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MCL coexpression mm9:601: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0045069;regulation of viral genome replication;0.0119145437698286;12043!GO:0050792;regulation of viral reproduction;0.0119145437698286;12043!GO:0019079;viral genome replication;0.0119145437698286;12043!GO:0046902;regulation of mitochondrial membrane permeability;0.0119145437698286;12043!GO:0019058;viral infectious cycle;0.0119145437698286;12043!GO:0051881;regulation of mitochondrial membrane potential;0.0119145437698286;12043!GO:0004652;polynucleotide adenylyltransferase activity;0.0136158753894981;216578!GO:0022415;viral reproductive process;0.0148915477320502;12043!GO:0016032;viral reproduction;0.0158834472390889;12043!GO:0001836;release of cytochrome c from mitochondria;0.0238186440108132;12043!GO:0043631;RNA polyadenylation;0.0238186440108132;216578!GO:0007006;mitochondrial membrane organization and biogenesis;0.0256466306647956;12043!GO:0031069;hair follicle morphogenesis;0.0256466306647956;12043!GO:0031123;RNA 3'-end processing;0.0289131305174863;216578!GO:0008637;apoptotic mitochondrial changes;0.0301570578102471;12043!GO:0006839;mitochondrial transport;0.0322040377729354;12043!GO:0043524;negative regulation of neuron apoptosis;0.0322040377729354;12043!GO:0043523;regulation of neuron apoptosis;0.0408962687220554;12043!GO:0051402;neuron apoptosis;0.0408962687220554;12043!GO:0022404;molting cycle process;0.0408962687220554;12043!GO:0001942;hair follicle development;0.0408962687220554;12043!GO:0022405;hair cycle process;0.0408962687220554;12043!GO:0042391;regulation of membrane potential;0.0408962687220554;12043!GO:0042633;hair cycle;0.0408962687220554;12043!GO:0042303;molting cycle;0.0408962687220554;12043!GO:0008632;apoptotic program;0.0421101746110773;12043!GO:0048730;epidermis morphogenesis;0.0421101746110773;12043!GO:0016772;transferase activity, transferring phosphorus-containing groups;0.0421101746110773;216578,18712!GO:0046982;protein heterodimerization activity;0.0483232202533136;12043!GO:0005634;nucleus;0.0483232202533136;216578,18712,12043!}}
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of viral genome replication;0.0119145437698286;12043!GO:0050792;regulation of viral reproduction;0.0119145437698286;12043!GO:0019079;viral genome replication;0.0119145437698286;12043!GO:0046902;regulation of mitochondrial membrane permeability;0.0119145437698286;12043!GO:0019058;viral infectious cycle;0.0119145437698286;12043!GO:0051881;regulation of mitochondrial membrane potential;0.0119145437698286;12043!GO:0004652;polynucleotide adenylyltransferase activity;0.0136158753894981;216578!GO:0022415;viral reproductive process;0.0148915477320502;12043!GO:0016032;viral reproduction;0.0158834472390889;12043!GO:0001836;release of cytochrome c from mitochondria;0.0238186440108132;12043!GO:0043631;RNA polyadenylation;0.0238186440108132;216578!GO:0007006;mitochondrial membrane organization and biogenesis;0.0256466306647956;12043!GO:0031069;hair follicle morphogenesis;0.0256466306647956;12043!GO:0031123;RNA 3'-end processing;0.0289131305174863;216578!GO:0008637;apoptotic mitochondrial changes;0.0301570578102471;12043!GO:0006839;mitochondrial transport;0.0322040377729354;12043!GO:0043524;negative regulation of neuron apoptosis;0.0322040377729354;12043!GO:0043523;regulation of