chr18:23656049..23656109,+p3@Dtna
Mm9::chr19:10379357..10379444,-p1@Dagla
Mm9::chr19:42506268..42506282,-p1@Crtac1
Mm9::chr3:123393724..123393765,-p2@Ndst3
Mm9::chr3:75361452..75361483,+p1@Serpini1
Mm9::chr4:152857048..152857081,-p1@Ajap1
Mm9::chr4:66007191..66007194,-p@chr4:66007191..66007194
-
Mm9::chr4:66065468..66065490,-p2@Astn2
Mm9::chr4:66065492..66065543,-p1@Astn2
Mm9::chr4:9196485..9196509,+p2@Clvs1
Mm9::chr6:82889553..82889581,-p2@Sema4f
Mm9::chr7:51842709..51842745,+p@chr7:51842709..51842745
+
Mm9::chr7:98691475..98691503,+p12@Dlg2
Mm9::chr7:98691504..98691553,+p5@Dlg2
Mm9::chr7:99473169..99473173,+p@chr7:99473169..99473173
+
Mm9::chr9:4635267..4635271,-p@chr9:4635267..4635271
-
Mm9::chr9:4765243..4765247,-p@chr9:4765243..4765247
-
Mm9::chr9:4795561..4795644,-p3@Gria4
Mm9::chr9:4796022..4796033,-p10@Gria4
Mm9::chr9:4796034..4796066,-p5@Gria4
Mm9::chr9:4796070..4796081,-p9@Gria4
Mm9::chr9:4796141..4796159,-p6@Gria4
Mm9::chr9:4796160..4796195,-p2@Gria4
Mm9::chr9:4796196..4796216,-p4@Gria4
Mm9::chr9:62384753..62384758,-p16@Coro2b


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:0045211postsynaptic membrane0.00470690023203389
GO:0005234extracellular-glutamate-gated ion channel activity0.00470690023203389
GO:0004970ionotropic glutamate receptor activity0.00470690023203389
GO:0044456synapse part0.00470690023203389
GO:0030054cell junction0.00620867731463551
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0139163769570832
GO:0008066glutamate receptor activity0.0139163769570832
GO:0016014dystrobrevin complex0.01840793294253
GO:0005230extracellular ligand-gated ion channel activity0.0235807865386546
GO:0015277kainate selective glutamate receptor activity0.026499165811143
GO:0007411axon guidance0.026499165811143
GO:0015276ligand-gated ion channel activity0.026499165811143
GO:0022834ligand-gated channel activity0.026499165811143
GO:0007638mechanosensory behavior0.0392283199289765
GO:0015016[heparan sulfate]-glucosamine N-sulfotransferase activity0.0392283199289765



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 system7.36e-2973
nervous system2.05e-2875
ectoderm-derived structure9.93e-2895
ectoderm9.93e-2895
presumptive ectoderm9.93e-2895
neurectoderm2.86e-2464
neural plate2.86e-2464
presumptive neural plate2.86e-2464
ecto-epithelium4.86e-2273
regional part of nervous system1.07e-2054
structure with developmental contribution from neural crest1.15e-1992
neural tube1.49e-1952
neural rod1.49e-1952
future spinal cord1.49e-1952
neural keel1.49e-1952
pre-chordal neural plate5.68e-1749
brain6.11e-1747
future brain6.11e-1747
regional part of brain2.68e-1646
anterior neural tube1.20e-1440
gray matter4.62e-1434
regional part of forebrain4.71e-1439
forebrain4.71e-1439
future forebrain4.71e-1439
brain grey matter1.62e-1129
regional part of telencephalon1.62e-1129
telencephalon1.62e-1129
multi-cellular organism2.54e-09333
cerebral cortex7.12e-0821
cerebral hemisphere7.12e-0821
pallium7.12e-0821
regional part of cerebral cortex1.63e-0717
autonomic nervous system1.64e-079
occipital lobe2.82e-0710
visual cortex2.82e-0710
neocortex2.82e-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)
MA0003.12.63589
MA0004.10.0858689
MA0006.10.786458
MA0007.10.271387
MA0009.10.98466
MA0014.12.28807
MA0017.10.0322854
MA0019.10.671243
MA0024.10.342622
MA0025.10.57681
MA0027.11.94532
MA0028.10.116488
MA0029.10.325591
MA0030.10.330711
MA0031.10.303242
MA0038.10.494825
MA0040.10.387805
MA0041.10.0540602
MA0042.10.0492946
MA0043.10.457929
MA0046.10.407017
MA0048.10.0310795
MA0050.10.104869
MA0051.10.170484
MA0052.10.394392
MA0055.10.614002
MA0056.10
MA0057.11.02207
MA0058.10.0469235
MA0059.10.0512607
MA0060.10.485647
MA0061.10.180685
MA0063.10
MA0066.10.158169
MA0067.10.677115
MA0068.10.00730072
MA0069.10.39467
MA0070.10.386747
MA0071.10.340616
MA0072.10.379853
MA0073.10.000728854
MA0074.10.136938
MA0076.10.149319
MA0077.10.36238
MA0078.10.191654
MA0081.11.73582
MA0083.10.457256
MA0084.10.985399
MA0087.10.421024
MA0088.10.123781
MA0089.10
MA0090.10.070593
MA0091.10.092107
MA0092.10.530193
MA0093.10.0301253
MA0095.10
MA0098.10
MA0100.10.408164
MA0101.10.443304
MA0103.10.141239
MA0105.10.625989
MA0106.10.572177
MA0107.10.135394
MA0108.20.709125
MA0109.10
MA0111.10.265025
MA0113.10.178447
MA0114.10.0143817
MA0115.10.460306
MA0116.10.107342
MA0117.10.433078
MA0119.10.444528
MA0122.10.449781
MA0124.10.628716
MA0125.10.562419
MA0130.10
MA0131.10.235509
MA0132.10
MA0133.10
MA0135.10.489063
MA0136.10.889206
MA0139.10.866511
MA0140.10.130298
MA0141.10.0414652
MA0142.10.292245
MA0143.10.188991
MA0144.10.0149196
MA0145.10.53959
MA0146.10.344756
MA0147.10.0782471
MA0148.10.311535
MA0149.12.22987
MA0062.20.0197237
MA0035.20.132954
MA0039.20.00949757
MA0138.20.229939
MA0002.20.103645
MA0137.20.040538
MA0104.20.120647
MA0047.20.16444
MA0112.21.51234
MA0065.20.145939
MA0150.10.0789524
MA0151.10
MA0152.10.493821
MA0153.10.503426
MA0154.12.10704
MA0155.10.100044
MA0156.10.619633
MA0157.10.26838
MA0158.10
MA0159.10.0857096
MA0160.10.095069
MA0161.10
MA0162.10.584704
MA0163.12.88524
MA0164.10.454747
MA0080.22.83852
MA0018.20.154575
MA0099.20.22555
MA0079.20.353785
MA0102.21.03585
MA0258.11.14049
MA0259.10.0707314
MA0442.10
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