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MCL coexpression mm9:1287: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0019932;second-messenger-mediated signaling;0.0041889307110198;18707,11513!GO:0046934;phosphatidylinositol-4,5-bisphosphate 3-kinase activity;0.0101825686755877;18707!GO:0046854;phosphoinositide phosphorylation;0.0101825686755877;18707!GO:0035004;phosphoinositide 3-kinase activity;0.0101825686755877;18707!GO:0016303;1-phosphatidylinositol-3-kinase activity;0.0101825686755877;18707!GO:0005942;phosphoinositide 3-kinase complex;0.0101825686755877;18707!GO:0001782;B cell homeostasis;0.0101825686755877;18707!GO:0046834;lipid phosphorylation;0.0101825686755877;18707!GO:0004016;adenylate cyclase activity;0.0101825686755877;11513!GO:0007190;adenylate cyclase activation;0.0101825686755877;11513!GO:0031281;positive regulation of cyclase activity;0.0101825686755877;11513!GO:0051349;positive regulation of lyase activity;0.0101825686755877;11513!GO:0045762;positive regulation of adenylate cyclase activity;0.0101825686755877;11513!GO:0045761;regulation of adenylate cyclase activity;0.0101825686755877;11513!GO:0006171;cAMP biosynthetic process;0.0101825686755877;11513!GO:0031279;regulation of cyclase activity;0.0101825686755877;11513!GO:0051339;regulation of lyase activity;0.0101825686755877;11513!GO:0002260;lymphocyte homeostasis;0.0101825686755877;18707!GO:0046058;cAMP metabolic process;0.0101825686755877;11513!GO:0001727;lipid kinase activity;0.0101825686755877;18707!GO:0009975;cyclase activity;0.0101825686755877;11513!GO:0016849;phosphorus-oxygen lyase activity;0.0101825686755877;11513!GO:0030258;lipid modification;0.0101825686755877;18707!GO:0001776;leukocyte homeostasis;0.0101825686755877;18707!GO:0007242;intracellular signaling cascade;0.0101825686755877;18707,11513!GO:0009190;cyclic nucleotide biosynthetic process;0.0101825686755877;11513!GO:0048872;homeostasis of number of cells;0.0101825686755877;18707!GO:0004428;inositol or phosphatidylinositol kinase activity;0.0101825686755877;18707!GO:0007189;G-protein signaling, adenylate cyclase activating pathway;0.0122869486827826;11513!GO:0009187;cyclic nucleotide metabolic process;0.0125554027972597;11513!GO:0048015;phosphoinositide-mediated signaling;0.0139948906204137;18707!GO:0030384;phosphoinositide metabolic process;0.0139948906204137;18707!GO:0007188;G-protein signaling, coupled to cAMP nucleotide second messenger;0.016860093186008;11513!GO:0006650;glycerophospholipid metabolic process;0.016860093186008;18707!GO:0007187;G-protein signaling, coupled to cyclic nucleotide second messenger;0.016860093186008;11513!GO:0019933;cAMP-mediated signaling;0.0169560597719931;11513!GO:0019935;cyclic-nucleotide-mediated signaling;0.0173212513502202;11513!GO:0042113;B cell activation;0.0227412066789144;18707!GO:0044445;cytosolic part;0.0244981950385326;18707!GO:0006644;phospholipid metabolic process;0.0294582099803791;18707!GO:0009165;nucleotide biosynthetic process;0.0302212702873356;11513!GO:0043085;positive regulation of catalytic activity;0.0323928369149597;11513!GO:0006643;membrane lipid metabolic process;0.0350565684588753;18707!GO:0016829;lyase activity;0.0350565684588753;11513!GO:0007166;cell surface receptor linked signal transduction;0.0374638801911031;18707,11513!GO:0009117;nucleotide metabolic process;0.0398981395349427;11513!GO:0046649;lymphocyte activation;0.0407661960117566;18707!GO:0055086;nucleobase, nucleoside and nucleotide metabolic process;0.040967261749857;11513!GO:0045321;leukocyte activation;0.0425994543014596;18707!GO:0001775;cell activation;0.0447688215167534;18707!}}