neuron apoptosis;0.0408962687220554;12043!GO:0051402;neuron apoptosis;0.0408962687220554;12043!GO:0022404;molting cycle process;0.0408962687220554;12043!GO:0001942;hair follicle development;0.0408962687220554;12043!GO:0022405;hair cycle process;0.0408962687220554;12043!GO:0042391;regulation of membrane potential;0.0408962687220554;12043!GO:0042633;hair cycle;0.0408962687220554;12043!GO:0042303;molting cycle;0.0408962687220554;12043!GO:0008632;apoptotic program;0.0421101746110773;12043!GO:0048730;epidermis morphogenesis;0.0421101746110773;12043!GO:0016772;transferase activity, transferring phosphorus-containing groups;0.0421101746110773;216578,18712!GO:0046982;protein heterodimerization activity;0.0483232202533136;12043!GO:0005634;nucleus;0.0483232202533136;216578,18712,12043!|ontology_enrichment_celltype=CL:0000838!1.47e-18!12;CL:0000084!1.90e-17!11;CL:0000827!1.90e-17!11;CL:0000542!7.65e-17!13;CL:0000051!7.65e-17!13;CL:0000791!2.46e-14!9;CL:0000789!2.46e-14!9;CL:0002420!2.46e-14!9;CL:0002419!2.46e-14!9;CL:0000790!2.46e-14!9;CL:0000624!4.65e-13!8;CL:0002242!5.39e-13!16;CL:0000738!5.11e-12!17;CL:0002087!5.11e-12!17;CL:0000988!2.40e-11!32;CL:0002032!2.40e-11!32;CL:0000037!2.40e-11!32;CL:0000566!2.40e-11!32;CL:0000837!2.40e-11!32;CL:0002031!6.04e-11!25;CL:0000893!4.29e-10!6;CL:0002489!4.29e-10!6;CL:0000898!4.29e-10!6;CL:0000809!4.29e-10!6;CL:0000810!4.29e-10!6;CL:0000895!4.29e-10!6;CL:0000808!4.29e-10!6;CL:0000894!4.29e-10!6;CL:0000806!4.29e-10!6;CL:0000807!4.29e-10!6;CL:0000805!4.29e-10!6;CL:0002425!4.29e-10!6;CL:0002436!4.29e-10!6;CL:0002427!4.29e-10!6;CL:0002428!4.29e-10!6;CL:0002429!4.29e-10!6;CL:0002433!4.29e-10!6;CL:0002431!4.29e-10!6;CL:0002432!4.29e-10!6;CL:0002320!2.58e-07!46;CL:0000134!2.58e-07!46|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0004177!1.17e-24!29;UBERON:0005057!1.17e-24!29;UBERON:0000077!9.14e-23!35;UBERON:0002370!1.30e-22!23;UBERON:0000974!1.30e-22!23;UBERON:0004807!1.30e-22!23;UBERON:0005058!1.30e-22!23;UBERON:0003351!1.30e-22!23;UBERON:0009113!1.30e-22!23;UBERON:0003295!1.30e-22!23;UBERON:0009722!1.30e-22!23;UBERON:0005562!1.30e-22!23;UBERON:0007690!1.30e-22!23;UBERON:0006562!2.10e-21!24;UBERON:0003408!2.10e-21!24;UBERON:0001557!2.10e-21!24;UBERON:0001042!2.10e-21!24;UBERON:0008814!2.10e-21!24;UBERON:0009145!2.10e-21!24;UBERON:0002193!4.15e-20!48;UBERON:0002405!4.15e-20!48;UBERON:0002390!1.07e-18!45;UBERON:0003061!1.07e-18!45;UBERON:0000072!2.54e-18!27;UBERON:0000063!4.47e-14!35;UBERON:0000065!2.20e-12!41;UBERON:0007811!3.25e-12!36;UBERON:0001004!6.19e-12!42;UBERON:0000153!3.16e-10!43;UBERON:0003929!2.02e-09!55;UBERON:0003081!2.52e-09!87;UBERON:0001041!1.40e-08!80;UBERON:0000490!1.72e-08!66;UBERON:0002368!4.30e-08!60;UBERON:0005911!1.14e-07!69;UBERON:0002384!2.58e-07!46;UBERON:0002530!5.49e-07!65|tfbs_overrepresentation_for_novel_motifs=0.267173,0.110566,0.245304,0.818969,0.474017,0.847245,0.396495,0.0908011,0.320069,0.0641678,0.357058,0.385627,0.304329,0.407615,0.169024,0,0.587245,0.150639,0.0817508,0.602977,0.215242,0.0217402,0.406794,0.155356,0.251585,0.432737,0.951622,0.334131,0.191143,0.0536593,0.321757,0.683831,0.14899,0.0658632,0.169391,0.130126,0.142225,0.382372,0.79515,0.347926,0.910079,0.870859,0.990451,0.508662,0.153213,0.293566,0.512146,0.34807,1.19261,0.19345,0.570705,0.457464,0.0502729,0.82076,0.837732,0.414119,1.10033,0.37415,1.36955,0.412262,0.664611