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MCL coexpression mm9:1016: Difference between revisions

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{{MCL_coexpression_mm9
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structure morphogenesis;0.00296909382281702;11477,14561,14163!GO:0009887;organ morphogenesis;0.00646380487127128;11477,14561!GO:0001655;urogenital system development;0.00646380487127128;11477,14561!GO:0048856;anatomical structure development;0.00646380487127128;11477,14561,14163!GO:0050431;transforming growth factor beta binding;0.00959842217717636;11477!GO:0016361;activin receptor activity, type I;0.0121739696266195;11477!GO:0017002;activin receptor activity;0.0121739696266195;11477!GO:0007507;heart development;0.0121739696266195;11477!GO:0048514;blood vessel morphogenesis;0.0121739696266195;11477!GO:0032502;developmental process;0.0121739696266195;11477,14561,14163!GO:0005025;transforming growth factor beta receptor activity, type I;0.0126221882574342;11477!GO:0001568;blood vessel development;0.0126221882574342;11477!GO:0001944;vasculature development;0.0126221882574342;11477!GO:0048468;cell development;0.0127947411668825;11477,14561!GO:0060037;pharyngeal system development;0.0127947411668825;11477!GO:0050793;regulation of developmental process;0.0157949769515772;14561,14163!GO:0048185;activin binding;0.0169314328740094;11477!GO:0048513;organ development;0.017489293322562;11477,14561!GO:0051145;smooth muscle cell differentiation;0.0215822546795309;11477!GO:0048738;cardiac muscle development;0.0215822546795309;!GO:0004675;transmembrane receptor protein serine/threonine kinase activity;0.0239763413012367;11477!GO:0005024;transforming growth factor beta receptor activity;0.0239763413012367;11477!GO:0048731;system development;0.0242921967687915;11477,14561!GO:0031016;pancreas development;0.0242921967687915;14561!GO:0048869;cellular developmental process;0.0242921967687915;11477,14561!GO:0030154;cell differentiation;0.0242921967687915;11477,14561!GO:0048593;camera-type eye morphogenesis;0.0287550599656491;14561!GO:0022829;wide pore channel activity;0.0287550599656491;!GO:0005243;gap junction channel activity;0.0287550599656491;!GO:0005922;connexon 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|gostat_on_MCL_coexpression=GO:0009653;anatomical structure morphogenesis;0.00296909382281702;11477,14561,14163!GO:0009887;organ morphogenesis;0.00646380487127128;11477,14561!GO:0001655;urogenital system development;0.00646380487127128;11477,14561!GO:0048856;anatomical structure development;0.00646380487127128;11477,14561,14163!GO:0050431;transforming growth factor beta binding;0.00959842217717636;11477!GO:0016361;activin receptor activity, type I;0.0121739696266195;11477!GO:0017002;activin receptor activity;0.0121739696266195;11477!GO:0007507;heart development;0.0121739696266195;11477!GO:0048514;blood vessel morphogenesis;0.0121739696266195;11477!GO:0032502;developmental process;0.0121739696266195;11477,14561,14163!GO:0005025;transforming growth factor beta receptor activity, type I;0.0126221882574342;11477!GO:0001568;blood vessel development;0.0126221882574342;11477!GO:0001944;vasculature development;0.0126221882574342;11477!GO:0048468;cell development;0.0127947411668825;11477,14561!GO:0060037;pharyngeal system development;0.0127947411668825;11477!GO:0050793;regulation of developmental process;0.0157949769515772;14561,14163!GO:0048185;activin binding;0.0169314328740094;11477!GO:0048513;organ development;0.017489293322562;11477,14561!GO:0051145;smooth muscle cell differentiation;0.0215822546795309;11477!GO:0048738;cardiac muscle development;0.0215822546795309;!GO:0004675;transmembrane receptor protein serine/threonine kinase