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MCL coexpression mm9:825: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=0.0484183606696472,-0.153383095200759,-0.169854142249236,-0.17519824975595,-0.187950005170534,-0.180461344010868,-0.177819026185741,-0.161996463781497,-0.175978354587531,-0.187950005170534,-0.187950005170534,-0.164609799532713,-0.166115144041473,-0.166407219113472,-0.149439102111965,-0.128900406458503,-0.145721932818731,-0.162186959273197,-0.181749541598492,-0.158296108422605,0.119259242147112,-0.0980824295848669,-0.145272623625417,-0.169032777956443,-0.169727640650791,-0.187950005170534,-0.153379472744294,-0.170658652702457,-0.118408493675839,-0.123764472903414,-0.150910460680117,-0.00991439713122499,-0.0687219373093861,-0.187950005170534,-0.153702423065559,-0.168426022069835,-0.130946084788868,-0.158602881613423,-0.160089373494767,-0.167633424387205,-0.187950005170534,-0.162828243713688,-0.168852707070819,0.0946661528369787,0.163212790561559,0.0821986969114653,0.248397108021665,0.0178728997799872,0.0704779121859486,0.0449793217508745,0.157088838817216,-0.0517678291840072,-0.187950005170534,-0.0806821834687584,-0.187950005170534,0.0848564482239371,0.19532485948359,0.210234286463894,-0.102855129161493,-0.0748256391871076,0.0115250277130035,0.069077702474902,0.0958411333598693,0.611248204650611,0.789406402643147,0.678592005022521,0.466252234117863,0.353181542921645,-0.0694264741145163,-0.0202187210575252,-0.0473871430184977,-0.0131011605752302,-0.0131488327978293,-0.117734698458852,-0.111419039896128,-0.0733933960744194,-0.0637618186214994,-0.0297224564832074,-0.0284030923591353,-0.0974840900992175,-0.0638886087347765,-0.080161520655634,-0.0504263634506932,-0.0588881458617195,0.00249595164184131,0.0379603168700985,0.00521719937823619,-0.0402452084818682,-0.0166313667976233,0.000908599775623939,0.142361112687179,-0.00960852998672373,-0.162916463928425,-0.187950005170534,-0.111274764618114,-0.128977874292089,0.061515713342445,0.103118759873035,0.116156998549718,0.0378778100259933,-0.0689395449321691,0.021479642066152,0.0151264582293129,-0.0565663698887993,-0.120963506102887,-0.120408099347364,-0.168206915004758,0.0509937510549588,0.166927481668089,0.388511827931141,0.111785520945216,0.321244572554486,0.214361002577111,0.316492653199609,0.30357044267421,0.243221871282702,0.961498851762084,0.127785720472678,-0.0169205092918182,0.108146735833888,0.0418788274992334,0.081765348792396,-0.00365363842008129,-0.0486180006590071,0.00914289309081659,-0.0240603873477261,-0.119694505809025,-0.165272940755773,-0.135000787434551,-0.00995299697971317,-0.0649522175883916,-0.125622095021549,-0.0587406708030431,-0.0486008554391193,-0.0154840164705603,-0.0483806544664793,0.181218551880192,0.117451589969438,0.294779854890374,0.0180767218245171,0.0474643314409972,0.00850847744314043,-0.0283405929246484,0.0344702512412806,-0.00741975514738141,0.0698326476020483,0.0213621278788138,0.029279870656335,-0.0263556802437796,0.0830630578554694,0.108565856373699,0.125386949258986,0.212130706260535,0.164247861219345,0.155380505597902,0.0775715415871672,-0.162281788421626,-0.13273346451281,-0.0656717112758088,0.0250088772105655,0.0837491544232071,0.0401221013800467,0.04299552512343,0.0107000378221454,0.0100916713946318,0.0292970998694011,0.00511175459563289,-0.013069379857634,0.00289124386036268,0.0485169031469346,0.0202569679530088,0.0482324682015818,0.069031568399238,0.038144665005356,-0.0489516073684312,-0.015585746701844,-0.163469209675971,-0.046366192783464,0.0512037135783454,0.0736796744127754,0.0501508139326343,0.0671977539598869,0.102666181548842,0.112509005082892,0.03675182128625,0.232267355395603,0.251218112371271,0.2454332285472,0.267625457004917,0.0235724121187209,0.00402551405873304,0.0290535738574608,0.0941490