,0.46618,0.104381,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.229771,0.313987,0.0239269,0.870406,0.0680008,0.483805,0.504564,0.50152,0.648171,0.218647,0.316038,0.60374,0.464847,1.52122,0.758319,0.367893,0.0395547,0.766772,1.28512,1.47691,1.03946,0.763136,0.696137,0.16091,0.391609,0.360425,0.622881,0.698838,0.512384,0.0434558,0.862562,0.683562,0.803823,0.571268,0.57027,0.3259,0.627019,0.911463,0.222586,0.216685,0.261228,0.805555,0.219561,1.69217,1.04639,0.152197,0.0493982,0.306448,0.58848,0.139554,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,4.84007,0.689622,0.969481,0.49047,0.787341,0.296885,0.940498,0.426575,1.06766,0.092963,0.274293,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,1.65731,0.564145,0.326684,0.515065,1.80426,0.276297,0.157809,0.445509,0.0825345,0.822286,0.115938,0.425729,0.901933,0.458393,0.178202,0.265096,0.274055,1.02862,0.757491,0.652135,0.25933,0.561023,1.07498,0.141416,0.384198,0.0476708|tfbs_overrepresentation_jaspar=MA0003.1;0.307389,MA0004.1;2.26768,MA0006.1;0.16569,MA0007.1;1.43999,MA0009.1;0.709264,MA0014.1;0.357292,MA0017.1;0.546298,MA0019.1;0.535691,MA0024.1;0.667197,MA0025.1;0.936082,MA0027.1;2.34178,MA0028.1;0.173587,MA0029.1;0.64639,MA0030.1;0.65267,MA0031.1;1.5004,MA0038.1;0.432665,MA0040.1;0.721328,MA0041.1;0.239557,MA0042.1;0.228771,MA0043.1;0.802848,MA0046.1;0.743934,MA0048.1;0.168666,MA0050.1;0.895831,MA0051.1;0.440863,MA0052.1;0.729105,MA0055.1;0.10681,MA0056.1;0,MA0057.1;0.350222,MA0058.1;5.27749,MA0059.1;6.40969,MA0060.1;0.108526,MA0061.1;0.129002,MA0063.1;0,MA0066.1;0.422624,MA0067.1;1.04514,MA0068.1;1.43405,MA0069.1;0.729433,MA0070.1;0.720077,MA0071.1;0.336739,MA0072.1;0.711905,MA0073.1;3.31298,MA0074.1;0.390075,MA0076.1;0.200996,MA0077.1;0.691048,MA0078.1;0.471303,MA0081.1;0.252371,MA0083.1;0.802078,MA0084.1;1.3693,MA0087.1;0.760279,MA0088.1;0.24301,MA0089.1;0,MA0090.1;1.38006,MA0091.1;0.845572,MA0092.1;0.274547,MA0093.1;3.87285,MA0095.1;0,MA0098.1;0,MA0100.1;0.379666,MA0101.1;0.240622,MA0103.1;0.566591,MA0105.1;0.0633795,MA0106.1;0.478503,MA0107.1;0.189625,MA0108.2;2.34884,MA0109.1;0,MA0111.1;0.78079,MA0113.1;0.452439,MA0114.1;0.127366,MA0115.1;0.805567,MA0116.1;0.165534,MA0117.1;0.774259,MA0119.1;0.241106,MA0122.1;0.793507,MA0124.1;0.992825,MA0125.1;0.920215,MA0130.1;0,MA0131.1;0.531427,MA0132.1;0,MA0133.1;0,MA0135.1;0.838263,MA0136.1;0.408073,MA0139.1;2.10637,MA0140.1;0.379562,MA0141.1;0.603844,MA0142.1;0.604892,MA0143.1;0.467531,MA0144.1;2.56311,MA0145.1;1.15539,MA0146.1;0.0622241,MA0147.1;1.36583,MA0148.1;0.317692,MA0149.1;0.245177,MA0062.2;0.0662974,MA0035.2;0.383789,MA0039.2;0.382143,MA0138.2;0.523978,MA0002.2;1.55322,MA0137.2;1.1287,MA0104.2;1.63782,MA0047.2;0.431964,MA0112.2;0.494696,MA0065.2;0.109524,MA0150.1;0.290598,MA0151.1;0,MA0152.1;0.432062,MA0153.1;0.854464,MA0154.1;1.03999,MA0155.1;0.127763,MA0156.1;0.200311,MA0157.1;2.40511,MA0158.1;0,MA0159.1;0.876351,MA0160.1;0.320315,MA0161.1;0,MA0162.1;0.317256,MA0163.1;1.62398,MA0164.1;1.052,MA0080.2;0.190316,MA0018.2;0.417217,MA0099.2;0.518072,MA0079.2;1.92054,MA0102.2;1.42135,MA0258.1;0.756558,MA0259.1;0.130633,MA0442.1;0}}

Latest revision as of 15:35, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:23795175..23795189,-p2@Papolg
Mm9::chr15:5187479..5187496,+p@chr15:5187479..5187496
+
Mm9::chr16:49856460..49856493,-p@chr16:49856460..49856493
-