activity;0.0239763413012367;11477!GO:0005024;transforming growth factor beta receptor activity;0.0239763413012367;11477!GO:0048731;system development;0.0242921967687915;11477,14561!GO:0031016;pancreas development;0.0242921967687915;14561!GO:0048869;cellular developmental process;0.0242921967687915;11477,14561!GO:0030154;cell differentiation;0.0242921967687915;11477,14561!GO:0048593;camera-type eye morphogenesis;0.0287550599656491;14561!GO:0022829;wide pore channel activity;0.0287550599656491;!GO:0005243;gap junction channel activity;0.0287550599656491;!GO:0005922;connexon complex;0.0287550599656491;!GO:0001569;patterning of blood vessels;0.0340001801508854;11477!GO:0001755;neural crest cell migration;0.0340268617337679;11477!GO:0001707;mesoderm formation;0.0340268617337679;11477!GO:0048332;mesoderm morphogenesis;0.0340268617337679;11477!GO:0005921;gap junction;0.0340268617337679;!GO:0007275;multicellular organismal development;0.0340268617337679;11477,14561!GO:0001704;formation of primary germ layer;0.0340268617337679;11477!GO:0007281;germ cell development;0.0340268617337679;11477!GO:0001570;vasculogenesis;0.0356044036869571;!GO:0001702;gastrulation with mouth forming second;0.0356241688914495;11477!GO:0014032;neural crest cell development;0.0356241688914495;11477!GO:0014033;neural crest cell differentiation;0.0356241688914495;11477!GO:0001657;ureteric bud development;0.0356241688914495;14561!GO:0007368;determination of left/right symmetry;0.0356390644170355;11477!GO:0001726;ruffle;0.0356390644170355;14163!GO:0009799;determination of symmetry;0.0356390644170355;11477!GO:0009855;determination of bilateral symmetry;0.0356390644170355;11477!GO:0048762;mesenchymal cell differentiation;0.0380786740322516;11477!GO:0014031;mesenchymal cell development;0.0380786740322516;11477!GO:0009880;embryonic pattern specification;0.0382708027366175;11477!GO:0048592;eye morphogenesis;0.0383992257020482;14561!GO:0014704;intercalated disc;0.0383992257020482;!GO:0001656;metanephros development;0.0383992257020482;14561!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0383992257020482;11477!GO:0004702;receptor signaling protein serine/threonine kinase activity;0.0383992257020482;11477!GO:0022603;regulation of anatomical structure morphogenesis;0.0383992257020482;14163!GO:0022604;regulation of cell morphogenesis;0.0383992257020482;14163!GO:0008360;regulation of cell shape;0.0383992257020482;14163!GO:0019838;growth factor binding;0.0383992257020482;11477!GO:0007498;mesoderm development;0.0383992257020482;11477!GO:0030027;lamellipodium;0.0383992257020482;14163!GO:0005089;Rho guanyl-nucleotide exchange factor activity;0.040850517821372;14163!GO:0035023;regulation of Rho protein signal transduction;0.042467210308323;14163!GO:0048754;branching morphogenesis of a tube;0.0432895282359754;11477!GO:0005088;Ras guanyl-nucleotide exchange factor activity;0.043354858875854;14163!GO:0007369;gastrulation;0.0442372284256234;11477!GO:0001763;morphogenesis of a branching structure;0.0442372284256234;11477!GO:0042692;muscle cell differentiation;0.0442372284256234;11477!GO:0019955;cytokine binding;0.0463488678699826;11477!GO:0001822;kidney development;0.047693177764072;14561!GO:0019199;transmembrane receptor protein kinase activity;0.047693177764072;11477!GO:0048469;cell maturation;0.047693177764072;14561!GO:0048729;tissue morphogenesis;0.047693177764072;11477!GO:0043010;camera-type eye development;0.047693177764072;14561!GO:0031252;leading edge;0.047693177764072;14163!GO:0002526;acute inflammatory response;0.047693177764072;11477!GO:0045177;apical part of cell;0.047693177764072;11477!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0482849740211149;11477!GO:0007266;Rho protein signal transduction;0.0482849740211149;14163!