235426702,0.083330323970453,0.115418223442034,0.167869311801102,0.127895551972128,0.149449129701112,0.264939541359792,0.261219713804911,0.299017033818608,0.277018318964765,-0.0382073771291447,-0.00109287033776497,0.00410792299103483,-0.000419390788258577,0.0126881121315634,-0.00465308579978262,0.0098986352961593,0.0162678674158397,0.082081301079108,0.0190347247356701,0.377536142634967,0.134771607261622,0.0996109741895175,0.0304762422412496,0.0134410012651967,0.0219816901506954,0.100318174402384,0.0403083223672403,0.0845711146194273,0.0336508431674184,0.0582794599263751,0.0756015544298613,0.102286100689303,0.0289218191988512,0.0535948644466228,0.0685839038909233,0.0254897959408126,0.0581246971743896,0.0928935691730026,0.0694067520467599,0.703132926847147,0.235554992667674,0.441820190607568,0.355611508808099,-0.0150867169489968,-0.0308243405837594,0.0257865763570125,0.0892275297558612,0.0120979756488835,0.0305177402378632,0.0833442725109321,-0.0247774320823059,-0.0262185428891009,-0.017321860651203,-0.06218206451723,-0.0315087820413775,0.00616200650994128,-0.0128658307655589,0.112121627246244,0.141356895258143,0.0997138014217634,0.0993216617598301,-0.0074158041615374,0.11104081962371,0.12153337911186,0.0940672248946356,0.0550529707588838,0.0398411435449368,0.079524744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during locomotory behavior;0.00552222860125881;76524!GO:0045851;pH reduction;0.00552222860125881;76524!GO:0051452;cellular pH reduction;0.00552222860125881;76524!GO:0051453;regulation of cellular pH;0.00552222860125881;76524!GO:0007042;lysosomal lumen acidification;0.00552222860125881;76524!GO:0030641;cellular hydrogen ion homeostasis;0.00591651141402709;76524!GO:0006907;pinocytosis;0.00591651141402709;13132!GO:0045862;positive regulation of proteolysis;0.00862777305743479;76524!GO:0055067;monovalent inorganic cation homeostasis;0.0092022015204295;76524!GO:0030004;cellular monovalent inorganic cation homeostasis;0.0092022015204295;76524!GO:0001573;ganglioside metabolic process;0.0092022015204295;76524!GO:0005788;endoplasmic reticulum lumen;0.0092022015204295;76524!GO:0006687;glycosphingolipid metabolic process;0.010617342979341;76524!GO:0030162;regulation of proteolysis;0.0119174408521997;76524!GO:0007588;excretion;0.0119174408521997;13132!GO:0007040;lysosome organization and biogenesis;0.0119174408521997;76524!GO:0006664;glycolipid metabolic process;0.0119174408521997;76524!GO:0006898;receptor-mediated endocytosis;0.0119174408521997;13132!GO:0006885;regulation of pH;0.0119174408521997;76524!GO:0006022;aminoglycan metabolic process;0.0119174408521997;76524!GO:0030203;glycosaminoglycan metabolic process;0.0119174408521997;76524!GO:0007033;vacuole organization and biogenesis;0.0119174408521997;76524!GO:0006672;ceramide metabolic process;0.0137976292243873;76524!GO:0046519;sphingoid metabolic process;0.01437174251759;76524!GO:0005905;coated pit;0.0171053084570357;13132!GO:0006665;sphingolipid metabolic process;0.0222768700319768;76524!GO:0008203;cholesterol metabolic process;0.0326687356933175;76524!GO:0016125;sterol metabolic process;0.0337359571224111;76524!GO:0051247;positive regulation of protein metabolic process;0.0337359571224111;76524!GO:0044432;endoplasmic reticulum part;0.0367361909616291;76524!GO:0003008;system process;0.0408793113802752;13132,76524!GO:0042803;protein homodimerization activity;0.0424400708242353;76524!GO:0030003;cellular cation homeostasis;0.0424400708242353;76524!GO:0055080;cation homeostasis;0.0424400708242353;76524!GO:0007601;visual perception;0.0424400708242353;76524!GO:0050953;sensory perception of light stimulus;0.0424400708242353;76524!GO:0001701;in utero embryonic development;0.044259385893427;13132!GO:0008202;steroid metabolic process;0.0493293550094;76524!GO:0055082;cellular chemical homeostasis;0.0493293550094;76524!GO:0006873;cellular ion homeostasis;0.0493293550094;76524!GO:0016043;cellular component organization and biogenesis;0.0493293550094;13132,76524!GO:0006643;membrane lipid metabolic 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|ontology_enrichment_uberon=UBERON:0006554!5.73e-07!18
