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MCL coexpression mm9:1702: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0007268;synaptic transmission;0.0035803288377154;14805!GO:0048172;regulation of short-term neuronal synaptic plasticity;0.0035803288377154;14805!GO:0019226;transmission of nerve impulse;0.0035803288377154;14805!GO:0015277;kainate selective glutamate receptor activity;0.00388966498699777;14805!GO:0007267;cell-cell signaling;0.00389749695633027;14805!GO:0022803;passive transmembrane transporter activity;0.00389749695633027;14805!GO:0015267;channel activity;0.00389749695633027;14805!GO:0030054;cell junction;0.00389749695633027;14805!GO:0008328;ionotropic glutamate receptor complex;0.00777741194068963;14805!GO:0065008;regulation of biological quality;0.00777741194068963;14805!GO:0048169;regulation of long-term neuronal synaptic plasticity;0.00777741194068963;14805!GO:0048168;regulation of neuronal synaptic plasticity;0.00808773078604848;14805!GO:0005234;extracellular-glutamate-gated ion channel activity;0.00808773078604848;14805!GO:0005243;gap junction channel activity;0.00808773078604848;!GO:0004970;ionotropic glutamate receptor activity;0.00808773078604848;14805!GO:0022829;wide pore channel activity;0.00808773078604848;!GO:0005922;connexon complex;0.00808773078604848;!GO:0022857;transmembrane transporter activity;0.00808773078604848;14805!GO:0048167;regulation of synaptic plasticity;0.00859373140231635;14805!GO:0050803;regulation of synapse structure and activity;0.00894108274739065;14805!GO:0005921;gap junction;0.00962521884196859;!GO:0001508;regulation of action potential;0.0130708738798452;!GO:0005231;excitatory extracellular ligand-gated ion channel activity;0.0139862988667611;14805!GO:0008066;glutamate receptor activity;0.0139862988667611;14805!GO:0014704;intercalated disc;0.0139862988667611;!GO:0044459;plasma membrane part;0.0174841030919808;14805!GO:0005230;extracellular ligand-gated ion channel activity;0.0184633996099129;14805!GO:0043234;protein complex;0.0184633996099129;14805!GO:0043235;receptor complex;0.0192771606715988;14805!GO:0050877;neurological system process;0.0201328630300659;14805!GO:0015276;ligand-gated ion channel activity;0.0201328630300659;14805!GO:0022834;ligand-gated channel activity;0.0201328630300659;14805!GO:0003008;system process;0.0216390967647873;14805!GO:0005886;plasma membrane;0.0224257707744585;14805!GO:0032991;macromolecular complex;0.0226559776580504;14805!GO:0045211;postsynaptic membrane;0.0226559776580504;14805!GO:0007601;visual perception;0.0226559776580504;!GO:0050953;sensory perception of light stimulus;0.0226559776580504;!GO:0044456;synapse part;0.024057186837918;14805!GO:0005911;intercellular junction;0.0290542086819516;!GO:0042802;identical protein binding;0.0324832506934418;14805!GO:0005261;cation channel activity;0.0445290510818903;14805!GO:0022836;gated channel activity;0.0465269977220717;14805!GO:0046873;metal ion transmembrane transporter activity;0.0496500648514648;14805!}}
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activity;0.00808773078604848;!GO:0004970;ionotropic glutamate receptor activity;0.00808773078604848;14805!GO:0022829;wide pore channel activity;0.00808773078604848;!GO:0005922;connexon complex;0.00808773078604848;!GO:0022857;transmembrane transporter activity;0.00808773078604848;14805!GO:0048167;regulation of synaptic plasticity;0.00859373140231635;14805!GO:0050803;regulation of synapse structure and activity;0.00894108274739065;14805!GO:0005921;gap junction;0.00962521884196859;!GO:0001508;regulation of action potential;0.0130708738798452;!GO:0005231;excitatory extracellular ligand-gated ion channel activity;0.0139862988667611;14805!GO:0008066;glutamate receptor activity;0.0139862988667611;14805!GO:0014704;intercalated disc;0.0139862988667611;!GO:0044459;plasma membrane part;0.0174841030919808;14805!GO:0005230;extracellular ligand-gated ion channel activity;0.0184633996099129;14805!GO:0043234;protein complex;0.0184633996099129;14805!GO:0043235;receptor complex;0.0192771606715988;14805!GO:0050877;neurological system process;0.0201328630300659;14805!GO:0015276;ligand-gated ion channel activity;0.0201328630300659;14805!GO:0022834;ligand-gated channel activity;0.0201328630300659;14805!GO:0003008;system process;0.0216390967647873;14805!GO:0005886;plasma membrane;0.0224257707744585;14805!GO:0032991;macromolecular complex;0.0226559776580504;14805!GO:0045211;postsynaptic membrane;0.0226559776580504;14805!GO:0007601;visual perception;0.0226559776580504;!GO:0050953;sensory perception of light stimulus;0.0226559776580504;!GO:0044456;synapse part;0.024057186837918;14805!GO:0005911;intercellular junction;0.0290542086819516;!GO:0042802;identical protein binding;0.0324832506934418;14805!GO:0005261;cation channel activity;0.0445290510818903;14805!GO:0022836;gated channel activity;0.0465269977220717;14805!GO:0046873;metal ion transmembrane transporter activity;0.0496500648514648;14805!