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MCL coexpression mm9:429: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002365!5.75e-11!25;UBERON:0002330!5.75e-11!25;UBERON:0002107!8.29e-10!22;UBERON:0007499!8.29e-10!22;UBERON:0006925!8.29e-10!22;UBERON:0009497!8.29e-10!22;UBERON:0000015!8.29e-10!22;UBERON:0002423!8.29e-10!22;UBERON:0006235!8.29e-10!22;UBERON:0008835!8.29e-10!22;UBERON:0003894!8.29e-10!22;UBERON:0004161!8.29e-10!22;UBERON:0008836!8.29e-10!22;UBERON:0009854!3.52e-09!23;UBERON:0009856!3.52e-09!23
|tfbs_overrepresentation_for_novel_motifs=0.48778,1.31277,0.873196,0.191238,0.271545,0.201606,0.270195,0.340454,0.361988,0.115943,0.236307,0.260789,1.84857,0.27987,0.295744,0,0.44163,0.0750368,1.28115,0.136088,0.121654,0.0267127,0.279154,0.0782709,0.149704,1.48051,0.534309,0.216938,0.338701,0.648885,0.206597,0.531719,0.546575,3.02067,0.0880674,5.83218,0.0693463,0.257981,0.0591424,1.539,0.0770075,0.210373,0.00374448,0.0888852,0.142379,0.539875,0.372907,0.228683,0.0147531,0.699131,0.426383,0.323798,0.922321,0.661847,0.67813,0.28555,1.18914,0.25091,3.15223,0.283926,0.513661,0.331566,0.172226,0.4166,0.294453,0.451957,0.806865,1.14503,0.509463,1.00145,0.132733,0.153772,0.0300638,0.709559,0.0246496,3.5015,0.468707,0.363297,4.30656,1.2779,0.0397272,0.456892,0.330377,0.930992,0.602212,0.0199438,0.138203,0.649538,0.377064,1.30447,0.873554,0.606796,0.543309,0.280055,0.057338,0.186449,1.35973,0.545856,0.373124,4.08624,0.523231,1.31644,0.645628,0.4269,0.425983,0.21005,0.478524,0.225669,0.127231,0.122746,0.925979,0.647285,0.124928,0.240232,0.880323,0.557702,1.50366,2.39839,0.442771,0.0675617,0.714636,0.398522,0.303371,0.362534,0.932468,0.501574,0.276618,0.53717,0.805419,0.0836776,0.629874,0.186072,4.39639,0.296474,0.9011,0.0259009,0.167758,0.211406,0.853868,1.66928,1.27308,0.811357,0.313144,0.541193,1.078,1.14027,0.375553,1.62988,2.95441,0.0799646,3.89449,0.0678237,0.66331,0.0522757,1.45824,0.739975,0.324625,0.0943424,5.386,0.501353,0.862985,0.601424,0.501973,0.15582,1.07177,0.289792,0.0688048,0.259556,0.273375
}}

Latest revision as of 15:17, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:99553856..99553873,+p@chr15:99553856..99553873
+
Mm9::chr3:14863235..14863254,-p@chr3:14863235..14863254
-
Mm9::chr3:14863476..14863483,+p3@Car3
Mm9::chr3:14863486..14863494,+p5@Car3
Mm9::chr3:14863495..14863521,+p1@Car3
Mm9::chr3:14870039..14870084,+p@chr3:14870039..14870084
+
Mm9::chr3:14870094..14870137,+p@chr3:14870094..14870137
+
Mm9::chr3:14870141..14870163,+p@chr3:14870141..14870163
+
Mm9::chr3:14871545..14871546,+p@chr3:14871545..14871546
+
Mm9::chr3:14871599..14871610,+p@chr3:14871599..14871610
+
Mm9::chr3:14871636..14871653,+p@chr3:14871636..14871653
+
Mm9::chr3:14871661..14871670,+p@chr3:14871661..14871670
+
Mm9::chr3:14871682..14871692,+p@chr3:14871682..14871692
+
Mm9::chr3:14871700..14871705,+p@chr3:14871700..14871705
+
Mm9::chr3:14871709..14871717,+p@chr3:14871709..14871717
+
Mm9::chr3:14871724..14871735,+p@chr3:14871724..14871735
+
Mm9::chr3:14871767..14871772,+p@chr3:14871767..14871772
+
Mm9::chr7:123175510..123175523,+p@chr7:123175510..123175523
+


