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MCL coexpression mm9:1050: Difference between revisions

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{{MCL_coexpression_mm9
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collagen;7.68413969194452e-07;12841,12840!GO:0005593;FACIT collagen;7.68413969194452e-07;12841,12840!GO:0005594;collagen type IX;7.68413969194452e-07;12841,12840!GO:0005578;proteinaceous extracellular matrix;0.000186816617471087;12841,13516,12840!GO:0030020;extracellular matrix structural constituent conferring tensile strength;0.000186816617471087;12841,12840!GO:0005581;collagen;0.000228052395601774;12841,12840!GO:0005201;extracellular matrix structural constituent;0.000580429918189773;12841,12840!GO:0044420;extracellular matrix part;0.00119830147109974;12841,12840!GO:0030948;negative regulation of vascular endothelial growth factor receptor signaling pathway;0.00155834352952635;16840!GO:0001501;skeletal development;0.00366562736125257;16840,12840!GO:0030947;regulation of vascular endothelial growth factor receptor signaling pathway;0.00637294626688134;16840!GO:0048010;vascular endothelial growth factor receptor signaling pathway;0.0163451333037402;16840!GO:0016525;negative regulation of angiogenesis;0.0172403831278707;16840!GO:0005615;extracellular space;0.0211013759293603;12841,13516,12840!GO:0044421;extracellular region part;0.0224121950137161;12841,13516,12840!GO:0022610;biological adhesion;0.0224121950137161;12841,12840!GO:0007155;cell adhesion;0.0224121950137161;12841,12840!GO:0045765;regulation of angiogenesis;0.023319499887863;16840!GO:0051216;cartilage development;0.0352951820224402;16840!GO:0006817;phosphate 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|gostat_on_MCL_coexpression=GO:0030934;anchoring collagen;7.68413969194452e-07;12841,12840!GO:0005593;FACIT collagen;7.68413969194452e-07;12841,12840!GO:0005594;collagen type IX;7.68413969194452e-07;12841,12840!GO:0005578;proteinaceous extracellular matrix;0.000186816617471087;12841,13516,12840!GO:0030020;extracellular matrix structural constituent conferring tensile strength;0.000186816617471087;12841,12840!GO:0005581;collagen;0.000228052395601774;12841,12840!GO:0005201;extracellular matrix structural constituent;0.000580429918189773;12841,12840!GO:0044420;extracellular matrix part;0.00119830147109974;12841,12840!GO:0030948;negative regulation of vascular endothelial growth factor receptor signaling pathway;0.00155834352952635;16840!GO:0001501;skeletal development;0.00366562736125257;16840,12840!GO:0030947;regulation of vascular endothelial growth factor receptor signaling pathway;0.00637294626688134;16840!GO:0048010;vascular endothelial growth factor receptor signaling pathway;0.0163451333037402;16840!GO:0016525;negative regulation of angiogenesis;0.0172403831278707;16840!GO:0005615;extracellular space;0.0211013759293603;12841,13516,12840!GO:0044421;extracellular region part;0.0224121950137161;12841,13516,12840!GO:0022610;biological adhesion;0.0224121950137161;12841,12840!GO:0007155;cell adhesion;0.0224121950137161;12841,12840!GO:0045765;regulation of angiogenesis;0.023319499887863;16840!GO:0051216;cartilage development;0.0352951820224402;16840!GO:0006817;phosphate transport;0.046729817468914;12840!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!3.17e-09!333;UBERON:0000026!4.38e-08!12;UBERON:0004708!4.38e-08!12;UBERON:0002101!4.38e-08!12;UBERON:0004357!4.38e-08!12;UBERON:0004347!4.38e-08!12;UBERON:0005732!4.38e-08!12;UBERON:0005733!4.38e-08!12;UBERON:0010707!4.24e-07!13
}}

Latest revision as of 16:18, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:97110040..97110070,+p2@Epyc
Mm9::chr14:80061897..80061908,-p3@Lect1
Mm9::chr14:80061914..80061919,-p4@Lect1
Mm9::chr14:80061926..80061952,-p2@Lect1
Mm9::chr14:80061955..80061980,-p1@Lect1
Mm9::chr2:180332924..180332931,+p2@Col9a3
Mm9::chr4:120712161..120712285,+p1@Col9a2


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:0030934anchoring collagen7.68413969194452e-07
GO:0005593FACIT collagen7.68413969194452e-07
GO:0005594collagen type IX7.68413969194452e-07
GO:0005578proteinaceous extracellular matrix0.000186816617471087
GO:0030020extracellular matrix structural constituent conferring tensile strength0.000186816617471087
GO:0005581collagen0.000228052395601774
GO:0005201extracellular matrix structural constituent0.000580429918189773
GO:0044420extracellular matrix part0.00119830147109974
GO:0030948negative regulation of vascular endothelial growth factor receptor signaling pathway0.00155834352952635
GO:0001501skeletal development0.00366562736125257
GO:0030947regulation of vascular endothelial growth factor receptor signaling pathway0.00637294626688134
GO:0048010vascular endothelial growth factor receptor signaling pathway0.0163451333037402
GO:0016525negative regulation of angiogenesis0.0172403831278707
GO:0005615extracellular space0.0211013759293603
GO:0044421extracellular region part0.0224121950137161
GO:0022610biological adhesion0.0224121950137161
GO:0007155cell adhesion0.0224121950137161
GO:0045765regulation of angiogenesis0.023319499887863
GO:0051216cartilage development0.0352951820224402
GO:0006817phosphate transport0.046729817468914



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 organism3.17e-09333
appendage4.38e-0812
paired limb/fin4.38e-0812
limb4.38e-0812
paired limb/fin bud4.38e-0812
limb bud4.38e-0812
limb/fin field4.38e-0812
limb field4.38e-0812
appendage girdle complex4.24e-0713


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)
MA0003.10.0861444
MA0004.10.481116
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.10.222567
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.11.99617
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.40238
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.127.6241
MA0056.10
MA0057.12.44114
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.239558
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.12.38523
MA0101.10.406019
MA0103.10.348572
MA0105.10.488671
MA0106.10.677988
MA0107.10.906859
MA0108.20.763162
MA0109.10
MA0111.11.16549
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.12.77751
MA0146.10.0256827
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.21.72008
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.20.304722
MA0065.21.56466
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.687925
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.11.4173
MA0160.10.50056
MA0161.10
MA0162.10.302441
MA0163.10.0280055
MA0164.11.46244
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.323753
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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