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pathway;0.0122869486827826;11513!GO:0009187;cyclic nucleotide metabolic process;0.0125554027972597;11513!GO:0048015;phosphoinositide-mediated signaling;0.0139948906204137;18707!GO:0030384;phosphoinositide metabolic process;0.0139948906204137;18707!GO:0007188;G-protein signaling, coupled to cAMP nucleotide second messenger;0.016860093186008;11513!GO:0006650;glycerophospholipid metabolic process;0.016860093186008;18707!GO:0007187;G-protein signaling, coupled to cyclic nucleotide second messenger;0.016860093186008;11513!GO:0019933;cAMP-mediated signaling;0.0169560597719931;11513!GO:0019935;cyclic-nucleotide-mediated signaling;0.0173212513502202;11513!GO:0042113;B cell activation;0.0227412066789144;18707!GO:0044445;cytosolic part;0.0244981950385326;18707!GO:0006644;phospholipid metabolic process;0.0294582099803791;18707!GO:0009165;nucleotide biosynthetic process;0.0302212702873356;11513!GO:0043085;positive regulation of catalytic activity;0.0323928369149597;11513!GO:0006643;membrane lipid metabolic process;0.0350565684588753;18707!GO:0016829;lyase activity;0.0350565684588753;11513!GO:0007166;cell surface receptor linked signal transduction;0.0374638801911031;18707,11513!GO:0009117;nucleotide metabolic process;0.0398981395349427;11513!GO:0046649;lymphocyte activation;0.0407661960117566;18707!GO:0055086;nucleobase, nucleoside and nucleotide metabolic process;0.040967261749857;11513!GO:0045321;leukocyte activation;0.0425994543014596;18707!GO:0001775;cell activation;0.0447688215167534;18707!|ontology_enrichment_celltype=CL:0000838!3.30e-12!12;CL:0000084!1.26e-11!11;CL:0000827!1.26e-11!11;CL:0000542!6.39e-11!13;CL:0000051!6.39e-11!13;CL:0000988!1.04e-10!32;CL:0002032!1.04e-10!32;CL:0000037!1.04e-10!32;CL:0000566!1.04e-10!32;CL:0000837!1.04e-10!32;CL:0002031!3.07e-10!25;CL:0000791!1.51e-09!9;CL:0000789!1.51e-09!9;CL:0002420!1.51e-09!9;CL:0002419!1.51e-09!9;CL:0000790!1.51e-09!9;CL:0000738!1.40e-08!17;CL:0002087!1.40e-08!17;CL:0000624!1.74e-08!8;CL:0002242!4.60e-08!16|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0004177!9.83e-20!29;UBERON:0005057!9.83e-20!29;UBERON:0002193!1.16e-19!48;UBERON:0002405!1.16e-19!48;UBERON:0002390!1.13e-17!45;UBERON:0003061!1.13e-17!45;UBERON:0000077!4.99e-17!35;UBERON:0003408!1.67e-16!24;UBERON:0002370!1.03e-15!23;UBERON:0000974!1.03e-15!23;UBERON:0004807!1.03e-15!23;UBERON:0005058!1.03e-15!23;UBERON:0003351!1.03e-15!23;UBERON:0009113!1.03e-15!23;UBERON:0003295!1.03e-15!23;UBERON:0009722!1.03e-15!23;UBERON:0005562!1.03e-15!23;UBERON:0007690!1.03e-15!23;UBERON:0006562!1.01e-14!24;UBERON:0001557!1.01e-14!24;UBERON:0001042!1.01e-14!24;UBERON:0008814!1.01e-14!24;UBERON:0009145!1.01e-14!24;UBERON:0000072!3.24e-12!27;UBERON:0003081!2.24e-11!87;UBERON:0001004!1.68e-10!42;UBERON:0000065!7.21e-10!41;UBERON:0000063!1.10e-08!35;UBERON:0004119!1.11e-08!118;UBERON:0000925!1.11e-08!118;UBERON:0006595!1.11e-08!118;UBERON:0001007!1.41e-08!116;UBERON:0001555!1.41e-08!116;UBERON:0007026!1.41e-08!116;UBERON:0001041!1.51e-08!80;UBERON:0007811!2.29e-08!36;UBERON:0004921!6.85e-08!114;UBERON:0000926!9.70e-08!120;UBERON:0004120!9.70e-08!120;UBERON:0006603!9.70e-08!120|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.7141,0.0835344,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.143775,0.426133,0.35122,0.657163,0.345236,0.472505,0.686615,0.63639,0.572827,0.394364,0.534301,0.558142,0.960397,0.892985,0.589948,0.364821,0.144368,0.326478,0.629145,0.820134,0.27383,0.342638,0.56353,0.327433,0.959963,0.368882,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.742129,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.366795,1.156,0.208101,0.19692,0.204132,0.763395,0.922432,2.875,0.708505,0.874787,1.71704,0.676326,1.03903,0.198949,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