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MCL coexpression mm9:202: Difference between revisions

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{{MCL_coexpression_mm9
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of mononuclear cell proliferation;0.00475871526897105;57916,108723,93675!GO:0050670;regulation of lymphocyte proliferation;0.00475871526897105;57916,108723,93675!GO:0032943;mononuclear cell proliferation;0.00555133419886413;57916,108723,93675!GO:0046651;lymphocyte proliferation;0.00555133419886413;57916,108723,93675!GO:0045076;regulation of interleukin-2 biosynthetic process;0.00555133419886413;108723,93675!GO:0051249;regulation of lymphocyte activation;0.00555133419886413;57916,108723,93675!GO:0050865;regulation of cell activation;0.00555133419886413;57916,108723,93675!GO:0042094;interleukin-2 biosynthetic process;0.00555133419886413;108723,93675!GO:0032623;interleukin-2 production;0.0056357446767541;108723,93675!GO:0030041;actin filament polymerization;0.0057446821543281;211401,93675!GO:0030888;regulation of B cell proliferation;0.00804288610178782;57916,108723!GO:0042100;B cell proliferation;0.0122743599463278;57916,108723!GO:0030036;actin cytoskeleton organization and biogenesis;0.0173835408549393;211401,14248,93675!GO:0030029;actin filament-based process;0.0185098557713758;211401,14248,93675!GO:0050864;regulation of B cell activation;0.0185098557713758;57916,108723!GO:0051258;protein polymerization;0.0186270750013696;211401,93675!GO:0008154;actin polymerization and/or depolymerization;0.0186270750013696;211401,93675!GO:0042129;regulation of T cell proliferation;0.0186270750013696;108723,93675!GO:0046649;lymphocyte activation;0.0186270750013696;57916,108723,93675!GO:0045610;regulation of hemocyte differentiation;0.0186270750013696;26411!GO:0042386;hemocyte differentiation;0.0186270750013696;26411!GO:0004633;phosphopantothenoylcysteine decarboxylase activity;0.0186270750013696;66812!GO:0042035;regulation of cytokine biosynthetic process;0.0218420849105439;108723,93675!GO:0045321;leukocyte activation;0.0218420849105439;57916,108723,93675!GO:0042098;T cell proliferation;0.0244722713607449;108723,93675!GO:0001775;cell activation;0.0246598869635554;57916,108723,93675!GO:0042089;cytokine biosynthetic process;0.0264246680723444;108723,93675!GO:0042107;cytokine metabolic process;0.0264246680723444;108723,93675!GO:0050863;regulation of T cell activation;0.0264246680723444;108723,93675!GO:0004144;diacylglycerol O-acyltransferase activity;0.0264246680723444;68393!GO:0051014;actin filament severing;0.0264246680723444;14248!GO:0051239;regulation of multicellular organismal process;0.0384332951015432;57916,108723,93675!GO:0030695;GTPase regulator activity;0.0424162388366757;108995,26411,76088!GO:0042113;B cell activation;0.0424162388366757;57916,108723!GO:0003846;2-acylglycerol O-acyltransferase activity;0.0454617984365382;68393!GO:0006651;diacylglycerol biosynthetic process;0.0454617984365382;68393!GO:0042127;regulation of cell 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|gostat_on_MCL_coexpression=GO:0032944;regulation of mononuclear cell proliferation;0.00475871526897105;57916,108723,93675!GO:0050670;regulation of lymphocyte proliferation;0.00475871526897105;57916,108723,93675!GO:0032943;mononuclear cell proliferation;0.00555133419886413;57916,108723,93675!GO:0046651;lymphocyte