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MCL coexpression mm9:308: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0009055;electron carrier activity;0.0235749622765852;68194,30926!GO:0015035;protein disulfide oxidoreductase activity;0.030000362435492;30926!GO:0006118;electron transport;0.030000362435492;68194,30926!GO:0031975;envelope;0.030000362435492;69482,68194!GO:0031967;organelle envelope;0.030000362435492;69482,68194!GO:0015036;disulfide oxidoreductase activity;0.030000362435492;30926!GO:0006091;generation of precursor metabolites and energy;0.030000362435492;68194,30926!GO:0031090;organelle membrane;0.0382432531186327;69482,68194!GO:0045454;cell redox homeostasis;0.0382432531186327;30926!GO:0016491;oxidoreductase activity;0.0382432531186327;68194,30926!GO:0008137;NADH dehydrogenase (ubiquinone) activity;0.0382432531186327;68194!GO:0003954;NADH dehydrogenase activity;0.0382432531186327;68194!GO:0050136;NADH dehydrogenase (quinone) activity;0.0382432531186327;68194!GO:0051028;mRNA transport;0.0382432531186327;69482!GO:0016655;oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor;0.0382432531186327;68194!GO:0050658;RNA transport;0.0382432531186327;69482!GO:0051236;establishment of RNA localization;0.0382432531186327;69482!GO:0050657;nucleic acid transport;0.0382432531186327;69482!GO:0006403;RNA localization;0.0382432531186327;69482!GO:0005643;nuclear pore;0.0382432531186327;69482!GO:0065002;intracellular protein transport across a membrane;0.0382432531186327;69482!GO:0015931;nucleobase, nucleoside, nucleotide and nucleic acid transport;0.0382432531186327;69482!GO:0046930;pore complex;0.0382432531186327;69482!GO:0044453;nuclear membrane part;0.0395589900222561;69482!GO:0031965;nuclear membrane;0.0395589900222561;69482!GO:0016651;oxidoreductase activity, acting on NADH or NADPH;0.0398389700056067;68194!}}
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carrier activity;0.0235749622765852;68194,30926!GO:0015035;protein disulfide oxidoreductase activity;0.030000362435492;30926!GO:0006118;electron transport;0.030000362435492;68194,30926!GO:0031975;envelope;0.030000362435492;69482,68194!GO:0031967;organelle envelope;0.030000362435492;69482,68194!GO:0015036;disulfide oxidoreductase activity;0.030000362435492;30926!GO:0006091;generation of precursor metabolites and energy;0.030000362435492;68194,30926!GO:0031090;organelle membrane;0.0382432531186327;69482,68194!GO:0045454;cell redox homeostasis;0.0382432531186327;30926!GO:0016491;oxidoreductase activity;0.0382432531186327;68194,30926!GO:0008137;NADH dehydrogenase (ubiquinone) activity;0.0382432531186327;68194!GO:0003954;NADH dehydrogenase activity;0.0382432531186327;68194!GO:0050136;NADH dehydrogenase (quinone) activity;0.0382432531186327;68194!GO:0051028;mRNA transport;0.0382432531186327;69482!GO:0016655;oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor;0.0382432531186327;68194!GO:0050658;RNA transport;0.0382432531186327;69482!GO:0051236;establishment of RNA localization;0.0382432531186327;69482!GO:0050657;nucleic acid transport;0.0382432531186327;69482!GO:0006403;RNA localization;0.0382432531186327;69482!GO:0005643;nuclear pore;0.0382432531186327;69482!GO:0065002;intracellular protein transport across a membrane;0.0382432531186327;69482!GO:0015931;nucleobase, nucleoside, nucleotide and nucleic acid transport;0.0382432531186327;69482!GO:0046930;pore complex;0.0382432531186327;69482!GO:0044453;nuclear membrane part;0.0395589900222561;69482!GO:0031965;nuclear membrane;0.0395589900222561;69482!GO:0016651;oxidoreductase activity, acting on NADH or NADPH;0.0398389700056067;68194!