|ontology_enrichment_celltype=CL:0000221!6.17e-13!44;CL:0000133!6.17e-13!44;CL:0000055!7.47e-13!49;CL:0002319!1.77e-12!43;CL:0000393!5.77e-10!39;CL:0000211!5.77e-10!39;CL:0000540!1.25e-09!33;CL:0000047!1.25e-09!33;CL:0000031!1.25e-09!33;CL:0000404!1.25e-09!33
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004121!1.30e-08!95;UBERON:0000924!1.30e-08!95;UBERON:0006601!1.30e-08!95;UBERON:0000468!3.23e-08!333;UBERON:0001017!4.31e-08!73;UBERON:0001016!5.55e-08!75;UBERON:0000922!2.39e-07!320;UBERON:0010314!5.63e-07!92
|tfbs_overrepresentation_for_novel_motifs=0.438063,1.9469,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.616096,1.7494,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.291368,0.561256,0.731589,0.374752,0.586604,0.598814,0.29769,0.419327,0.62766,1.0368,0.516511,0.344372,0.876948,0.50223,0.897561,0.78719,0.498917,1.53201,2.47396,1.40094,0.57142,0.258564,1.89251,0.295233,0.507468,0.54842,0.317766,0.515031,0.469348,0.714592,0.532496,0.219744,0.917701,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,1.3814,0.176152,0.604914,0.877332,1.59614,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,1.02583,1.09164,1.55661,0.936963,0.963958,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,5.61226,0.164297,0.877485,1.71058,1.70793,1.26498,0.980512,0.910485,0.823238,1.30733,0.237542,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,1.74385,1.10097,1.02459,0.380122,0.547992,1.27206,0.293461,2.11126,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,2.19037,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.886471,1.92168,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,5.353
}}

Latest revision as of 16:15, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128328730..128328771,-p1@Gdf11
Mm9::chr11:102680428..102680528,-p1@Gjc1
Mm9::chr14:52604501..52604531,+p2@Arhgef40
Mm9::chr17:28314586..28314627,-p@chr17:28314586..28314627
-
Mm9::chr2:58419568..58419699,-p1@Acvr1
Mm9::chr9:56842884..56842924,+p2@Ptpn9
Mm9::chrX:147481455..147481476,+p2@Fgd1


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:0009653anatomical structure morphogenesis0.00296909382281702
GO:0009887organ morphogenesis0.00646380487127128
GO:0001655urogenital system development0.00646380487127128
GO:0048856anatomical structure development0.00646380487127128
GO:0050431transforming growth factor beta binding0.00959842217717636
GO:0016361activin receptor activity, type I0.0121739696266195
GO:0017002activin receptor activity0.0121739696266195
GO:0007507heart development0.0121739696266195
GO:0048514blood vessel morphogenesis0.0121739696266195
GO:0032502developmental process0.0121739696266195
GO:0005025transforming growth factor beta receptor activity, type I0.0126221882574342
GO:0001568blood vessel development0.0126221882574342
GO:0001944vasculature development0.0126221882574342
GO:0048468cell development0.0127947411668825
GO:0060037pharyngeal system development0.0127947411668825
GO:0050793regulation of developmental process0.0157949769515772
GO:0048185activin binding0.0169314328740094
GO:0048513organ development0.017489293322562
GO:0051145smooth muscle cell differentiation0.0215822546795309
GO:0048738cardiac muscle development0.0215822546795309
GO:0004675transmembrane receptor protein serine/threonine kinase activity0.0239763413012367
GO:0005024transforming growth factor beta receptor activity0.0239763413012367
GO:0048731system development0.0242921967687915
GO:0031016pancreas development0.0242921967687915
GO:0048869cellular developmental process0.0242921967687915
GO:0030154cell differentiation0.0242921967687915
GO:0048593camera-type eye morphogenesis0.0287550599656491
GO:0022829wide pore channel activity0.0287550599656491
GO:0005243gap junction channel activity0.0287550599656491
GO:0005922connexon complex0.0287550599656491
GO:0001569patterning of blood vessels0.0340001801508854
GO:0001755neural crest cell migration0.0340268617337679
GO:0001707mesoderm formation0.0340268617337679
GO:0048332mesoderm morphogenesis0.0340268617337679
GO:0005921gap junction0.0340268617337679
GO:0007275multicellular organismal development0.0340268617337679
GO:0001704formation of primary germ layer0.0340268617337679
GO:0007281germ cell development0.0340268617337679
GO:0001570vasculogenesis0.0356044036869571
