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MCL coexpression mm9:628: Difference between revisions

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{{MCL_coexpression_mm9
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receptor binding;0.0046019832356325;20348!GO:0001974;blood vessel remodeling;0.0224113141921173;20348!GO:0001755;neural crest cell migration;0.0224113141921173;20348!GO:0009791;post-embryonic development;0.0224113141921173;20348!GO:0014033;neural crest cell differentiation;0.0224113141921173;20348!GO:0014032;neural crest cell development;0.0224113141921173;20348!GO:0048762;mesenchymal cell differentiation;0.0224113141921173;20348!GO:0014031;mesenchymal cell development;0.0224113141921173;20348!GO:0004867;serine-type endopeptidase inhibitor activity;0.046250788779941;67866!GO:0005615;extracellular space;0.046250788779941;67866,20348!GO:0044421;extracellular region part;0.046250788779941;67866,20348!GO:0048771;tissue remodeling;0.046250788779941;20348!GO:0004866;endopeptidase inhibitor activity;0.0466112836959704;67866!GO:0030414;protease inhibitor activity;0.0466112836959704;67866!GO:0007169;transmembrane receptor protein tyrosine kinase signaling pathway;0.0466112836959704;20348!GO:0007507;heart development;0.0466112836959704;20348!GO:0048514;blood vessel morphogenesis;0.0466112836959704;20348!GO:0001568;blood vessel development;0.0471342349206472;20348!GO:0001944;vasculature development;0.0471342349206472;20348!GO:0004857;enzyme inhibitor 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|gostat_on_MCL_coexpression=GO:0030215;semaphorin receptor binding;0.0046019832356325;20348!GO:0001974;blood vessel remodeling;0.0224113141921173;20348!GO:0001755;neural crest cell migration;0.0224113141921173;20348!GO:0009791;post-embryonic development;0.0224113141921173;20348!GO:0014033;neural crest cell differentiation;0.0224113141921173;20348!GO:0014032;neural crest cell development;0.0224113141921173;20348!GO:0048762;mesenchymal cell differentiation;0.0224113141921173;20348!GO:0014031;mesenchymal cell development;0.0224113141921173;20348!GO:0004867;serine-type endopeptidase inhibitor activity;0.046250788779941;67866!GO:0005615;extracellular space;0.046250788779941;67866,20348!GO:0044421;extracellular region part;0.046250788779941;67866,20348!GO:0048771;tissue remodeling;0.046250788779941;20348!GO:0004866;endopeptidase inhibitor activity;0.0466112836959704;67866!GO:0030414;protease inhibitor activity;0.0466112836959704;67866!GO:0007169;transmembrane receptor protein tyrosine kinase signaling pathway;0.0466112836959704;20348!GO:0007507;heart development;0.0466112836959704;20348!GO:0048514;blood vessel morphogenesis;0.0466112836959704;20348!GO:0001568;blood vessel development;0.0471342349206472;20348!GO:0001944;vasculature development;0.0471342349206472;20348!GO:0004857;enzyme inhibitor activity;0.0471342349206472;67866!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!1.91e-10!333;UBERON:0000464!2.10e-09!57;UBERON:0005178!4.27e-07!17;UBERON:0005181!4.27e-07!17;UBERON:0002224!4.27e-07!17;UBERON:0000915!4.27e-07!17;UBERON:0008947!4.27e-07!17;UBERON:0003258!4.27e-07!17;UBERON:0005156!6.24e-07!26;UBERON:0000990!6.24e-07!26
|tfbs_overrepresentation_for_novel_motifs=0.267173,0.2332,5.53254,0.303186,0.1565,0.315748,2.71625,0.0908011,0.0967611,0.852117,1.67609,0.385627,1.05446,0.407615,0.169024,0,1.43434,0.150639,1.47146,1.82035,2.5506,0.235703,0.406794,0.155356,0.701128,0.432737,5.46255,1.59553,0.191143,0.0536593,0.321757,0.683831,0.14899,1.81823,1.55237,0.00280939,0.862318,0.382372,0.126724,0.107198,0.153518,4.2638,0.0834993,0.170547,0.685271,0.293566,0.512146,2.48564,0.0642028,0.564214,0.570705,0.457464,2.11345,0.82076,0.837732,0.414119,0.200484,0.37415,0.0716833,1.0604,1.59636,0.46618,0.104381,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.229771,0.0945081,6.30637,0.870406,4.45738,0.222652,0.504564,0.50152,0.648171,0.624196,0.0952669,0.60374,1.17414,0.0868537,0.758319,0.0325399,0.00753188,0.43877,0.516731,1.47691,1.03946,0.763136,0.696137,0.484945,0.12392,0.11194,1.04257,0.698838,0.512384,0.0434558,0.142282,0.683562,0.803823,0.571268,0.57027,0.3259,0.627019,0.344504,0.222586,1.16343,0.261228,0.805555,0.219561,0.361667,1.04639,0.152197,2.71606,4.11096,0.58848,0.139554,0.875675,0.540309,1.94166,0.500675,1.09972,0.651709,0.403884,0.689622,0.969481,0.163147,0.787341,0.296885,0.940498,0.426575,1.06766,0.0212043,3.85719,0.327523,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,1.56915,0.515065,1.80426,0.276297,2.84471,4.10924,0.209642,0.822286,0.115938,0.425729,0.901933,0.458393,0.178202,0.265096,0.274055,1.02862,1.78909,0.652135,0.25933,0.561023,2.82128,0.141416,0.384198,6.72706
}}