|ontology_enrichment_celltype=CL:0002371!4.06e-24!118;CL:0000548!6.87e-22!115;CL:0000255!6.87e-22!115;CL:0000988!5.21e-20!32;CL:0002032!5.21e-20!32;CL:0000037!5.21e-20!32;CL:0000566!5.21e-20!32;CL:0000837!5.21e-20!32;CL:0002320!6.79e-18!46;CL:0000134!6.79e-18!46;CL:0000219!6.78e-17!54;CL:0002031!1.03e-16!25;CL:0000066!4.03e-16!25;CL:0002076!1.32e-14!15;CL:0000034!3.94e-14!97;CL:0000838!3.33e-12!12;CL:0000223!7.66e-12!20;CL:0000738!1.05e-11!17;CL:0002087!1.05e-11!17;CL:0000084!4.41e-11!11;CL:0000827!4.41e-11!11;CL:0000542!4.84e-11!13;CL:0000051!4.84e-11!13;CL:0000791!5.42e-11!9;CL:0000789!5.42e-11!9;CL:0002420!5.42e-11!9;CL:0002419!5.42e-11!9;CL:0000790!5.42e-11!9;CL:0000723!3.08e-10!91;CL:0000048!3.08e-10!91;CL:0000049!3.16e-10!19;CL:0002242!3.78e-10!16;CL:0000624!4.81e-10!8;CL:0002563!1.61e-09!9;CL:0002251!1.61e-09!9;CL:0000893!5.16e-08!6;CL:0002489!5.16e-08!6;CL:0000898!5.16e-08!6;CL:0000809!5.16e-08!6;CL:0000810!5.16e-08!6;CL:0000895!5.16e-08!6;CL:0000808!5.16e-08!6;CL:0000894!5.16e-08!6;CL:0000806!5.16e-08!6;CL:0000807!5.16e-08!6;CL:0000805!5.16e-08!6;CL:0002425!5.16e-08!6;CL:0002436!5.16e-08!6;CL:0002427!5.16e-08!6;CL:0002428!5.16e-08!6;CL:0002429!5.16e-08!6;CL:0002433!5.16e-08!6;CL:0002431!5.16e-08!6;CL:0002432!5.16e-08!6;CL:0000075!9.20e-08!7;CL:0000763!1.43e-07!16;CL:0000239!6.22e-07!6;CL:0000677!6.22e-07!6;CL:0000212!6.22e-07!6;CL:0000584!6.22e-07!6|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0002384!6.79e-18!46;UBERON:0000344!6.87e-14!15;UBERON:0001242!2.57e-11!13;UBERON:0000060!2.57e-11!13;UBERON:0001262!2.57e-11!13;UBERON:0004786!2.57e-11!13;UBERON:0000485!3.80e-11!11;UBERON:0003350!1.61e-09!9;UBERON:0004808!1.61e-09!9;UBERON:0001277!1.61e-09!9;UBERON:0004923!2.43e-07!24;UBERON:0002193!6.25e-07!48;UBERON:0002405!6.25e-07!48|tfbs_overrepresentation_for_novel_motifs=0.621914,0.734167,0.264934,0.357342,0.13626,0.378043,0.173296,0.802044,0.169209,0.201274,0.44746,0.165604,0.52939,0.181267,0.633867,0,0.321317,0.882528,1.03294,0.980393,1.25234,0.195815,1.61733,0.316587,0.0801894,0.199623,0.444085,0.811999,0.0490134,0.0736806,0.388015,0.403236,0.0308777,0.377102,0.153647,0.069489,0.28244,0.95082,1.08815,0.626782,0.132316,0.395563,1.04718,0.640187,0.0101868,0.696406,0.260475,0.139809,0.639076,0.187406,0.307679,0.218134,0.680586,0.524674,0.540069,0.546195,0.197567,0.927074,0.235144,0.184626,0.386651,0.638588,0.187517,0.80944,1.07232,0.880487,0.662968,0.992392,0.382806,0.851665,0.517607,0.550805,0.057172,0.569888,0.0357104,1.11649,0.098925,0.702334,1.73008,0.22435,0.165658,0.890404,0.636199,0.295929,0.468641,0.00212005,0.00317853,0.164918,0.729995,1.14963,0.72731,0.472928,0.41392,0.600223,0.021752,0.20598,0.151563,0.416272,0.722077,1.45087,0.0283065,0.403003,0.509378,0.308141,0.828295,0.394918,0.354606,0.137427,0.497774,0.831712,0.0856504,0.510939,0.225717,0.149001,0.733862,0.564124,0.0814819,0.732983,0.322341,1.18719,0.574718,1.41182,0.20086,0.251444,0.784453,0.375593