proliferation;0.00555133419886413;57916,108723,93675!GO:0045076;regulation of interleukin-2 biosynthetic process;0.00555133419886413;108723,93675!GO:0051249;regulation of lymphocyte activation;0.00555133419886413;57916,108723,93675!GO:0050865;regulation of cell activation;0.00555133419886413;57916,108723,93675!GO:0042094;interleukin-2 biosynthetic process;0.00555133419886413;108723,93675!GO:0032623;interleukin-2 production;0.0056357446767541;108723,93675!GO:0030041;actin filament polymerization;0.0057446821543281;211401,93675!GO:0030888;regulation of B cell proliferation;0.00804288610178782;57916,108723!GO:0042100;B cell proliferation;0.0122743599463278;57916,108723!GO:0030036;actin cytoskeleton organization and biogenesis;0.0173835408549393;211401,14248,93675!GO:0030029;actin filament-based process;0.0185098557713758;211401,14248,93675!GO:0050864;regulation of B cell activation;0.0185098557713758;57916,108723!GO:0051258;protein polymerization;0.0186270750013696;211401,93675!GO:0008154;actin polymerization and/or depolymerization;0.0186270750013696;211401,93675!GO:0042129;regulation of T cell proliferation;0.0186270750013696;108723,93675!GO:0046649;lymphocyte activation;0.0186270750013696;57916,108723,93675!GO:0045610;regulation of hemocyte differentiation;0.0186270750013696;26411!GO:0042386;hemocyte differentiation;0.0186270750013696;26411!GO:0004633;phosphopantothenoylcysteine decarboxylase activity;0.0186270750013696;66812!GO:0042035;regulation of cytokine biosynthetic process;0.0218420849105439;108723,93675!GO:0045321;leukocyte activation;0.0218420849105439;57916,108723,93675!GO:0042098;T cell proliferation;0.0244722713607449;108723,93675!GO:0001775;cell activation;0.0246598869635554;57916,108723,93675!GO:0042089;cytokine biosynthetic process;0.0264246680723444;108723,93675!GO:0042107;cytokine metabolic process;0.0264246680723444;108723,93675!GO:0050863;regulation of T cell activation;0.0264246680723444;108723,93675!GO:0004144;diacylglycerol O-acyltransferase activity;0.0264246680723444;68393!GO:0051014;actin filament severing;0.0264246680723444;14248!GO:0051239;regulation of multicellular organismal process;0.0384332951015432;57916,108723,93675!GO:0030695;GTPase regulator activity;0.0424162388366757;108995,26411,76088!GO:0042113;B cell activation;0.0424162388366757;57916,108723!GO:0003846;2-acylglycerol O-acyltransferase activity;0.0454617984365382;68393!GO:0006651;diacylglycerol biosynthetic process;0.0454617984365382;68393!GO:0042127;regulation of cell proliferation;0.0480240436370861;57916,108723,93675!
|ontology_enrichment_celltype=CL:0000838!1.55e-11!12;CL:0002031!4.64e-11!25;CL:0000084!2.19e-10!11;CL:0000827!2.19e-10!11;CL:0000542!2.29e-10!13;CL:0000051!2.29e-10!13;CL:0000988!2.56e-09!32;CL:0002032!2.56e-09!32;CL:0000037!2.56e-09!32;CL:0000566!2.56e-09!32;CL:0000837!2.56e-09!32;CL:0000791!9.43e-09!9;CL:0000789!9.43e-09!9;CL:0002420!9.43e-09!9;CL:0002419!9.43e-09!9;CL:0000790!9.43e-09!9;CL:0000624!8.99e-08!8;CL:0002242!9.21e-08!16;CL:0000553!1.15e-07!6;CL:0000556!1.15e-07!6;CL:0000738!4.16e-07!17;CL:0002087!4.16e-07!17
