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MCL coexpression mm9:164: Difference between revisions

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{{MCL_coexpression_mm9
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reductase activity;0.00240073715954517;68428,20321!GO:0016723;oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor;0.00240073715954517;68428,20321!GO:0016722;oxidoreductase activity, oxidizing metal ions;0.00447156352393819;68428,20321!GO:0004733;pyridoxamine-phosphate oxidase activity;0.0439991598606532;103711!GO:0008480;sarcosine dehydrogenase activity;0.0439991598606532;192166!GO:0006096;glycolysis;0.0439991598606532;18770,15275!GO:0016491;oxidoreductase activity;0.0439991598606532;68428,192166,103711,20321,12892!GO:0006007;glucose catabolic process;0.0439991598606532;18770,15275!GO:0046365;monosaccharide catabolic process;0.0439991598606532;18770,15275!GO:0019320;hexose catabolic process;0.0439991598606532;18770,15275!GO:0046164;alcohol catabolic process;0.0439991598606532;18770,15275!GO:0000041;transition metal ion transport;0.0439991598606532;68428,226781!GO:0042816;vitamin B6 metabolic process;0.0439991598606532;103711!GO:0004743;pyruvate kinase activity;0.0439991598606532;18770!GO:0008614;pyridoxine metabolic process;0.0439991598606532;103711!GO:0004109;coproporphyrinogen oxidase activity;0.0439991598606532;12892!GO:0000780;condensed nuclear chromosome, pericentric region;0.0439991598606532;232811!GO:0042819;vitamin B6 biosynthetic process;0.0439991598606532;103711!GO:0008615;pyridoxine biosynthetic process;0.0439991598606532;103711!GO:0044275;cellular carbohydrate catabolic 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|gostat_on_MCL_coexpression=GO:0000293;ferric-chelate reductase activity;0.00240073715954517;68428,20321!GO:0016723;oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor;0.00240073715954517;68428,20321!GO:0016722;oxidoreductase activity, oxidizing metal ions;0.00447156352393819;68428,20321!GO:0004733;pyridoxamine-phosphate oxidase activity;0.0439991598606532;103711!GO:0008480;sarcosine dehydrogenase activity;0.0439991598606532;192166!GO:0006096;glycolysis;0.0439991598606532;18770,15275!GO:0016491;oxidoreductase activity;0.0439991598606532;68428,192166,103711,20321,12892!GO:0006007;glucose catabolic process;0.0439991598606532;18770,15275!GO:0046365;monosaccharide catabolic process;0.0439991598606532;18770,15275!GO:0019320;hexose catabolic process;0.0439991598606532;18770,15275!GO:0046164;alcohol catabolic process;0.0439991598606532;18770,15275!GO:0000041;transition metal ion transport;0.0439991598606532;68428,226781!GO:0042816;vitamin B6 metabolic process;0.0439991598606532;103711!GO:0004743;pyruvate kinase activity;0.0439991598606532;18770!GO:0008614;pyridoxine metabolic process;0.0439991598606532;103711!GO:0004109;coproporphyrinogen oxidase activity;0.0439991598606532;12892!GO:0000780;condensed nuclear chromosome, pericentric region;0.0439991598606532;232811!GO:0042819;vitamin B6 biosynthetic process;0.0439991598606532;103711!GO:0008615;pyridoxine biosynthetic process;0.0439991598606532;103711!GO:0044275;cellular carbohydrate catabolic process;0.0492542329247989;18770,15275!