|ontology_enrichment_celltype=CL:0000540!1.42e-16!33;CL:0000047!1.42e-16!33;CL:0000031!1.42e-16!33;CL:0000404!1.42e-16!33;CL:0000393!5.97e-12!39;CL:0000211!5.97e-12!39;CL:0000221!3.27e-11!44;CL:0000133!3.27e-11!44;CL:0002319!6.99e-11!43;CL:0000117!3.36e-10!23;CL:0000337!3.36e-10!23;CL:0000055!4.85e-08!49;CL:0000107!1.84e-07!9|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0001017!6.30e-25!73;UBERON:0001016!3.14e-24!75;UBERON:0002346!3.76e-24!64;UBERON:0003075!3.76e-24!64;UBERON:0007284!3.76e-24!64;UBERON:0004121!2.92e-23!95;UBERON:0000924!2.92e-23!95;UBERON:0006601!2.92e-23!95;UBERON:0010371!3.36e-20!73;UBERON:0000073!3.82e-18!54;UBERON:0001049!3.35e-17!52;UBERON:0005068!3.35e-17!52;UBERON:0006241!3.35e-17!52;UBERON:0007135!3.35e-17!52;UBERON:0003056!1.41e-16!49;UBERON:0002020!1.49e-16!34;UBERON:0000955!1.61e-13!47;UBERON:0006238!1.61e-13!47;UBERON:0010314!1.67e-13!92;UBERON:0002616!6.42e-13!46;UBERON:0003528!1.50e-12!29;UBERON:0002791!1.50e-12!29;UBERON:0001893!1.50e-12!29;UBERON:0003080!1.99e-12!40;UBERON:0002780!7.71e-12!39;UBERON:0001890!7.71e-12!39;UBERON:0006240!7.71e-12!39;UBERON:0002021!1.22e-08!10;UBERON:0000411!1.22e-08!10;UBERON:0001950!1.22e-08!10;UBERON:0000956!3.50e-08!21;UBERON:0001869!3.50e-08!21;UBERON:0000203!3.50e-08!21;UBERON:0002410!1.84e-07!9;UBERON:0002619!3.60e-07!17|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.115752,1.60538,0.702872,1.47559,0.728641,1.0876,0,0.930881,0.397593,0.775038,1.0421,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,0.425309,1.68786,1.7724,0.699032,0.360612,0.876199,0.401916,0.631725,0.419293,0.426986,0.0637209,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,1.74061,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,4.38414,1.23259,0.714607,0.245132,0.70455,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,1.44773,8.42284,1.87702,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,3.46853,0.3366,1.46478,1.05152,0.848095,0.590368,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,1.23125,0.550229,1.16464,0.495367,1.61686,1.41481,0.399936,1.11665,0.607321,0.932233,0.380707,1.23809,0.879184,1.7936,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.44142,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,1.05179,0.230371,5.85111,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.997706,0.701187,0.191104|tfbs_overrepresentation_jaspar=MA0003.1;0.211284,MA0004.1;1.46913,MA0006.1;1.07705,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.187732,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;0.43138,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;0.593503,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;0.0851423,MA0056.1;0,MA0057.1;0.562607,MA0058.1;0.50032,MA0059.1;1.27866,MA0060.1;0.330907,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;0.197245,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;2.09333,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;0.453686,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;1.39225,MA0093.1;1.12162,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;1.28296,MA0106.1;0.809991,MA0107.1;0.454197,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;0.361633,MA0115.1;1.16466,MA0116.1;1.07655,MA0117.1;1.13165,MA0119.1;0.524046,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;0.295945,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;0.157686,MA0146.1;0.0604336,MA0147.1;1.75115,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;0.749235,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;1.52809,MA0047.2;0.75686,MA0112.2;0.157681,MA0065.2;0.477991,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.203217,MA0155.1;0.173445,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;1.35147,MA0163.1;0.855539,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;1.7149,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;1.71005,MA0442.1;0}}

Latest revision as of 17:21, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:88290431..88290442,-p3@Grik1
Mm9::chr16:88290444..88290471,-p1@Grik1
Mm9::chr2:113839356..113839374,-p1@Gjd2
Mm9::chr5:46030532..46030550,-p2@Fam184b
Mm9::chr7:48153974..48153989,-p1@A230077H06Rik


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:0007268synaptic transmission0.0035803288377154
GO:0048172regulation of short-term neuronal synaptic plasticity0.0035803288377154