,0.178582,0.408257,0.661578,0.337079,0.494561,0.106861,0.634573,0.195077,0.753996,0.0177816,0.310556,0.126256,0.708276,1.51166,1.11861,0.667289,0.209097,0.411967,0.302305,0.125712,0.726958,1.47245,0.0944245,0.0343953,0.076247,0.0140779,1.30495,1.38393,0.566627,0.598868,0.624647,0.165822,0.0878751,0.0931012,0.717087,0.467905,0.375957,0.0845658,0.811218,0.1895,0.280354,0.494051,0.0956157|tfbs_overrepresentation_jaspar=MA0003.1;0.0276344,MA0004.1;0.358028,MA0006.1;0.148601,MA0007.1;0.103069,MA0009.1;0.425374,MA0014.1;0.0519867,MA0017.1;0.176804,MA0019.1;0.279241,MA0024.1;0.388875,MA0025.1;0.630472,MA0027.1;2.00714,MA0028.1;0.159417,MA0029.1;0.371051,MA0030.1;0.376415,MA0031.1;0.347586,MA0038.1;0.578883,MA0040.1;0.435948,MA0041.1;1.92078,MA0042.1;1.84423,MA0043.1;0.5085,MA0046.1;0.45588,MA0048.1;0.00273976,MA0050.1;0.414313,MA0051.1;0.593414,MA0052.1;0.442788,MA0055.1;0.388062,MA0056.1;0,MA0057.1;0.0453438,MA0058.1;0.231244,MA0059.1;0.246439,MA0060.1;0.6347,MA0061.1;0.1011,MA0063.1;0,MA0066.1;0.192176,MA0067.1;0.732677,MA0068.1;0.0146006,MA0069.1;0.443076,MA0070.1;1.94315,MA0071.1;0.413073,MA0072.1;0.427684,MA0073.1;7.40327e-09,MA0074.1;0.504232,MA0076.1;0.198312,MA0077.1;0.409496,MA0078.1;0.228674,MA0081.1;0.58044,MA0083.1;0.507806,MA0084.1;1.04444,MA0087.1;1.18604,MA0088.1;0.0198605,MA0089.1;0,MA0090.1;0.310535,MA0091.1;0.118208,MA0092.1;0.310962,MA0093.1;0.381754,MA0095.1;0,MA0098.1;0,MA0100.1;0.943001,MA0101.1;0.257705,MA0103.1;0.188828,MA0105.1;0.202372,MA0106.1;0.234207,MA0107.1;0.0483046,MA0108.2;0.296634,MA0109.1;0,MA0111.1;0.675922,MA0113.1;0.214338,MA0114.1;0.244479,MA0115.1;0.51095,MA0116.1;0.34339,MA0117.1;0.48285,MA0119.1;0.258451,MA0122.1;0.500096,MA0124.1;0.683426,MA0125.1;0.615761,MA0130.1;0,MA0131.1;2.12774,MA0132.1;0,MA0133.1;0,MA0135.1;0.540552,MA0136.1;0.535598,MA0139.1;0.149499,MA0140.1;0.161354,MA0141.1;0.463338,MA0142.1;0.336004,MA0143.1;0.22579,MA0144.1;0.10174,MA0145.1;0.131485,MA0146.1;0.0209843,MA0147.1;0.11258,MA0148.1;1.25018,MA0149.1;0.0766295,MA0062.2;0.213838,MA0035.2;0.493344,MA0039.2;0.0213518,MA0138.2;0.269868,MA0002.2;0.309453,MA0137.2;0.208165,MA0104.2;0.0666678,MA0047.2;0.199051,MA0112.2;0.763683,MA0065.2;0.23538,MA0150.1;0.10301,MA0151.1;0,MA0152.1;0.199123,MA0153.1;0.55531,MA0154.1;0.236552,MA0155.1;0.285814,MA0156.1;0.197316,MA0157.1;0.310784,MA0158.1;0,MA0159.1;0.121887,MA0160.1;0.772496,MA0161.1;0,MA0162.1;0.0318231,MA0163.1;0.0105696,MA0164.1;0.181834,MA0080.2;0.182919,MA0018.2;0.188226,MA0099.2;0.26517,MA0079.2;2.97167e-09,MA0102.2;2.47957,MA0258.1;0.423098,MA0259.1;1.11848,MA0442.1;0}}

Latest revision as of 15:04, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:28749875..28749924,+p@chr10:28749875..28749924
+
Mm9::chr10:43243886..43243899,+p2@ENSMUST00000057649
Mm9::chr12:24587988..24588001,+p@chr12:24587988..24588001
+
Mm9::chr12:70223961..70223973,+p@chr12:70223961..70223973
+
Mm9::chr13:118018159..118018169,+p@chr13:118018159..118018169
+
Mm9::chr14:28023521..28023536,+p@chr14:28023521..28023536
+
Mm9::chr15:81296769..81296795,+p1@Gm9840
p1@Rbx1
Mm9::chr17:47547801..47547833,+p@chr17:47547801..47547833
+
Mm9::chr18:38873969..38873988,+p@chr18:38873969..38873988
+
Mm9::chr19:25107619..25107626,+p@chr19:25107619..25107626
+
Mm9::chr19:28838027..28838030,-p1@Gm6788