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|ontology_enrichment_uberon=UBERON:0002106!2.03e-08!6;UBERON:0004457!2.03e-08!6;UBERON:0000042!2.03e-08!6;UBERON:0004854!2.03e-08!6;UBERON:0009034!2.03e-08!6;UBERON:0002095!2.03e-08!6;UBERON:0004782!2.03e-08!6;UBERON:0003281!2.03e-08!6;UBERON:0009664!2.03e-08!6;UBERON:0002296!2.03e-08!6;UBERON:0005602!2.03e-08!6;UBERON:0001179!2.03e-08!6;UBERON:0006293!2.03e-08!6;UBERON:0005172!6.45e-08!49;UBERON:0005173!6.45e-08!49;UBERON:0002417!6.45e-08!49;UBERON:0000916!6.45e-08!49
|tfbs_overrepresentation_for_novel_motifs=0.200398,0.660888,0.161731,0.27151,0.0995255,0.147294,0.262978,1.04264,0.170462,0.0894013,0.202892,0.0997278,0.233875,0.281056,1.88427,0,0.302987,1.05373,0.116237,0.259236,0.369478,0.598105,0.279706,0.0976018,0.505722,0.0344857,1.03693,0.171055,0.0330444,0.639273,0.0575697,0.848079,0.270968,0.846886,0.122437,2.46415,0.0341499,0.240721,1.0472,0.212807,0.436335,0.542808,0.888822,0.737796,0.237382,0.0428588,0.471989,0.190128,0.506655,0.29487,0.282905,0.160907,0.447481,0.222347,0.659609,0.122329,0.957121,0.0912703,0.755215,0.120787,0.803006,0.0441965,0.440885,0.27026,0.0322441,0.316837,0.878384,0.616867,0.126144,0.49015,0.0592317,0.682105,0.0511536,0.256208,0.0745294,0.242829,0.381938,0.0559266,0.119914,1.09499,1.3583,0.0980457,0.381206,0.0174454,0.182353,0.000186934,0.176041,0.184578,0.0614341,0.763142,0.382871,0.544637,0.877261,0.318118,0.00714873,0.877149,0.332808,0.147254,0.472464,0.470858,0.542568,1.36907,0.211201,0.283579,0.0829573,0.0599356,0.109249,0.185164,0.0537142,0.00236174,0.794479,0.212331,0.231228,0.0825035,0.388387,0.429301,0.00506197,0.0492808,0.0910151,1.48137,2.04602,0.247408,0.326513,0.204057,0.431518,0.121742,0.0271978,0.142099,0.328524,0.327252,0.581258,0.448191,1.49803,0.57146,0.40544,0.71185,0.86415,0.546912,0.366944,1.11117,0.733971,0.886234,0.0380209,0.144477,0.977567,0.161235,0.219396,1.07297,0.101978,0.186815,0.0768305,0.00144193,0.635304,0.711282,0.311503,0.278572,0.161787,0.390885,2.26356,0.0340959,0.374299,0.536197,0.121963,0.0282454,0.271396,0.550882,0.373176,0.744165,0.00226347
|tfbs_overrepresentation_jaspar=MA0003.1;4.11118e-05,MA0004.1;0.469306,MA0006.1;0.11563,MA0007.1;0.117589,MA0009.1;0.15318,MA0014.1;0.0109589,MA0017.1;0.27081,MA0019.1;0.0686792,MA0024.1;0.12989,MA0025.1;0.303494,MA0027.1;1.59941,MA0028.1;0.0239536,MA0029.1;0.76088,MA0030.1;0.775333,MA0031.1;0.342575,MA0038.1;0.323478,MA0040.1;0.483091,MA0041.1;2.40516,MA0042.1;0.880026,MA0043.1;0.210566,MA0046.1;0.516091,MA0048.1;0.772043,MA0050.1;0.066821,MA0051.1;0.33785,MA0052.1;0.956628,MA0055.1;1.0172,MA0056.1;0,MA0057.1;0.0931481,MA0058.1;0.398282,MA0059.1;0.43537,MA0060.1;0.331005,MA0061.1;0.311612,MA0063.1;0,MA0066.1;1.72535,MA0067.1;0.387388,MA0068.1;0.00842135,MA0069.1;0.494844,MA0070.1;0.15943,MA0071.1;