GO:0001702gastrulation with mouth forming second0.0356241688914495
GO:0014032neural crest cell development0.0356241688914495
GO:0014033neural crest cell differentiation0.0356241688914495
GO:0001657ureteric bud development0.0356241688914495
GO:0007368determination of left/right symmetry0.0356390644170355
GO:0001726ruffle0.0356390644170355
GO:0009799determination of symmetry0.0356390644170355
GO:0009855determination of bilateral symmetry0.0356390644170355
GO:0048762mesenchymal cell differentiation0.0380786740322516
GO:0014031mesenchymal cell development0.0380786740322516
GO:0009880embryonic pattern specification0.0382708027366175
GO:0048592eye morphogenesis0.0383992257020482
GO:0014704intercalated disc0.0383992257020482
GO:0001656metanephros development0.0383992257020482
GO:0007179transforming growth factor beta receptor signaling pathway0.0383992257020482
GO:0004702receptor signaling protein serine/threonine kinase activity0.0383992257020482
GO:0022603regulation of anatomical structure morphogenesis0.0383992257020482
GO:0022604regulation of cell morphogenesis0.0383992257020482
GO:0008360regulation of cell shape0.0383992257020482
GO:0019838growth factor binding0.0383992257020482
GO:0007498mesoderm development0.0383992257020482
GO:0030027lamellipodium0.0383992257020482
GO:0005089Rho guanyl-nucleotide exchange factor activity0.040850517821372
GO:0035023regulation of Rho protein signal transduction0.042467210308323
GO:0048754branching morphogenesis of a tube0.0432895282359754
GO:0005088Ras guanyl-nucleotide exchange factor activity0.043354858875854
GO:0007369gastrulation0.0442372284256234
GO:0001763morphogenesis of a branching structure0.0442372284256234
GO:0042692muscle cell differentiation0.0442372284256234
GO:0019955cytokine binding0.0463488678699826
GO:0001822kidney development0.047693177764072
GO:0019199transmembrane receptor protein kinase activity0.047693177764072
GO:0048469cell maturation0.047693177764072
GO:0048729tissue morphogenesis0.047693177764072
GO:0043010camera-type eye development0.047693177764072
GO:0031252leading edge0.047693177764072
GO:0002526acute inflammatory response0.047693177764072
GO:0045177apical part of cell0.047693177764072
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0482849740211149
GO:0007266Rho protein signal transduction0.0482849740211149



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
ectodermal cell6.17e-1344
neurectodermal cell6.17e-1344
non-terminally differentiated cell7.47e-1349
neural cell1.77e-1243
electrically responsive cell5.77e-1039
electrically active cell5.77e-1039
neuron1.25e-0933
neuronal stem cell1.25e-0933
neuroblast1.25e-0933
electrically signaling cell1.25e-0933

Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure1.30e-0895
ectoderm1.30e-0895
presumptive ectoderm1.30e-0895
multi-cellular organism3.23e-08333
central nervous system4.31e-0873
nervous system5.55e-0875
embryo2.39e-07320
structure with developmental contribution from neural crest5.63e-0792


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)
MA0003.16.59917
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.14.64523
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.860672
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.801219
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.648475
MA0056.10
MA0057.11.80315
MA0058.10.384683
MA0059.10.397033
MA0060.10.656954
MA0061.12.05557
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.845602
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.12.05511
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.14.5223
MA0106.11.62423
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.836994
MA0117.10.992087
MA0119.11.04809
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.11.7399
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.631666
MA0146.12.55638
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.23.91294
MA0138.20.727395
MA0002.20.592533
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.20.631649
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.792589
MA0155.13.66586
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.13.96582
MA0163.15.14538
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.214.9487
MA0102.21.65195
MA0258.10.246285
MA0259.10.729797
MA0442.10
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