,1.47187,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.247162,0.53982,0.858327,0.862623,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.0987301,1.10596,0.287383,0.678689,1.18867,1.70209,0.376898,0.48935,0.500417,1.31911,1.03816,2.1365,0.482185,0.82857,0.671017,0.325308,1.52669,0.30995|tfbs_overrepresentation_jaspar=MA0003.1;0.04894,MA0004.1;1.3269,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.0315641,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;1.97265,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.161427,MA0050.1;1.41229,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.212634,MA0056.1;0,MA0057.1;0.457693,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.911705,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.0960184,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.111145,MA0089.1;0,MA0090.1;1.25093,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.988233,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;0.199622,MA0106.1;0.737893,MA0107.1;1.0169,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;2.2889,MA0145.1;0.761789,MA0146.1;0.353523,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.181031,MA0138.2;0.788113,MA0002.2;2.76558,MA0137.2;1.88035,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;0.132921,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.0465447,MA0163.1;0.0423021,MA0164.1;0.658997,MA0080.2;1.01893,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.000341844,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0}}

Latest revision as of 16:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:48805759..48805781,-p3@Tgtp1
p3@Tgtp2
Mm9::chr2:167766298..167766302,+p@chr2:167766298..167766302
+
Mm9::chr4:149075690..149075711,-p2@Pik3cd
Mm9::chr5:122683421..122683445,+p@chr5:122683421..122683445
+
Mm9::chr8:90812977..90812990,+p8@Adcy7
Mm9::chrX:50113602..50113611,+p@chrX:50113602..50113611
+


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:0019932second-messenger-mediated signaling0.0041889307110198
GO:0046934phosphatidylinositol-4,5-bisphosphate 3-kinase activity0.0101825686755877
GO:0046854phosphoinositide phosphorylation0.0101825686755877
GO:0035004phosphoinositide 3-kinase activity0.0101825686755877
GO:00163031-phosphatidylinositol-3-kinase activity0.0101825686755877
GO:0005942phosphoinositide 3-kinase complex0.0101825686755877
GO:0001782B cell homeostasis0.0101825686755877
GO:0046834lipid phosphorylation0.0101825686755877
GO:0004016adenylate cyclase activity0.0101825686755877
GO:0007190adenylate cyclase activation0.0101825686755877
GO:0031281positive regulation of cyclase activity0.0101825686755877
GO:0051349positive regulation of lyase activity0.0101825686755877
GO:0045762positive regulation of adenylate cyclase activity0.0101825686755877
GO:0045761regulation of adenylate cyclase activity0.0101825686755877
GO:0006171cAMP biosynthetic process0.0101825686755877
GO:0031279regulation of cyclase activity0.0101825686755877
GO:0051339regulation of lyase activity0.0101825686755877
GO:0002260lymphocyte homeostasis0.0101825686755877
GO:0046058cAMP metabolic process0.0101825686755877
GO:0001727lipid kinase activity0.0101825686755877
GO:0009975cyclase activity0.0101825686755877
GO:0016849phosphorus-oxygen lyase activity0.0101825686755877
GO:0030258lipid modification0.0101825686755877
GO:0001776leukocyte homeostasis0.0101825686755877
GO:0007242intracellular signaling cascade0.0101825686755877
GO:0009190cyclic nucleotide biosynthetic process0.0101825686755877
GO:0048872homeostasis of number of cells0.0101825686755877
GO:0004428inositol or phosphatidylinositol kinase activity0.0101825686755877
GO:0007189G-protein signaling, adenylate cyclase activating pathway0.0122869486827826
