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MCL coexpression mm9:89: Difference between revisions

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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-0

Latest revision as of 14:40, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:41405744..41405758,-p@chr10:41405744..41405758
-
Mm9::chr10:41405776..41405787,-p@chr10:41405776..41405787
-
Mm9::chr10:95540375..95540381,-p@chr10:95540375..95540381
-
Mm9::chr12:55962069..55962086,-p@chr12:55962069..55962086
-
Mm9::chr13:109654585..109654595,+p@chr13:109654585..109654595
+
Mm9::chr13:85266235..85266244,-p@chr13:85266235..85266244
-
Mm9::chr15:77034193..77034206,-p@chr15:77034193..77034206
-
Mm9::chr16:4707125..4707130,+p@chr16:4707125..4707130
+
Mm9::chr18:78014527..78014544,+p@chr18:78014527..78014544
+
Mm9::chr19:19110006..19110007,-p@chr19:19110006..19110007
-
Mm9::chr19:57240306..57240308,-p@chr19:57240306..57240308
-
Mm9::chr19:57316202..57316205,-p@chr19:57316202..57316205
-
Mm9::chr19:57326171..57326175,-p@chr19:57326171..57326175
-
Mm9::chr2:160642405..160642410,-p@chr2:160642405..160642410
-
Mm9::chr2:22445817..22445825,-p1@ENSMUST00000120651
Mm9::chr3:114530566..114530569,+p@chr3:114530566..114530569
+
Mm9::chr4:19511896..19511899,+p@chr4:19511896..19511899
+
Mm9::chr4:33258985..33258989,-p@chr4:33258985..33258989
-
Mm9::chr4:79649068..79649076,+p@chr4:79649068..79649076
+
Mm9::chr4:79649373..79649403,+p2@ENSMUST00000120053
Mm9::chr4:79649894..79649896,+p1@ENSMUST00000120053
Mm9::chr5:122906995..122907008,-p@chr5:122906995..122907008
-
Mm9::chr5:30446334..30446350,-p@chr5:30446334..30446350
-
Mm9::chr6:133056370..133056385,+p@chr6:133056370..133056385
+
Mm9::chr6:142538447..142538468,-p@chr6:142538447..142538468
-
Mm9::chr6:87950283..87950322,-p@chr6:87950283..87950322
-
Mm9::chr8:71428515..71428535,+p@chr8:71428515..71428535
+
Mm9::chr9:101023058..101023062,-p@chr9:101023058..101023062
-
Mm9::chr9:24388430..24388435,+p@chr9:24388430..24388435
+
Mm9::chrM:11083..11106,+p@chrM:11083..11106
+
Mm9::chrM:11108..11119,+p@chrM:11108..11119
+
Mm9::chrM:11120..11134,+p@chrM:11120..11134
+
Mm9::chrM:11143..11229,-p@chrM:11143..11229
-
Mm9::chrM:11172..11190,+p@chrM:11172..11190
+
Mm9::chrM:11194..11230,+p@chrM:11194..11230
+
Mm9::chrM:11241..11283,+p@chrM:11241..11283
+
Mm9::chrM:11260..11281,-p@chrM:11260..11281
-
Mm9::chrM:11291..11305,+p@chrM:11291..11305
+
Mm9::chrM:11323..11336,+p@chrM:11323..11336
+
Mm9::chrM:11351..11362,+p@chrM:11351..11362
+
Mm9::chrM:11371..11423,+p@chrM:11371..11423
+
Mm9::chrM:11411..11545,-p@chrM:11411..11545
-
Mm9::chrM:11425..11457,+p@chrM:11425..11457
+
Mm9::chrM:11734..11757,+p1@ND5
Mm9::chrM:11924..11936,-p@chrM:11924..11936
-
Mm9::chrM:11989..12000,-p@chrM:11989..12000
-
Mm9::chrM:12012..12033,-p@chrM:12012..12033
-
Mm9::chrM:12061..12098,-p@chrM:12061..12098
-
Mm9::chrM:12124..12146,-p@chrM:12124..12146
-
Mm9::chrM:12150..12168,-p@chrM:12150..12168
-
Mm9::chrM:12186..12202,-p@chrM:12186..12202
-
Mm9::chrM:12218..12271,-p@chrM:12218..12271
-
Mm9::chrM:12356..12383,-p@chrM:12356..12383
-
Mm9::chrM:12387..12432,-p@chrM:12387..12432