0.0663704,MA0072.1;0.154697,MA0073.1;0.346984,MA0074.1;0.474988,MA0076.1;0.0389122,MA0077.1;0.142892,MA0078.1;0.174236,MA0081.1;0.17383,MA0083.1;0.210065,MA0084.1;0.664822,MA0087.1;0.183562,MA0088.1;0.927817,MA0089.1;0,MA0090.1;0.213725,MA0091.1;0.146366,MA0092.1;0.214232,MA0093.1;0.251703,MA0095.1;0,MA0098.1;0,MA0100.1;0.0952876,MA0101.1;0.285073,MA0103.1;0.463373,MA0105.1;0.17048,MA0106.1;0.406725,MA0107.1;0.0808299,MA0108.2;0.266897,MA0109.1;0,MA0111.1;0.112742,MA0113.1;0.156186,MA0114.1;0.44565,MA0115.1;1.79377,MA0116.1;0.501752,MA0117.1;0.192271,MA0119.1;1.61879,MA0122.1;0.590697,MA0124.1;0.915629,MA0125.1;0.793271,MA0130.1;0,MA0131.1;0.0670133,MA0132.1;0,MA0133.1;0,MA0135.1;0.660449,MA0136.1;0.28181,MA0139.1;0.0804221,MA0140.1;20.3222,MA0141.1;0.00206375,MA0142.1;0.667303,MA0143.1;0.386175,MA0144.1;0.115884,MA0145.1;0.142572,MA0146.1;0.257985,MA0147.1;0.0710004,MA0148.1;0.302543,MA0149.1;0.29728,MA0062.2;0.0174888,MA0035.2;6.21496,MA0039.2;0.154758,MA0138.2;0.229129,MA0002.2;0.635072,MA0137.2;0.748825,MA0104.2;0.0575311,MA0047.2;0.322259,MA0112.2;0.0198594,MA0065.2;0.205058,MA0150.1;1.6658,MA0151.1;0,MA0152.1;0.137701,MA0153.1;0.245148,MA0154.1;0.348918,MA0155.1;0.0176013,MA0156.1;0.18603,MA0157.1;0.287446,MA0158.1;0,MA0159.1;0.154222,MA0160.1;0.0567586,MA0161.1;0,MA0162.1;0.000449654,MA0163.1;1.67525,MA0164.1;0.282353,MA0080.2;1.46378,MA0018.2;0.0304402,MA0099.2;0.48382,MA0079.2;0.00810396,MA0102.2;0.712096,MA0258.1;0.0914295,MA0259.1;0.319498,MA0442.1;0
}}

Latest revision as of 14:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:61790414..61790427,-p13@Hk1
Mm9::chr10:80598968..80599012,+p5@Zbtb7a
Mm9::chr11:117659040..117659062,+p1@6030468B19Rik
Mm9::chr11:74433178..74433216,+p2@E130309D14Rik
Mm9::chr11:77885415..77885418,+p@chr11:77885415..77885418
+
Mm9::chr11:84637090..84637112,-p@chr11:84637090..84637112
-
Mm9::chr11:84637170..84637197,-p@chr11:84637170..84637197
-
Mm9::chr11:84637220..84637231,-p@chr11:84637220..84637231
-
Mm9::chr11:96805245..96805254,-p5@Pnpo
Mm9::chr12:52930846..52930857,-p7@Hectd1
Mm9::chr13:53537276..53537281,+p@chr13:53537276..53537281
+
Mm9::chr13:76154994..76155011,-p@chr13:76154994..76155011
-
Mm9::chr13:76193135..76193185,+p@chr13:76193135..76193185
+
Mm9::chr14:27813679..27813693,+p2@Hesx1
Mm9::chr14:55681772..55681781,+p@chr14:55681772..55681781
+
Mm9::chr14:70019476..70019481,-p@chr14:70019476..70019481
-
Mm9::chr15:35130686..35130729,+p@chr15:35130686..35130729
+
Mm9::chr15:78091332..78091357,+p5@Ncf4
Mm9::chr16:11584601..11584606,+p@chr16:11584601..11584606
+
Mm9::chr16:58670163..58670203,+p3@Cpox
Mm9::chr16:58670348..58670359,+p2@Cpox
Mm9::chr17:25223888..25223930,+p@chr17:25223888..25223930
+
Mm9::chr17:29580791..29580806,-p@chr17:29580791..29580806
-
Mm9::chr17:71619652..71619694,-p@chr17:71619652..71619694