Mm9::chr1:13426571..13426575,+p@chr1:13426571..13426575
+
Mm9::chr1:15057084..15057123,+p@chr1:15057084..15057123
+
Mm9::chr2:150131486..150131493,+p1@ENSMUST00000120921
Mm9::chr2:36244522..36244568,+p1@ENSMUST00000121366
Mm9::chr2:52475255..52475266,+p2@Bloc1s2
p2@Gm13540
Mm9::chr2:80479001..80479013,+p3@Nup35
Mm9::chr4:116821517..116821519,+p1@ENSMUST00000118674
Mm9::chr4:34432983..34433015,+p2@ENSMUST00000117487
Mm9::chr7:144629334..144629355,+p1@Gm12669
Mm9::chr7:3181067..3181081,+p@chr7:3181067..3181081
+
Mm9::chr7:54087766..54087785,+p2@Gm5331
Mm9::chr7:54087805..54087833,+p1@Gm5331
Mm9::chr9:120293968..120293975,+p1@ENSMUST00000118890
Mm9::chr9:48258428..48258437,+p5@Gm5616
p5@LOC100045968
p5@LOC100505330
p5@Nhp2l1
Mm9::chrX:101543820..101543838,-p1@ENSMUST00000120233


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:0009055electron carrier activity0.0235749622765852
GO:0015035protein disulfide oxidoreductase activity0.030000362435492
GO:0006118electron transport0.030000362435492
GO:0031975envelope0.030000362435492
GO:0031967organelle envelope0.030000362435492
GO:0015036disulfide oxidoreductase activity0.030000362435492
GO:0006091generation of precursor metabolites and energy0.030000362435492
GO:0031090organelle membrane0.0382432531186327
GO:0045454cell redox homeostasis0.0382432531186327
GO:0016491oxidoreductase activity0.0382432531186327
GO:0008137NADH dehydrogenase (ubiquinone) activity0.0382432531186327
GO:0003954NADH dehydrogenase activity0.0382432531186327
GO:0050136NADH dehydrogenase (quinone) activity0.0382432531186327
GO:0051028mRNA transport0.0382432531186327
GO:0016655oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor0.0382432531186327
GO:0050658RNA transport0.0382432531186327
GO:0051236establishment of RNA localization0.0382432531186327
GO:0050657nucleic acid transport0.0382432531186327
GO:0006403RNA localization0.0382432531186327
GO:0005643nuclear pore0.0382432531186327
GO:0065002intracellular protein transport across a membrane0.0382432531186327
GO:0015931nucleobase, nucleoside, nucleotide and nucleic acid transport0.0382432531186327
GO:0046930pore complex0.0382432531186327
GO:0044453nuclear membrane part0.0395589900222561
GO:0031965nuclear membrane0.0395589900222561
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.0398389700056067



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
somatic cell4.06e-24118
animal cell6.87e-22115
eukaryotic cell6.87e-22115
hematopoietic cell5.21e-2032
hematopoietic oligopotent progenitor cell5.21e-2032
hematopoietic stem cell5.21e-2032
angioblastic mesenchymal cell5.21e-2032
hematopoietic multipotent progenitor cell5.21e-2032
connective tissue cell6.79e-1846
mesenchymal cell6.79e-1846
motile cell6.78e-1754
hematopoietic lineage restricted progenitor cell1.03e-1625
epithelial cell4.03e-1625
endo-epithelial cell1.32e-1415
stem cell3.94e-1497
lymphoid lineage restricted progenitor cell3.33e-1212
endodermal cell7.66e-1220
leukocyte1.05e-1117
nongranular leukocyte1.05e-1117
T cell4.41e-1111
pro-T cell4.41e-1111
lymphocyte4.84e-1113
common lymphoid progenitor4.84e-1113
mature alpha-beta T cell5.42e-119
alpha-beta T cell5.42e-119
immature T cell5.42e-119
mature T cell5.42e-119
immature alpha-beta T cell5.42e-119
somatic stem cell3.08e-1091