Latest revision as of 15:37, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr5:17080038..17080058,+p14@Sema3c
Mm9::chr5:17080241..17080257,+p8@Sema3c
Mm9::chr5:17080288..17080304,+p2@Sema3c
Mm9::chr5:17080358..17080367,+p10@Sema3c
Mm9::chr5:17080389..17080396,+p13@Sema3c
Mm9::chr5:17080403..17080423,+p7@Sema3c
Mm9::chr5:17080426..17080449,+p3@Sema3c
Mm9::chr5:17080456..17080484,+p4@Sema3c
Mm9::chr5:17080485..17080504,+p6@Sema3c
Mm9::chr5:17080513..17080532,+p5@Sema3c
Mm9::chr5:17082856..17082864,+p@chr5:17082856..17082864
+
Mm9::chr8:122190143..122190152,+p5@Wfdc1


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:0030215semaphorin receptor binding0.0046019832356325
GO:0001974blood vessel remodeling0.0224113141921173
GO:0001755neural crest cell migration0.0224113141921173
GO:0009791post-embryonic development0.0224113141921173
GO:0014033neural crest cell differentiation0.0224113141921173
GO:0014032neural crest cell development0.0224113141921173
GO:0048762mesenchymal cell differentiation0.0224113141921173
GO:0014031mesenchymal cell development0.0224113141921173
GO:0004867serine-type endopeptidase inhibitor activity0.046250788779941
GO:0005615extracellular space0.046250788779941
GO:0044421extracellular region part0.046250788779941
GO:0048771tissue remodeling0.046250788779941
GO:0004866endopeptidase inhibitor activity0.0466112836959704
GO:0030414protease inhibitor activity0.0466112836959704
GO:0007169transmembrane receptor protein tyrosine kinase signaling pathway0.0466112836959704
GO:0007507heart development0.0466112836959704
GO:0048514blood vessel morphogenesis0.0466112836959704
GO:0001568blood vessel development0.0471342349206472
GO:0001944vasculature development0.0471342349206472
GO:0004857enzyme inhibitor activity0.0471342349206472



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
multi-cellular organism1.91e-10333
anatomical space2.10e-0957
thoracic cavity element4.27e-0717
thoracic segment organ4.27e-0717
thoracic cavity4.27e-0717
thoracic segment of trunk4.27e-0717
respiratory primordium4.27e-0717
endoderm of foregut4.27e-0717
reproductive structure6.24e-0726
reproductive system6.24e-0726


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)
MA0003.13.86695
MA0004.10.303605
MA0006.10.960584
MA0007.10.290695
MA0009.10.709264
MA0014.10.0136923
MA0017.10.546298
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.173587
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.680396
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.12.4347
MA0056.10
MA0057.10.0386961
MA0058.10.223242
MA0059.10.233271
MA0060.10.108526
MA0061.10.129002
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.0405002
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.18.11254e-06
MA0074.10.390075
MA0076.10.200996
MA0077.10.691048
MA0078.10.471303
MA0081.12.00694
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.0227266
MA0089.10
MA0090.10.27428
MA0091.10.315003
MA0092.10.274547
MA0093.10.179936
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.675688
MA0103.10.19444
MA0105.10.491577
MA0106.10.478503
MA0107.10.555009
MA0108.20.557195
MA0109.10
MA0111.10.286331
MA0113.11.14743
MA0114.10.127366
MA0115.10.805567
MA0116.10.165534
MA0117.10.774259
MA0119.13.58594
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.61859
MA0140.10.988903
MA0141.10.603844
MA0142.10.604892
MA0143.10.467531
MA0144.10.807435
MA0145.11.15539
MA0146.10.0622241
MA0147.11.36583
MA0148.10.317692
MA0149.10.245177
MA0062.20.0662974
MA0035.20.383789
MA0039.22.26616
MA0138.20.523978
MA0002.20.0901987
MA0137.22.49754
MA0104.22.89279
MA0047.20.431964
MA0112.26.43985
MA0065.20.109524
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.042968
MA0155.11.26717
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.145521
MA0160.10.320315
MA0161.10
MA0162.10.00450899
MA0163.10.692813
MA0164.10.408402
MA0080.20.190316
MA0018.20.417217
MA0099.20.518072
MA0079.20.00392046
MA0102.21.42135
MA0258.10.118033
MA0259.10.130633
MA0442.10
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