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.433653,0.330161,1.8057,0.645379,0.40827,0.495658,0.448965,0.468136,0.314043,0.453212,0.484001,0.146657,0.507558,0.680035,0,0.696644,0.22065,1.94334,0.247067,0.802917,0.713323,0.50668,0.226287,0.337218,0.534339,0.128175,0.428336,0.268347,0.0963992,0.414842,0.796599,0.218674,0.113369,0.242923,0.137663,0.210533,0.480503,0.559915,0.500908,0.224094,0.419787,1.46325,0.244285,0.059071,0.383899,0.618203,0.443479,1.30029,0.745859,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.764433,0.471658,0.384731,0.512521,0.776777,0.569793,0.492158,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.460931,0.0512949,0.987652,0.371787,0.107966,0.364033,0.607043,0.759798,0.81171,0.152219,0.713779,0.568383,0.436063,0.873141,0.0800961,0.0211263,0.0965007,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.188213,0.17334,0.871972,0.812053,0.618454,0.0816605,0.605162,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.348012,0.921485,0.814064,0.458194,1.16629,0.222515,0.0259088,0.398075,0.697928,1.12703,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.956381,0.229209,0.098204,0.041769,0.938577,0.527659,0.526881,1.01974,0.561556,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.254444
|tfbs_overrepresentation_jaspar=MA0003.1;0.0854318,MA0004.1;0.394951,MA0006.1;0.238555,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.00813637,MA0017.1;0.726051,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.24786,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.0824771,MA0050.1;1.10321,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.0198867,MA0056.1;0,MA0057.1;0.549903,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.169058,MA0061.1;0.56663,MA0063.1;0,MA0066.1;1.29967,MA0067.1;1.16502,MA0068.1;0.266547,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;1.10147,MA0072.1;1.92922,MA0073.1;0.000250057,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.18495,MA0089.1;0,MA0090.1;0.362551,MA0091.1;1.04993,MA0092.1;0.362847,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.109964,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.561811,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;2.10074,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.143341,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.442138,MA0146.1;0.0111657,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;0.113962,MA0035.2;0.482026,MA0039.2;0.000502396,MA0138.2;0.630612,MA0002.2;0.145685,MA0137.2;0.287486,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;0.200175,MA0065.2;0.44341,MA0150.1;0.991233,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.982083,MA0155.1;0.490492,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.0143037,MA0163.1;0.0600297,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.000240419,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.196451,MA0442.1;0
}}

Latest revision as of 15:57, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:6336759..6336785,+p1@Dab2
Mm9::chr15:6372301..6372327,+p@chr15:6372301..6372327
+
Mm9::chr15:6374201..6374212,+p@chr15:6374201..6374212
+
Mm9::chr15:6374660..6374664,+p@chr15:6374660..6374664
+
Mm9::chr15:6385332..6385355,-p@chr15:6385332..6385355
-
Mm9::chr15:6385439..6385449,+p@chr15:6385439..6385449
+
Mm9::chr15:6389228..6389240,+p@chr15:6389228..6389240
+
Mm9::chr9:62692398..62692419,+p6@Cln6
Mm9::chr9:62693807..62693811,+p8@Cln6