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!9.07e-21!48;UBERON:0002405!9.07e-21!48;UBERON:0004177!3.28e-20!29;UBERON:0005057!3.28e-20!29;UBERON:0002390!3.56e-18!45;UBERON:0003061!3.56e-18!45;UBERON:0003408!2.44e-17!24;UBERON:0000077!1.64e-16!35;UBERON:0002370!1.73e-16!23;UBERON:0000974!1.73e-16!23;UBERON:0004807!1.73e-16!23;UBERON:0005058!1.73e-16!23;UBERON:0003351!1.73e-16!23;UBERON:0009113!1.73e-16!23;UBERON:0003295!1.73e-16!23;UBERON:0009722!1.73e-16!23;UBERON:0005562!1.73e-16!23;UBERON:0007690!1.73e-16!23;UBERON:0001004!1.25e-15!42;UBERON:0006562!1.66e-15!24;UBERON:0001557!1.66e-15!24;UBERON:0001042!1.66e-15!24;UBERON:0008814!1.66e-15!24;UBERON:0009145!1.66e-15!24;UBERON:0000065!7.44e-15!41;UBERON:0000072!5.20e-13!27;UBERON:0003081!1.15e-11!87;UBERON:0001041!2.55e-11!80;UBERON:0000063!1.56e-09!35;UBERON:0007811!3.38e-09!36;UBERON:0000926!5.79e-09!120;UBERON:0004120!5.79e-09!120;UBERON:0006603!5.79e-09!120;UBERON:0005911!2.02e-08!69;UBERON:0001048!1.62e-07!134;UBERON:0001007!6.74e-07!116;UBERON:0001555!6.74e-07!116;UBERON:0007026!6.74e-07!116
|tfbs_overrepresentation_for_novel_motifs=0.457729,0.29905,0.651263,0.308831,0.315617,0.143218,0.502643,0.210961,0.132146,0.16578,0.187045,0.21991,0.211553,0.5274,0.568827,0,0.497195,0.478413,0.620117,0.740585,0.314143,0.310686,0.897959,1.34326,0.413127,0.278145,0.777889,0.370057,2.5804,0.35426,0.0378855,0.229773,0.157055,0.32068,0.201592,0.251214,0.143176,0.0596837,0.556201,0.160501,0.0747035,0.153958,0.254592,0.204228,0.650568,0.121663,0.773193,0.398692,0.441056,0.258712,0.472049,0.0932294,0.46202,0.882144,0.344664,1.38343,0.13469,0.206471,0.362834,0.537835,0.619092,0.66245,0.266948,0.456051,0.0775571,0.172879,0.453796,0.762091,0.611861,0.628327,0.179033,0.361846,0.104189,0.370715,1.40612,0.29271,0.204479,0.370963,0.592644,0.54512,0.128244,0.176256,0.0968899,1.45047,0.283628,0.237572,0.520515,1.11728,0.124296,0.913913,0.512525,1.4274,0.238418,0.330861,0.352921,0.29952,0.204904,0.240329,1.83692,0.168904,0.26783,0.229585,0.318186,0.472898,0.471392,0.0392163,0.191295,0.693922,0.333529,0.317925,0.0929617,0.855718,0.829405,0.427206,0.518556,0.0732384,0.531074,0.315124,0.166646,0.0598901,0.374962,0.842795,0.0822034,0.74521,0.565403,0.207718,0.88821,0.233828,0.452538,0.085768,0.305535,0.29679,0.428195,0.0786006,0.537141,1.52844,0.254916,0.155239,0.495055,1.26906,0.883804,0.457711,1.02922,0.236832,1.44814,0.154369,0.780349,1.23035,0.778921,0.0795505,0.244202,0.0180465,0.33253,0.0110786,0.568364,1.02561,0.644076,0.104386,0.238485,0.103944,0.503133,0.28301,0.208006,1.87441,0.894744,0.552976,0.434218,0.475632,0.91828
}}

Latest revision as of 14:52, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:110594409..110594448,-p@chr10:110594409..110594448
-
Mm9::chr11:11457391..11457401,+p2@ENSMUST00000146304
p2@uc007iag.1
Mm9::chr11:11457404..11457434,+p1@ENSMUST00000146304
p1@uc007iag.1
Mm9::chr11:49060964..49061014,+p5@Mgat1
Mm9::chr11:60955959..60955973,+p2@Tnfrsf13b
Mm9::chr11:98407234..98407259,-p2@Ikzf3
Mm9::chr11:98407264..98407295,-p1@Ikzf3
Mm9::chr11:98407305..98407321,-p6@Ikzf3
Mm9::chr11:98407340..98407359,-p4@Ikzf3
Mm9::chr11:98407370..98407395,-p3@Ikzf3
Mm9::chr11:98407512..98407517,-p13@Ikzf3
Mm9::chr12:100801772..100801861,-p1@Foxn3
Mm9::chr12:114660946..114660955,-p1@ENSMUST00000103426
Mm9::chr13:24821510..24821514,+p@chr13:24821510..24821514
+
Mm9::chr15:58913850..58913878,-p5@Mtss1
Mm9::chr15:74785926..74785937,-p@chr15:74785926..74785937
-
Mm9::chr15:74785945..74785971,-p@chr15:74785945..74785971
-
Mm9::chr15:74787899..74787904,+p@chr15:74787899..74787904
+
Mm9::chr15:74788002..74788006,+p@chr15:74788002..74788006
+
Mm9::chr17:50233579..50233599,-p3@Rftn1
Mm9::chr17:84177324..84177329,-p@chr17:84177324..84177329
-