Mm9::chr16:49856709..49856732,+p@chr16:49856709..49856732
+
Mm9::chr17:29629982..29630050,+p3@Pim1
Mm9::chr17:29630059..29630073,+p8@Pim1
Mm9::chr17:29630077..29630088,+p9@Pim1
Mm9::chr17:29630114..29630128,+p@chr17:29630114..29630128
+
Mm9::chr1:108610492..108610501,-p4@Bcl2
Mm9::chr3:58902298..58902304,-p@chr3:58902298..58902304
-
Mm9::chr6:129185107..129185119,+p@chr6:129185107..129185119
+
Mm9::chr7:31941253..31941263,-p@chr7:31941253..31941263
-


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:0045069regulation of viral genome replication0.0119145437698286
GO:0050792regulation of viral reproduction0.0119145437698286
GO:0019079viral genome replication0.0119145437698286
GO:0046902regulation of mitochondrial membrane permeability0.0119145437698286
GO:0019058viral infectious cycle0.0119145437698286
GO:0051881regulation of mitochondrial membrane potential0.0119145437698286
GO:0004652polynucleotide adenylyltransferase activity0.0136158753894981
GO:0022415viral reproductive process0.0148915477320502
GO:0016032viral reproduction0.0158834472390889
GO:0001836release of cytochrome c from mitochondria0.0238186440108132
GO:0043631RNA polyadenylation0.0238186440108132
GO:0007006mitochondrial membrane organization and biogenesis0.0256466306647956
GO:0031069hair follicle morphogenesis0.0256466306647956
GO:0031123RNA 3'-end processing0.0289131305174863
GO:0008637apoptotic mitochondrial changes0.0301570578102471
GO:0006839mitochondrial transport0.0322040377729354
GO:0043524negative regulation of neuron apoptosis0.0322040377729354
GO:0043523regulation of neuron apoptosis0.0408962687220554
GO:0051402neuron apoptosis0.0408962687220554
GO:0022404molting cycle process0.0408962687220554
GO:0001942hair follicle development0.0408962687220554
GO:0022405hair cycle process0.0408962687220554
GO:0042391regulation of membrane potential0.0408962687220554
GO:0042633hair cycle0.0408962687220554
GO:0042303molting cycle0.0408962687220554
GO:0008632apoptotic program0.0421101746110773
GO:0048730epidermis morphogenesis0.0421101746110773
GO:0016772transferase activity, transferring phosphorus-containing groups0.0421101746110773
GO:0046982protein heterodimerization activity0.0483232202533136
GO:0005634nucleus0.0483232202533136



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>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell1.47e-1812
T cell1.90e-1711
pro-T cell1.90e-1711
lymphocyte7.65e-1713
common lymphoid progenitor7.65e-1713
mature alpha-beta T cell2.46e-149
alpha-beta T cell2.46e-149
immature T cell2.46e-149
mature T cell2.46e-149
immature alpha-beta T cell2.46e-149
CD4-positive, alpha-beta T cell4.65e-138
nucleate cell5.39e-1316
leukocyte5.11e-1217
nongranular leukocyte5.11e-1217
hematopoietic cell2.40e-1132
hematopoietic oligopotent progenitor cell2.40e-1132
hematopoietic stem cell2.40e-1132
angioblastic mesenchymal cell2.40e-1132
hematopoietic multipotent progenitor cell2.40e-1132
hematopoietic lineage restricted progenitor cell6.04e-1125
thymocyte4.29e-106
double negative thymocyte4.29e-106
naive T cell4.29e-106
double-positive, alpha-beta thymocyte4.29e-106
CD4-positive, alpha-beta thymocyte4.29e-106
naive thymus-derived CD4-positive, alpha-beta T cell4.29e-106
DN4 thymocyte4.29e-106
DN1 thymic pro-T cell4.29e-106
DN2 thymocyte4.29e-106
DN3 thymocyte4.29e-106
immature single positive thymocyte4.29e-106
early T lineage precursor4.29e-106