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:0031987locomotion during locomotory behavior0.00552222860125881
GO:0045851pH reduction0.00552222860125881
GO:0051452cellular pH reduction0.00552222860125881
GO:0051453regulation of cellular pH0.00552222860125881
GO:0007042lysosomal lumen acidification0.00552222860125881
GO:0030641cellular hydrogen ion homeostasis0.00591651141402709
GO:0006907pinocytosis0.00591651141402709
GO:0045862positive regulation of proteolysis0.00862777305743479
GO:0055067monovalent inorganic cation homeostasis0.0092022015204295
GO:0030004cellular monovalent inorganic cation homeostasis0.0092022015204295
GO:0001573ganglioside metabolic process0.0092022015204295
GO:0005788endoplasmic reticulum lumen0.0092022015204295
GO:0006687glycosphingolipid metabolic process0.010617342979341
GO:0030162regulation of proteolysis0.0119174408521997
GO:0007588excretion0.0119174408521997
GO:0007040lysosome organization and biogenesis0.0119174408521997
GO:0006664glycolipid metabolic process0.0119174408521997
GO:0006898receptor-mediated endocytosis0.0119174408521997
GO:0006885regulation of pH0.0119174408521997
GO:0006022aminoglycan metabolic process0.0119174408521997
GO:0030203glycosaminoglycan metabolic process0.0119174408521997
GO:0007033vacuole organization and biogenesis0.0119174408521997
GO:0006672ceramide metabolic process0.0137976292243873
GO:0046519sphingoid metabolic process0.01437174251759
GO:0005905coated pit0.0171053084570357
GO:0006665sphingolipid metabolic process0.0222768700319768
GO:0008203cholesterol metabolic process0.0326687356933175
GO:0016125sterol metabolic process0.0337359571224111
GO:0051247positive regulation of protein metabolic process0.0337359571224111
GO:0044432endoplasmic reticulum part0.0367361909616291
GO:0003008system process0.0408793113802752
GO:0042803protein homodimerization activity0.0424400708242353
GO:0030003cellular cation homeostasis0.0424400708242353
GO:0055080cation homeostasis0.0424400708242353
GO:0007601visual perception0.0424400708242353
GO:0050953sensory perception of light stimulus0.0424400708242353
GO:0001701in utero embryonic development0.044259385893427
GO:0008202steroid metabolic process0.0493293550094
GO:0055082cellular chemical homeostasis0.0493293550094
GO:0006873cellular ion homeostasis0.0493293550094
GO:0016043cellular component organization and biogenesis0.0493293550094
GO:0006643membrane lipid metabolic process0.0494317164474651



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
urinary system structure5.73e-0718


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)
MA0003.10.0854318
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.00813637
MA0017.10.726051
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.0824771
MA0050.11.10321
MA0051.10.542972
MA0052.10.84317
MA0055.10.0198867
MA0056.10
MA0057.10.549903
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.10.56663
MA0063.10
MA0066.11.29967
MA0067.11.16502
MA0068.10.266547
MA0069.10.843506
MA0070.10.833895
MA0071.11.10147
MA0072.11.92922
MA0073.10.000250057
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.18495
MA0089.10
MA0090.10.362551
MA0091.11.04993
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.12.10074
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.442138
MA0146.10.0111657
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.20.113962
MA0035.20.482026
MA0039.20.000502396
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.20.200175
MA0065.20.44341
MA0150.10.991233
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.982083
MA0155.10.490492
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0143037
MA0163.10.0600297
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.000240419
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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