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MCL coexpression mm9:338: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002113!3.57e-20!14;UBERON:0003918!3.57e-20!14;UBERON:0011143!3.57e-20!14;UBERON:0005095!3.57e-20!14;UBERON:0007687!3.57e-20!14;UBERON:0005172!1.23e-18!49;UBERON:0005173!1.23e-18!49;UBERON:0002417!1.23e-18!49;UBERON:0000916!1.23e-18!49;UBERON:0006554!1.82e-15!18;UBERON:0001008!1.34e-14!19;UBERON:0003104!1.71e-14!61;UBERON:0009142!1.71e-14!61;UBERON:0009569!3.30e-13!66;UBERON:0000489!4.14e-13!21;UBERON:0005177!1.26e-10!79;UBERON:0002107!2.48e-09!22;UBERON:0007499!2.48e-09!22;UBERON:0006925!2.48e-09!22;UBERON:0009497!2.48e-09!22;UBERON:0000015!2.48e-09!22;UBERON:0002423!2.48e-09!22;UBERON:0006235!2.48e-09!22;UBERON:0008835!2.48e-09!22;UBERON:0003894!2.48e-09!22;UBERON:0004161!2.48e-09!22;UBERON:0008836!2.48e-09!22;UBERON:0002100!5.12e-09!90;UBERON:0009854!6.82e-09!23;UBERON:0009856!6.82e-09!23;UBERON:0002365!4.05e-08!25;UBERON:0002330!4.05e-08!25
|tfbs_overrepresentation_for_novel_motifs=0.110832,0.0209205,0.0967691,0.420313,0.39616,0.442517,0.203465,0.401523,0.22468,0.0457248,0.173735,1.07934,0.0181895,0.212045,0.757688,0,0.359959,0.166842,0.183035,0.146315,0.963216,0.284341,0.211409,1.52094,0.100751,0.23172,0.336826,0.475256,0.0645727,0.108097,0.148148,0.444875,0.374265,0.285662,0.0528656,0.0365673,0.0394039,0.19269,0.894921,0.0242476,0.0448336,0.151372,0.246433,0.437292,0.0487684,0.128506,0.296243,0.167123,0.451223,0.234067,0.345732,0.251452,0.034014,0.569522,0.585246,0.217101,0.525548,0.186482,0.155641,0.215654,0.427748,0.258489,0.246116,0.33663,0.22505,0.36962,0.710311,1.04299,0.423773,0.901202,0.0871308,1.0117,0.0015954,0.615662,0.0108504,0.00917144,0.0510296,0.287424,0.413185,0.978236,0.689839,0.374245,0.25741,0.383247,0.512157,0.00106719,0.180432,0.22906,0.300065,1.20106,0.775527,0.516553,0.455893,0.182585,0.127286,1.16319,0.649772,0.458317,0.803726,0.181167,0.154241,0.444635,0.553884,0.346214,0.34536,0.151097,0.394568,0.49385,0.281887,0.0792537,0.106955,0.555481,0.0809652,0.177151,0.78216,0.383607,0.00248467,0.137389,0.361025,0.624832,0.620583,2.34817,0.658005,1.42556,0.833329,0.416312,0.209158,0.450055,0.7089,0.731314,0.53872,0.812917,0.68148,0.643519,0.802533,0.631711,0.369821,0.152256,0.75625,1.56412,1.1699,0.714696,0.241832,0.45388,0.340119,0.461959,0.298675,1.52485,0.373295,0.0469598,0.23468,0.00693588,0.570933,0.115918,0.641956,0.645175,0.2522,0.0575142,0.353936,0.11537,0.765175,0.511402,1.07003,0.344026,0.895778,0.220885,0.352259,0.194075,0.000199279
}}

Latest revision as of 15:07, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127303468..127303473,+p6@BC089597
Mm9::chr12:85393097..85393107,+p2@Acot3
Mm9::chr13:23931446..23931456,+p4@Slc17a3
Mm9::chr13:23972751..23972753,+p@chr13:23972751..23972753
+
Mm9::chr14:49860853..49860856,-p@chr14:49860853..49860856
-
Mm9::chr15:27925075..27925093,-p@chr15:27925075..27925093
-
Mm9::chr18:35775051..35775061,-p@chr18:35775051..35775061
-
Mm9::chr19:12774597..12774607,+p@chr19:12774597..12774607
+
Mm9::chr19:40562058..40562081,-p@chr19:40562058..40562081
-
Mm9::chr2:162833196..162833199,+p@chr2:162833196..162833199
+
Mm9::chr2:163335366..163335380,-p@chr2:163335366..163335380
-
Mm9::chr2:167864910..167864915,-p@chr2:167864910..167864915
-
Mm9::chr3:121898002..121898005,-p@chr3:121898002..121898005
-
Mm9::chr4:128295560..128295571,-p@chr4:128295560..128295571
-
Mm9::chr4:137222270..137222274,-p@chr4:137222270..137222274
-
Mm9::chr5:89514525..89514545,+p@chr5:89514525..89514545
+
Mm9::chr5:89531075..89531084,+p@chr5:89531075..89531084
+
Mm9::chr5:89537758..89537769,+p@chr5:89537758..89537769
+
Mm9::chr7:126759226..126759230,-p@chr7:126759226..126759230
-
Mm9::chr7:31099193..31099204,-p@chr7:31099193..31099204
-
Mm9::chr8:62997035..62997039,+p@chr8:62997035..62997039
+
Mm9::chr8:63003002..63003009,+p@chr8:63003002..63003009
+
Mm9::chr9:71572350..71572363,-p@chr9:71572350..71572363
-