multi fate stem cell3.08e-1091
common myeloid progenitor3.16e-1019
nucleate cell3.78e-1016
CD4-positive, alpha-beta T cell4.81e-108
intestinal epithelial cell1.61e-099
epithelial cell of alimentary canal1.61e-099
thymocyte5.16e-086
double negative thymocyte5.16e-086
naive T cell5.16e-086
double-positive, alpha-beta thymocyte5.16e-086
CD4-positive, alpha-beta thymocyte5.16e-086
naive thymus-derived CD4-positive, alpha-beta T cell5.16e-086
DN4 thymocyte5.16e-086
DN1 thymic pro-T cell5.16e-086
DN2 thymocyte5.16e-086
DN3 thymocyte5.16e-086
immature single positive thymocyte5.16e-086
early T lineage precursor5.16e-086
mature CD4 single-positive thymocyte5.16e-086
resting double-positive thymocyte5.16e-086
double-positive blast5.16e-086
CD69-positive double-positive thymocyte5.16e-086
CD69-positive, CD4-positive single-positive thymocyte5.16e-086
CD4-positive, CD8-intermediate double-positive thymocyte5.16e-086
CD24-positive, CD4 single-positive thymocyte5.16e-086
columnar/cuboidal epithelial cell9.20e-087
myeloid cell1.43e-0716
brush border epithelial cell6.22e-076
gut absorptive cell6.22e-076
absorptive cell6.22e-076
enterocyte6.22e-076


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)
MA0003.10.0276344
MA0004.10.358028
MA0006.10.148601
MA0007.10.103069
MA0009.10.425374
MA0014.10.0519867
MA0017.10.176804
MA0019.10.279241
MA0024.10.388875
MA0025.10.630472
MA0027.12.00714
MA0028.10.159417
MA0029.10.371051
MA0030.10.376415
MA0031.10.347586
MA0038.10.578883
MA0040.10.435948
MA0041.11.92078
MA0042.11.84423
MA0043.10.5085
MA0046.10.45588
MA0048.10.00273976
MA0050.10.414313
MA0051.10.593414
MA0052.10.442788
MA0055.10.388062
MA0056.10
MA0057.10.0453438
MA0058.10.231244
MA0059.10.246439
MA0060.10.6347
MA0061.10.1011
MA0063.10
MA0066.10.192176
MA0067.10.732677
MA0068.10.0146006
MA0069.10.443076
MA0070.11.94315
MA0071.10.413073
MA0072.10.427684
MA0073.17.40327e-09
MA0074.10.504232
MA0076.10.198312
MA0077.10.409496
MA0078.10.228674
MA0081.10.58044
MA0083.10.507806
MA0084.11.04444
MA0087.11.18604
MA0088.10.0198605
MA0089.10
MA0090.10.310535
MA0091.10.118208
MA0092.10.310962
MA0093.10.381754
MA0095.10
MA0098.10
MA0100.10.943001
MA0101.10.257705
MA0103.10.188828
MA0105.10.202372
MA0106.10.234207
MA0107.10.0483046
MA0108.20.296634
MA0109.10
MA0111.10.675922
MA0113.10.214338
MA0114.10.244479
MA0115.10.51095
MA0116.10.34339
MA0117.10.48285
MA0119.10.258451
MA0122.10.500096
MA0124.10.683426
MA0125.10.615761
MA0130.10
MA0131.12.12774
MA0132.10
MA0133.10
MA0135.10.540552
MA0136.10.535598
MA0139.10.149499
MA0140.10.161354
MA0141.10.463338
MA0142.10.336004
MA0143.10.22579
MA0144.10.10174
MA0145.10.131485
MA0146.10.0209843
MA0147.10.11258
MA0148.11.25018
MA0149.10.0766295
MA0062.20.213838
MA0035.20.493344
MA0039.20.0213518
MA0138.20.269868
MA0002.20.309453
MA0137.20.208165
MA0104.20.0666678
MA0047.20.199051
MA0112.20.763683
MA0065.20.23538
MA0150.10.10301
MA0151.10
MA0152.10.199123
MA0153.10.55531
MA0154.10.236552
MA0155.10.285814
MA0156.10.197316
MA0157.10.310784
MA0158.10
MA0159.10.121887
MA0160.10.772496
MA0161.10
MA0162.10.0318231
MA0163.10.0105696
MA0164.10.181834
MA0080.20.182919
MA0018.20.188226
MA0099.20.26517
MA0079.22.97167e-09
MA0102.22.47957
MA0258.10.423098
MA0259.11.11848
MA0442.10
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