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:0016151nickel ion binding0.00372541500027393
GO:0004089carbonate dehydratase activity0.00884786062565058
GO:0016836hydro-lyase activity0.0137374678135101
GO:0016835carbon-oxygen lyase activity0.0137374678135101
GO:0006730one-carbon compound metabolic process0.0143428477510546
GO:0016829lyase activity0.0235942950017349



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
exocrine gland5.75e-1125
exocrine system5.75e-1125
liver8.29e-1022
epithelial sac8.29e-1022
digestive gland8.29e-1022
epithelium of foregut-midgut junction8.29e-1022
anatomical boundary8.29e-1022
hepatobiliary system8.29e-1022
foregut-midgut junction8.29e-1022
hepatic diverticulum8.29e-1022
liver primordium8.29e-1022
septum transversum8.29e-1022
liver bud8.29e-1022
digestive tract diverticulum3.52e-0923
sac3.52e-0923


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)
MA0003.10.012764
MA0004.11.06516
MA0006.10.0854592
MA0007.10.181021
MA0009.11.36778
MA0014.12.44372
MA0017.11.11747
MA0019.11.80507
MA0024.10.516087
MA0025.10.773017
MA0027.12.16618
MA0028.10.0910441
MA0029.10.496599
MA0030.10.502474
MA0031.11.18689
MA0038.10.815918
MA0040.10.567108
MA0041.10.140298
MA0042.10.131965
MA0043.10.644695
MA0046.10.58854
MA0048.12.47154
MA0050.11.17524
MA0051.14.13133
MA0052.10.574473
MA0055.10.543903
MA0056.10
MA0057.11.4568
MA0058.10.799579
MA0059.10.421089
MA0060.10.0476793
MA0061.10.060618
MA0063.10
MA0066.10.293002
MA0067.10.879099
MA0068.10.0569808
MA0069.10.574784
MA0070.10.565924
MA0071.11.17286
MA0072.10.558195
MA0073.12.0632e-11
MA0074.10.264633
MA0076.10.110983
MA0077.10.538513
MA0078.10.336143
MA0081.12.77212
MA0083.16.48843
MA0084.11.1979
MA0087.10.604077
MA0088.11.07738
MA0089.10
MA0090.10.167748
MA0091.10.582275
MA0092.10.167962
MA0093.10.653128
MA0095.10
MA0098.10
MA0100.10.255651
MA0101.10.141127
MA0103.10.106139
MA0105.10.0222933
MA0106.10.342589
MA0107.10.102611
MA0108.21.87232
MA0109.10
MA0111.11.59903
MA0113.10.319332
MA0114.10.470969
MA0115.10.647296
MA0116.10.288992
MA0117.10.617392
MA0119.11.99894
MA0122.10.635764
MA0124.10.828115
MA0125.10.757653
MA0130.10
MA0131.10.390422
MA0132.10
MA0133.10
MA0135.10.67864
MA0136.10.280269
MA0139.14.83608
MA0140.10.710317
MA0141.12.43904
MA0142.10.457961
MA0143.10.332773
MA0144.10.0609575
MA0145.10.584715
MA0146.10.343991
MA0147.10.509077
MA0148.10.203219
MA0149.10.144679
MA0062.20.0237736
MA0035.20.259203
MA0039.25.80504e-07
MA0138.20.383644
MA0002.28.78044
MA0137.20.116005
MA0104.20.662527
MA0047.20.301217
MA0112.21.15703
MA0065.21.16061
MA0150.10.180943
MA0151.10
MA0152.10.301303
MA0153.10.694211
MA0154.11.54588
MA0155.10.246884
MA0156.10.110475
MA0157.11.09863
MA0158.10
MA0159.11.3683
MA0160.10.205397
MA0161.10
MA0162.10.0894944
MA0163.10.0339329
MA0164.10.280556
MA0080.20.103116
MA0018.20.288261
MA0099.20.37828
MA0079.20.000152177
MA0102.21.24942
MA0258.11.17038
MA0259.10.482458
MA0442.10
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