GO:0019226transmission of nerve impulse0.0035803288377154
GO:0015277kainate selective glutamate receptor activity0.00388966498699777
GO:0007267cell-cell signaling0.00389749695633027
GO:0022803passive transmembrane transporter activity0.00389749695633027
GO:0015267channel activity0.00389749695633027
GO:0030054cell junction0.00389749695633027
GO:0008328ionotropic glutamate receptor complex0.00777741194068963
GO:0065008regulation of biological quality0.00777741194068963
GO:0048169regulation of long-term neuronal synaptic plasticity0.00777741194068963
GO:0048168regulation of neuronal synaptic plasticity0.00808773078604848
GO:0005234extracellular-glutamate-gated ion channel activity0.00808773078604848
GO:0005243gap junction channel activity0.00808773078604848
GO:0004970ionotropic glutamate receptor activity0.00808773078604848
GO:0022829wide pore channel activity0.00808773078604848
GO:0005922connexon complex0.00808773078604848
GO:0022857transmembrane transporter activity0.00808773078604848
GO:0048167regulation of synaptic plasticity0.00859373140231635
GO:0050803regulation of synapse structure and activity0.00894108274739065
GO:0005921gap junction0.00962521884196859
GO:0001508regulation of action potential0.0130708738798452
GO:0005231excitatory extracellular ligand-gated ion channel activity0.0139862988667611
GO:0008066glutamate receptor activity0.0139862988667611
GO:0014704intercalated disc0.0139862988667611
GO:0044459plasma membrane part0.0174841030919808
GO:0005230extracellular ligand-gated ion channel activity0.0184633996099129
GO:0043234protein complex0.0184633996099129
GO:0043235receptor complex0.0192771606715988
GO:0050877neurological system process0.0201328630300659
GO:0015276ligand-gated ion channel activity0.0201328630300659
GO:0022834ligand-gated channel activity0.0201328630300659
GO:0003008system process0.0216390967647873
GO:0005886plasma membrane0.0224257707744585
GO:0032991macromolecular complex0.0226559776580504
GO:0045211postsynaptic membrane0.0226559776580504
GO:0007601visual perception0.0226559776580504
GO:0050953sensory perception of light stimulus0.0226559776580504
GO:0044456synapse part0.024057186837918
GO:0005911intercellular junction0.0290542086819516
GO:0042802identical protein binding0.0324832506934418
GO:0005261cation channel activity0.0445290510818903
GO:0022836gated channel activity0.0465269977220717
GO:0046873metal ion transmembrane transporter activity0.0496500648514648



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 system6.30e-2573
nervous system3.14e-2475
neurectoderm3.76e-2464
neural plate3.76e-2464
presumptive neural plate3.76e-2464
ectoderm-derived structure2.92e-2395
ectoderm2.92e-2395
presumptive ectoderm2.92e-2395
ecto-epithelium3.36e-2073
regional part of nervous system3.82e-1854
neural tube3.35e-1752
neural rod3.35e-1752
future spinal cord3.35e-1752
neural keel3.35e-1752
pre-chordal neural plate1.41e-1649
gray matter1.49e-1634
brain1.61e-1347
future brain1.61e-1347
structure with developmental contribution from neural crest1.67e-1392
regional part of brain6.42e-1346
brain grey matter1.50e-1229
regional part of telencephalon1.50e-1229
telencephalon1.50e-1229
anterior neural tube1.99e-1240
regional part of forebrain7.71e-1239
forebrain7.71e-1239
future forebrain7.71e-1239
occipital lobe1.22e-0810
visual cortex1.22e-0810
neocortex1.22e-0810
cerebral cortex3.50e-0821
cerebral hemisphere3.50e-0821
pallium3.50e-0821
autonomic nervous system1.84e-079
regional part of cerebral cortex3.60e-0717


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)
MA0003.10.211284
MA0004.11.46913
MA0006.11.07705
MA0007.10.587678
MA0009.11.06266
MA0014.10.187732
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.593503
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.10.562607
MA0058.10.50032
MA0059.11.27866
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.12.09333
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.453686
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.11.39225
MA0093.11.12162
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.11.28296
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.11.07655
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.157686
MA0146.10.0604336
MA0147.11.75115
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.749235
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.21.52809
MA0047.20.75686
MA0112.20.157681
MA0065.20.477991
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.11.35147
MA0163.10.855539
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.21.7149
MA0102.21.79669
MA0258.10.346619
MA0259.11.71005
MA0442.10