mature CD4 single-positive thymocyte4.29e-106
resting double-positive thymocyte4.29e-106
double-positive blast4.29e-106
CD69-positive double-positive thymocyte4.29e-106
CD69-positive, CD4-positive single-positive thymocyte4.29e-106
CD4-positive, CD8-intermediate double-positive thymocyte4.29e-106
CD24-positive, CD4 single-positive thymocyte4.29e-106
connective tissue cell2.58e-0746
mesenchymal cell2.58e-0746

Uber Anatomy
Ontology termp-valuen
hemopoietic organ1.17e-2429
immune organ1.17e-2429
mixed endoderm/mesoderm-derived structure9.14e-2335
thymus1.30e-2223
neck1.30e-2223
respiratory system epithelium1.30e-2223
hemolymphoid system gland1.30e-2223
pharyngeal epithelium1.30e-2223
thymic region1.30e-2223
pharyngeal gland1.30e-2223
entire pharyngeal arch endoderm1.30e-2223
thymus primordium1.30e-2223
early pharyngeal endoderm1.30e-2223
pharynx2.10e-2124
gland of gut2.10e-2124
upper respiratory tract2.10e-2124
chordate pharynx2.10e-2124
pharyngeal arch system2.10e-2124
pharyngeal region of foregut2.10e-2124
hemolymphoid system4.15e-2048
immune system4.15e-2048
hematopoietic system1.07e-1845
blood island1.07e-1845
segment of respiratory tract2.54e-1827
organ segment4.47e-1435
respiratory tract2.20e-1241
craniocervical region3.25e-1236
respiratory system6.19e-1242
anterior region of body3.16e-1043
gut epithelium2.02e-0955
lateral plate mesoderm2.52e-0987
foregut1.40e-0880
unilaminar epithelium1.72e-0866
endocrine gland4.30e-0860
endo-epithelium1.14e-0769
connective tissue2.58e-0746
gland5.49e-0765


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)
MA0003.10.307389
MA0004.12.26768
MA0006.10.16569
MA0007.11.43999
MA0009.10.709264
MA0014.10.357292
MA0017.10.546298
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.173587
MA0029.10.64639
MA0030.10.65267
MA0031.11.5004
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.168666
MA0050.10.895831
MA0051.10.440863
MA0052.10.729105
MA0055.10.10681
MA0056.10
MA0057.10.350222
MA0058.15.27749
MA0059.16.40969
MA0060.10.108526
MA0061.10.129002
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.11.43405
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.13.31298
MA0074.10.390075
MA0076.10.200996
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.24301
MA0089.10
MA0090.11.38006
MA0091.10.845572
MA0092.10.274547
MA0093.13.87285
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.240622
MA0103.10.566591
MA0105.10.0633795
MA0106.10.478503
MA0107.10.189625
MA0108.22.34884
MA0109.10
MA0111.10.78079
MA0113.10.452439
MA0114.10.127366
MA0115.10.805567
MA0116.10.165534
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.12.10637
MA0140.10.379562
MA0141.10.603844
MA0142.10.604892
MA0143.10.467531
MA0144.12.56311
MA0145.11.15539
MA0146.10.0622241
MA0147.11.36583
MA0148.10.317692
MA0149.10.245177
MA0062.20.0662974
MA0035.20.383789
MA0039.20.382143
MA0138.20.523978
MA0002.21.55322
MA0137.21.1287
MA0104.21.63782
MA0047.20.431964
MA0112.20.494696
MA0065.20.109524
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.11.03999
MA0155.10.127763
MA0156.10.200311
MA0157.12.40511
MA0158.10
MA0159.10.876351
MA0160.10.320315
MA0161.10
MA0162.10.317256
MA0163.11.62398
MA0164.11.052
MA0080.20.190316
MA0018.20.417217
MA0099.20.518072
MA0079.21.92054
MA0102.21.42135
MA0258.10.756558
MA0259.10.130633
MA0442.10
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