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:0032788saturated monocarboxylic acid metabolic process0.0124900708008226
GO:0032789unsaturated monocarboxylic acid metabolic process0.0124900708008226
GO:0000038very-long-chain fatty acid metabolic process0.0249514138627973
GO:0016290palmitoyl-CoA hydrolase activity0.0249514138627973
GO:0006637acyl-CoA metabolic process0.0249514138627973
GO:0016291acyl-CoA thioesterase activity0.0249514138627973
GO:0001676long-chain fatty acid metabolic process0.0249514138627973
GO:0016289CoA hydrolase activity0.0249514138627973



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
kidney3.57e-2014
kidney mesenchyme3.57e-2014
upper urinary tract3.57e-2014
kidney rudiment3.57e-2014
kidney field3.57e-2014
abdomen element1.23e-1849
abdominal segment element1.23e-1849
abdominal segment of trunk1.23e-1849
abdomen1.23e-1849
urinary system structure1.82e-1518
renal system1.34e-1419
mesenchyme1.71e-1461
entire embryonic mesenchyme1.71e-1461
subdivision of trunk3.30e-1366
cavitated compound organ4.14e-1321
trunk region element1.26e-1079
liver2.48e-0922
epithelial sac2.48e-0922
digestive gland2.48e-0922
epithelium of foregut-midgut junction2.48e-0922
anatomical boundary2.48e-0922
hepatobiliary system2.48e-0922
foregut-midgut junction2.48e-0922
hepatic diverticulum2.48e-0922
liver primordium2.48e-0922
septum transversum2.48e-0922
liver bud2.48e-0922
trunk5.12e-0990
digestive tract diverticulum6.82e-0923
sac6.82e-0923
exocrine gland4.05e-0825
exocrine system4.05e-0825


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)
MA0003.12.4147e-05
MA0004.10.135415
MA0006.10.19
MA0007.10.126548
MA0009.10.467692
MA0014.11.63329e-05
MA0017.10.222109
MA0019.10.847739
MA0024.10.430047
MA0025.10.677312
MA0027.12.06014
MA0028.10.055063
MA0029.11.05899
MA0030.10.417163
MA0031.10.387282
MA0038.10.231663
MA0040.10.478574
MA0041.11.58124
MA0042.11.0228
MA0043.10.552986
MA0046.13.18746
MA0048.10.00492967
MA0050.10.934661
MA0051.10.669966
MA0052.10.485607
MA0055.10.00631096
MA0056.10
MA0057.10.159059
MA0058.10.0831725
MA0059.10.299763
MA0060.10.105577
MA0061.10.134639
MA0063.10
MA0066.10.223752
MA0067.10.78096
MA0068.11.32896
MA0069.10.485904
MA0070.10.477443
MA0071.10.932447
MA0072.10.470071
MA0073.10.00822401
MA0074.10.576444
MA0076.10.0701228
MA0077.10.451332
MA0078.10.262644
MA0081.10.332119
MA0083.10.552276
MA0084.11.09535
MA0087.10.513946
MA0088.10.00144909
MA0089.10
MA0090.11.22154
MA0091.10.867225
MA0092.10.746053
MA0093.10.0584444
MA0095.10
MA0098.10
MA0100.10.190641
MA0101.10.312158
MA0103.10.235667
MA0105.10.0482315
MA0106.10.268507
MA0107.10.0637309
MA0108.20.334189
MA0109.10
MA0111.10.390754
MA0113.10.691468
MA0114.10.311671
MA0115.10.555491
MA0116.10.189758
MA0117.10.526724
MA0119.10.0941347
MA0122.10.544387
MA0124.10.731064
MA0125.10.662359
MA0130.10
MA0131.10.312378
MA0132.10
MA0133.10
MA0135.10.585739
MA0136.10.2124
MA0139.10.201354
MA0140.10.190563
MA0141.10.553875
MA0142.10.375247
MA0143.10.71959
MA0144.10.317884
MA0145.10.195303
MA0146.10.00198396
MA0147.10.0375422
MA0148.10.445966
MA0149.10.0966891
MA0062.20.0103676
MA0035.20.193764
MA0039.21.39354e-05
MA0138.20.306125
MA0002.20.0810037
MA0137.20.257328
MA0104.20.0212101
MA0047.20.231108
MA0112.20.0119941
MA0065.20.100318
MA0150.10.794087
MA0151.10
MA0152.10.653663
MA0153.12.49036
MA0154.10.324988
MA0155.10.124879
MA0156.10.245195
MA0157.10.348973
MA0158.10
MA0159.10.364174
MA0160.10.450623
MA0161.10
MA0162.10.000662752
MA0163.10.00247972
MA0164.10.61003
MA0080.20.229013
MA0018.20.219518
MA0099.20.301184
MA0079.21.20455e-09
MA0102.21.14642
MA0258.10.11888
MA0259.10.137016
MA0442.10
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