Mm9::chr18:39678978..39678987,-p@chr18:39678978..39678987
-
Mm9::chr18:75438430..75438451,-p@chr18:75438430..75438451
-
Mm9::chr19:25126919..25126938,+p3@Dock8
Mm9::chr19:4190959..4190976,-p3@Tbc1d10c
Mm9::chr19:4190985..4191029,-p2@Tbc1d10c
Mm9::chr19:45547285..45547303,+p@chr19:45547285..45547303
+
Mm9::chr1:21315817..21315821,-p@chr1:21315817..21315821
-
Mm9::chr1:87627728..87627734,-p@chr1:87627728..87627734
-
Mm9::chr1:89749839..89749881,+p1@Dgkd
Mm9::chr2:112106018..112106082,+p3@Slc12a6
Mm9::chr2:158526707..158526708,+p@chr2:158526707..158526708
+
Mm9::chr4:56929012..56929023,-p@chr4:56929012..56929023
-
Mm9::chr5:141476512..141476543,-p3@Card11
Mm9::chr5:34575662..34575684,-p4@Zfyve28
Mm9::chr6:121222718..121222745,-p@chr6:121222718..121222745
-
Mm9::chr6:128837604..128837610,+p1@Clec2i
Mm9::chr7:29767851..29767911,+p1@Map4k1
Mm9::chr7:29769748..29769749,+p@chr7:29769748..29769749
+
Mm9::chr7:4412289..4412332,+p1@Eps8l1
Mm9::chr7:4412340..4412351,+p2@Eps8l1
Mm9::chr7:53314509..53314565,-p@chr7:53314509..53314565
-
Mm9::chr7:87343276..87343344,+p3@Sema4b
Mm9::chr8:11556867..11556918,+p@chr8:11556867..11556918
+
Mm9::chr9:32348906..32348920,-p3@Fli1
Mm9::chr9:57269180..57269193,-p@chr9:57269180..57269193
-


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:0032944regulation of mononuclear cell proliferation0.00475871526897105
GO:0050670regulation of lymphocyte proliferation0.00475871526897105
GO:0032943mononuclear cell proliferation0.00555133419886413
GO:0046651lymphocyte proliferation0.00555133419886413
GO:0045076regulation of interleukin-2 biosynthetic process0.00555133419886413
GO:0051249regulation of lymphocyte activation0.00555133419886413
GO:0050865regulation of cell activation0.00555133419886413
GO:0042094interleukin-2 biosynthetic process0.00555133419886413
GO:0032623interleukin-2 production0.0056357446767541
GO:0030041actin filament polymerization0.0057446821543281
GO:0030888regulation of B cell proliferation0.00804288610178782
GO:0042100B cell proliferation0.0122743599463278
GO:0030036actin cytoskeleton organization and biogenesis0.0173835408549393
GO:0030029actin filament-based process0.0185098557713758
GO:0050864regulation of B cell activation0.0185098557713758
GO:0051258protein polymerization0.0186270750013696
GO:0008154actin polymerization and/or depolymerization0.0186270750013696
GO:0042129regulation of T cell proliferation0.0186270750013696
GO:0046649lymphocyte activation0.0186270750013696
GO:0045610regulation of hemocyte differentiation0.0186270750013696
GO:0042386hemocyte differentiation0.0186270750013696
GO:0004633phosphopantothenoylcysteine decarboxylase activity0.0186270750013696
GO:0042035regulation of cytokine biosynthetic process0.0218420849105439
GO:0045321leukocyte activation0.0218420849105439
GO:0042098T cell proliferation0.0244722713607449
GO:0001775cell activation0.0246598869635554
GO:0042089cytokine biosynthetic process0.0264246680723444
GO:0042107cytokine metabolic process0.0264246680723444
GO:0050863regulation of T cell activation0.0264246680723444
GO:0004144diacylglycerol O-acyltransferase activity0.0264246680723444
GO:0051014actin filament severing0.0264246680723444
GO:0051239regulation of multicellular organismal process0.0384332951015432
GO:0030695GTPase regulator activity0.0424162388366757
GO:0042113B cell activation0.0424162388366757
GO:00038462-acylglycerol O-acyltransferase activity0.0454617984365382