GO:0009187cyclic nucleotide metabolic process0.0125554027972597
GO:0048015phosphoinositide-mediated signaling0.0139948906204137
GO:0030384phosphoinositide metabolic process0.0139948906204137
GO:0007188G-protein signaling, coupled to cAMP nucleotide second messenger0.016860093186008
GO:0006650glycerophospholipid metabolic process0.016860093186008
GO:0007187G-protein signaling, coupled to cyclic nucleotide second messenger0.016860093186008
GO:0019933cAMP-mediated signaling0.0169560597719931
GO:0019935cyclic-nucleotide-mediated signaling0.0173212513502202
GO:0042113B cell activation0.0227412066789144
GO:0044445cytosolic part0.0244981950385326
GO:0006644phospholipid metabolic process0.0294582099803791
GO:0009165nucleotide biosynthetic process0.0302212702873356
GO:0043085positive regulation of catalytic activity0.0323928369149597
GO:0006643membrane lipid metabolic process0.0350565684588753
GO:0016829lyase activity0.0350565684588753
GO:0007166cell surface receptor linked signal transduction0.0374638801911031
GO:0009117nucleotide metabolic process0.0398981395349427
GO:0046649lymphocyte activation0.0407661960117566
GO:0055086nucleobase, nucleoside and nucleotide metabolic process0.040967261749857
GO:0045321leukocyte activation0.0425994543014596
GO:0001775cell activation0.0447688215167534



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
hemopoietic organ9.83e-2029
immune organ9.83e-2029
hemolymphoid system1.16e-1948
immune system1.16e-1948
hematopoietic system1.13e-1745
blood island1.13e-1745
mixed endoderm/mesoderm-derived structure4.99e-1735
gland of gut1.67e-1624
thymus1.03e-1523
neck1.03e-1523
respiratory system epithelium1.03e-1523
hemolymphoid system gland1.03e-1523
pharyngeal epithelium1.03e-1523
thymic region1.03e-1523
pharyngeal gland1.03e-1523
entire pharyngeal arch endoderm1.03e-1523
thymus primordium1.03e-1523
early pharyngeal endoderm1.03e-1523
pharynx1.01e-1424
upper respiratory tract1.01e-1424
chordate pharynx1.01e-1424
pharyngeal arch system1.01e-1424
pharyngeal region of foregut1.01e-1424
segment of respiratory tract3.24e-1227
lateral plate mesoderm2.24e-1187
respiratory system1.68e-1042
respiratory tract7.21e-1041
organ segment1.10e-0835
endoderm-derived structure1.11e-08118
endoderm1.11e-08118
presumptive endoderm1.11e-08118
digestive system1.41e-08116
digestive tract1.41e-08116
primitive gut1.41e-08116
foregut1.51e-0880
craniocervical region2.29e-0836
subdivision of digestive tract6.85e-08114
mesoderm9.70e-08120
mesoderm-derived structure9.70e-08120
presumptive mesoderm9.70e-08120


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)
MA0003.10.04894
MA0004.11.3269
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.0315641
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.11.97265
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.11.41229
MA0051.10.695779
MA0052.11.00829
MA0055.10.212634
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.911705
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.0960184
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.111145
MA0089.10
MA0090.11.25093
MA0091.10.55008
MA0092.10.501022
MA0093.10.988233
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.11.0169
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.12.2889
MA0145.10.761789
MA0146.10.353523
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.181031
MA0138.20.788113
MA0002.22.76558
MA0137.21.88035
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.0465447
MA0163.10.0423021
MA0164.10.658997
MA0080.21.01893
MA0018.20.669032
MA0099.20.781628
MA0079.20.000341844
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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