-
Mm9::chr18:54582024..54582035,+p2@9430076G02Rik
Mm9::chr19:56000423..56000437,+p@chr19:56000423..56000437
+
Mm9::chr19:56000441..56000469,+p@chr19:56000441..56000469
+
Mm9::chr19:56012976..56012990,+p@chr19:56012976..56012990
+
Mm9::chr1:122167601..122167610,-p6@Steap3
Mm9::chr1:122167651..122167662,-p3@Steap3
Mm9::chr1:175280282..175280308,+p@chr1:175280282..175280308
+
Mm9::chr1:181906066..181906070,+p10@Cdc42bpa
Mm9::chr1:187278654..187278679,+p4@Slc30a10
Mm9::chr1:187278682..187278696,+p5@Slc30a10
Mm9::chr1:194861845..194861922,-p1@Syt14
Mm9::chr2:145924938..145924957,-p@chr2:145924938..145924957
-
Mm9::chr2:155814929..155814968,-p@chr2:155814929..155814968
-
Mm9::chr2:155815043..155815067,+p@chr2:155815043..155815067
+
Mm9::chr2:27080713..27080729,-p16@Sardh
Mm9::chr3:116562475..116562486,+p4@Frrs1
Mm9::chr3:116562492..116562509,+p2@Frrs1
Mm9::chr3:116562511..116562523,+p5@Frrs1
Mm9::chr3:153396873..153396893,-p@chr3:153396873..153396893
-
Mm9::chr3:88940055..88940105,+p1@Pklr
Mm9::chr4:109078850..109078867,-p1@uc008uch.1
Mm9::chr4:116666344..116666359,-p3@Urod
Mm9::chr4:141573922..141573949,+p1@uc008vpq.1
Mm9::chr4:46417096..46417112,-p1@Hemgn
Mm9::chr4:87452236..87452249,-p9@Mllt3
Mm9::chr5:116397935..116397956,+p@chr5:116397935..116397956
+
Mm9::chr5:35317630..35317648,+p7@Rgs12
Mm9::chr5:37112052..37112057,-p@chr5:37112052..37112057
-
Mm9::chr5:38899296..38899314,+p@chr5:38899296..38899314
+
Mm9::chr6:41653083..41653097,-p@chr6:41653083..41653097
-
Mm9::chr6:83301229..83301242,+p3@Bola3
Mm9::chr7:110962582..110962608,+p@chr7:110962582..110962608
+
Mm9::chr7:111067471..111067472,+p@chr7:111067471..111067472
+
Mm9::chr7:148382749..148382757,+p6@Lrrc56
Mm9::chr7:17642177..17642223,-p3@Hif3a
Mm9::chr7:4693441..4693454,+p10@Suv420h2
Mm9::chr7:52184039..52184051,-p8@Ap2a1
Mm9::chr8:90824273..90824283,+p@chr8:90824273..90824283
+
Mm9::chr8:90824303..90824338,+p@chr8:90824303..90824338
+
Mm9::chr8:90824341..90824359,+p@chr8:90824341..90824359
+
Mm9::chr9:48147805..48147837,-p@chr9:48147805..48147837
-
Mm9::chrX:8834026..8834043,-p1@uc009spp.1
Mm9::chrX:8834052..8834063,-p2@uc009spp.1


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:0000293ferric-chelate reductase activity0.00240073715954517
GO:0016723oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor0.00240073715954517
GO:0016722oxidoreductase activity, oxidizing metal ions0.00447156352393819
GO:0004733pyridoxamine-phosphate oxidase activity0.0439991598606532
GO:0008480sarcosine dehydrogenase activity0.0439991598606532
GO:0006096glycolysis0.0439991598606532
GO:0016491oxidoreductase activity0.0439991598606532
GO:0006007glucose catabolic process0.0439991598606532
GO:0046365monosaccharide catabolic process0.0439991598606532
GO:0019320hexose catabolic process0.0439991598606532