GO:0006651diacylglycerol biosynthetic process0.0454617984365382
GO:0042127regulation of cell proliferation0.0480240436370861



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
hemolymphoid system9.07e-2148
immune system9.07e-2148
hemopoietic organ3.28e-2029
immune organ3.28e-2029
hematopoietic system3.56e-1845
blood island3.56e-1845
gland of gut2.44e-1724
mixed endoderm/mesoderm-derived structure1.64e-1635
thymus1.73e-1623
neck1.73e-1623
respiratory system epithelium1.73e-1623
hemolymphoid system gland1.73e-1623
pharyngeal epithelium1.73e-1623
thymic region1.73e-1623
pharyngeal gland1.73e-1623
entire pharyngeal arch endoderm1.73e-1623
thymus primordium1.73e-1623
early pharyngeal endoderm1.73e-1623
respiratory system1.25e-1542
pharynx1.66e-1524
upper respiratory tract1.66e-1524
chordate pharynx1.66e-1524
pharyngeal arch system1.66e-1524
pharyngeal region of foregut1.66e-1524
respiratory tract7.44e-1541
segment of respiratory tract5.20e-1327
lateral plate mesoderm1.15e-1187
foregut2.55e-1180
organ segment1.56e-0935
craniocervical region3.38e-0936
mesoderm5.79e-09120
mesoderm-derived structure5.79e-09120
presumptive mesoderm5.79e-09120
endo-epithelium2.02e-0869
primordium1.62e-07134
digestive system6.74e-07116
digestive tract6.74e-07116
primitive gut6.74e-07116


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)
MA0003.10.331539
MA0004.10.309636
MA0006.10.193228
MA0007.10.0286754
MA0009.10.692256
MA0014.10.0956489
MA0017.10.240574
MA0019.10.135009
MA0024.10.623278
MA0025.10.424514
MA0027.11.761
MA0028.10.098513
MA0029.10.20414
MA0030.10.208367
MA0031.11.04238
MA0038.10.0813956
MA0040.10.256435
MA0041.12.16905
MA0042.10.87835
MA0043.10.317434
MA0046.10.272953
MA0048.10.0543507
MA0050.11.972
MA0051.11.01345
MA0052.10.262081
MA0055.10.0620722
MA0056.10
MA0057.10.327755
MA0058.10.168735
MA0059.10.184648
MA0060.10.0816892
MA0061.10.570417
MA0063.10
MA0066.10.265247
MA0067.10.517464
MA0068.10.348402
MA0069.10.725888
MA0070.11.3107
MA0071.10.164915
MA0072.10.249646
MA0073.10.25552
MA0074.10.2252
MA0076.10.135424
MA0077.10.23483
MA0078.10.100141
MA0081.10.680001
MA0083.10.31684
MA0084.10.812114
MA0087.10.777974
MA0088.10.00499668
MA0089.10
MA0090.10.104141
MA0091.10.14247
MA0092.10.104375
MA0093.10.398655
MA0095.10
MA0098.10
MA0100.10.212891
MA0101.10.632354
MA0103.10.452314
MA0105.11.91652
MA0106.10.103821
MA0107.10.249327
MA0108.20.451773
MA0109.10
MA0111.10.821081
MA0113.10.30385
MA0114.10.114412
MA0115.10.319533
MA0116.10.192879
MA0117.10.2956
MA0119.10.197444
MA0122.10.310251
MA0124.10.472367
MA0125.10.411352
MA0130.10
MA0131.10.820712
MA0132.10
MA0133.10
MA0135.10.345083
MA0136.10.247061
MA0139.10.201408
MA0140.10.465555
MA0141.10.148633
MA0142.10.17699
MA0143.10.0982359
MA0144.10.050193
MA0145.10.273294
MA0146.10.29238
MA0147.10.0585619
MA0148.10.145175
MA0149.11.33698
MA0062.20.323794
MA0035.20.47474
MA0039.20.124552
MA0138.20.128348
MA0002.20.337037
MA0137.20.502812
MA0104.20.138802
MA0047.20.277151
MA0112.20.185081
MA0065.20.385921
MA0150.10.28493
MA0151.10
MA0152.10.277277
MA0153.10.357941
MA0154.10.165851
MA0155.10.097464
MA0156.10.474471
MA0157.10.928824
MA0158.10
MA0159.10.149878
MA0160.10.342305
MA0161.10
MA0162.10.119484
MA0163.10.541415
MA0164.10.247467
MA0080.21.30557
MA0018.20.074393
MA0099.20.125042
MA0079.20.118013
MA0102.20.861175
MA0258.10.502463
MA0259.10.0155432
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:202&oldid=3072201"