GO:0046164alcohol catabolic process0.0439991598606532
GO:0000041transition metal ion transport0.0439991598606532
GO:0042816vitamin B6 metabolic process0.0439991598606532
GO:0004743pyruvate kinase activity0.0439991598606532
GO:0008614pyridoxine metabolic process0.0439991598606532
GO:0004109coproporphyrinogen oxidase activity0.0439991598606532
GO:0000780condensed nuclear chromosome, pericentric region0.0439991598606532
GO:0042819vitamin B6 biosynthetic process0.0439991598606532
GO:0008615pyridoxine biosynthetic process0.0439991598606532
GO:0044275cellular carbohydrate catabolic process0.0492542329247989



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>


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)
MA0003.14.11118e-05
MA0004.10.469306
MA0006.10.11563
MA0007.10.117589
MA0009.10.15318
MA0014.10.0109589
MA0017.10.27081
MA0019.10.0686792
MA0024.10.12989
MA0025.10.303494
MA0027.11.59941
MA0028.10.0239536
MA0029.10.76088
MA0030.10.775333
MA0031.10.342575
MA0038.10.323478
MA0040.10.483091
MA0041.12.40516
MA0042.10.880026
MA0043.10.210566
MA0046.10.516091
MA0048.10.772043
MA0050.10.066821
MA0051.10.33785
MA0052.10.956628
MA0055.11.0172
MA0056.10
MA0057.10.0931481
MA0058.10.398282
MA0059.10.43537
MA0060.10.331005
MA0061.10.311612
MA0063.10
MA0066.11.72535
MA0067.10.387388
MA0068.10.00842135
MA0069.10.494844
MA0070.10.15943
MA0071.10.0663704
MA0072.10.154697
MA0073.10.346984
MA0074.10.474988
MA0076.10.0389122
MA0077.10.142892
MA0078.10.174236
MA0081.10.17383
MA0083.10.210065
MA0084.10.664822
MA0087.10.183562
MA0088.10.927817
MA0089.10
MA0090.10.213725
MA0091.10.146366
MA0092.10.214232
MA0093.10.251703
MA0095.10
MA0098.10
MA0100.10.0952876
MA0101.10.285073
MA0103.10.463373
MA0105.10.17048
MA0106.10.406725
MA0107.10.0808299
MA0108.20.266897
MA0109.10
MA0111.10.112742
MA0113.10.156186
MA0114.10.44565
MA0115.11.79377
MA0116.10.501752
MA0117.10.192271
MA0119.11.61879
MA0122.10.590697
MA0124.10.915629
MA0125.10.793271
MA0130.10
MA0131.10.0670133
MA0132.10
MA0133.10
MA0135.10.660449
MA0136.10.28181
MA0139.10.0804221
MA0140.120.3222
MA0141.10.00206375
MA0142.10.667303
MA0143.10.386175
MA0144.10.115884
MA0145.10.142572
MA0146.10.257985
MA0147.10.0710004
MA0148.10.302543
MA0149.10.29728
MA0062.20.0174888
MA0035.26.21496
MA0039.20.154758
MA0138.20.229129
MA0002.20.635072
MA0137.20.748825
MA0104.20.0575311
MA0047.20.322259
MA0112.20.0198594
MA0065.20.205058
MA0150.11.6658
MA0151.10
MA0152.10.137701
MA0153.10.245148
MA0154.10.348918
MA0155.10.0176013
MA0156.10.18603
MA0157.10.287446
MA0158.10
MA0159.10.154222
MA0160.10.0567586
MA0161.10
MA0162.10.000449654
MA0163.11.67525
MA0164.10.282353
MA0080.21.46378
MA0018.20.0304402
MA0099.20.48382
MA0079.20.00810396
MA0102.20.712096
MA0258.10.0914295
MA0259.10.319498
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:164&oldid=3072163"