-
Mm9::chrM:12441..12477,-p@chrM:12441..12477
-
Mm9::chrM:1248..1266,-p@chrM:1248..1266
-
Mm9::chrM:12657..12678,-p@chrM:12657..12678
-
Mm9::chrM:12684..12750,-p@chrM:12684..12750
-
Mm9::chrM:12689..12701,+p1@uc009vfc.1
Mm9::chrM:12844..12881,-p@chrM:12844..12881
-
Mm9::chrM:12904..12928,-p@chrM:12904..12928
-
Mm9::chrM:12952..12974,+p@chrM:12952..12974
+
Mm9::chrM:12975..13016,+p@chrM:12975..13016
+
Mm9::chrM:13010..13058,-p@chrM:13010..13058
-
Mm9::chrM:13023..13055,+p@chrM:13023..13055
+
Mm9::chrM:13130..13141,+p@chrM:13130..13141
+
Mm9::chrM:13153..13203,-p@chrM:13153..13203
-
Mm9::chrM:13281..13334,-p@chrM:13281..13334
-
Mm9::chrM:13314..13335,+p@chrM:13314..13335
+
Mm9::chrM:13343..13371,-p@chrM:13343..13371
-
Mm9::chrM:13371..13384,+p@chrM:13371..13384
+
Mm9::chrM:13407..13433,-p@chrM:13407..13433
-
Mm9::chrM:13423..13435,+p@chrM:13423..13435
+
Mm9::chrM:13445..13452,-p@chrM:13445..13452
-
Mm9::chrM:13456..13483,-p@chrM:13456..13483
-
Mm9::chrM:13481..13492,+p@chrM:13481..13492
+
Mm9::chrM:13486..13509,-p@chrM:13486..13509
-
Mm9::chrM:13523..13536,-p@chrM:13523..13536
-
Mm9::chrM:13538..13561,-p@chrM:13538..13561
-
Mm9::chrM:13563..13607,-p3@uc012hdm.1
Mm9::chrM:13639..13659,+p2@CYTB
Mm9::chrM:13683..13710,-p7@uc012hdm.1
Mm9::chrM:13725..13748,-p6@uc012hdm.1
Mm9::chrM:13749..13807,-p1@uc012hdm.1
Mm9::chrM:13814..13833,-p5@uc012hdm.1
Mm9::chrM:13835..13846,-p8@uc012hdm.1
Mm9::chrM:13856..13867,+p3@CYTB
Mm9::chrM:13930..13967,-p4@uc012hdm.1
Mm9::chrM:14025..14036,-p9@uc012hdm.1
Mm9::chrM:14060..14074,-p1@ND6
Mm9::chrM:14138..14154,+p1@CYTB
Mm9::chrM:14290..14302,+p@chrM:14290..14302
+
Mm9::chrM:14546..14557,+p@chrM:14546..14557
+
Mm9::chrM:14566..14577,+p@chrM:14566..14577
+
Mm9::chrM:14636..14662,+p@chrM:14636..14662
+
Mm9::chrM:14667..14678,+p@chrM:14667..14678
+
Mm9::chrM:14676..14692,-p@chrM:14676..14692
-
Mm9::chrM:14710..14722,+p@chrM:14710..14722
+
Mm9::chrM:14769..14783,-p@chrM:14769..14783
-
Mm9::chrM:14784..14824,-p@chrM:14784..14824
-
Mm9::chrM:14841..14867,-p@chrM:14841..14867
-
Mm9::chrM:14871..14887,-p@chrM:14871..14887
-
Mm9::chrM:14906..14954,-p@chrM:14906..14954
-
Mm9::chrM:14983..15032,-p@chrM:14983..15032
-
Mm9::chrM:15037..15053,-p@chrM:15037..15053
-
Mm9::chrM:1588..1619,-p@chrM:1588..1619
-
Mm9::chrM:1965..2009,-p@chrM:1965..2009
-
Mm9::chrM:2024..2056,-p@chrM:2024..2056
-
Mm9::chrM:2167..2182,-p5@uc012hdk.1
Mm9::chrM:2466..2504,-p1@uc012hdk.1
Mm9::chrM:2743..2761,+p1@ND1
Mm9::chrM:2853..2864,+p@chrM:2853..2864
+
Mm9::chrM:3021..3048,-p4@uc012hdk.1
Mm9::chrM:3064..3075,+p@chrM:3064..3075
+
Mm9::chrM:3111..3126,-p8@uc012hdk.1
Mm9::chrM:3240..3282,-p@chrM:3240..3282
-
Mm9::chrM:3398..3425,-p@chrM:3398..3425
-
Mm9::chrM:3434..3653,-p@chrM:3434..3653
-
Mm9::chrM:3755..3776,-p@chrM:3755..3776
-
Mm9::chrM:4042..4055,-p@chrM:4042..4055
-
Mm9::chrM:4088..4126,-p@chrM:4088..4126
-
Mm9::chrM:4277..4328,-p@chrM:4277..4328
-
Mm9::chrM:4286..4297,+p1@uc009vex.1
Mm9::chrM:4329..4352,-p@chrM:4329..4352
-
Mm9::chrM:4356..4385,-p@chrM:4356..4385
-
Mm9::chrM:4386..4452,-p@chrM:4386..4452
-
Mm9::chrM:4404..4426,+p@chrM:4404..4426
+
Mm9::chrM:4458..4469,-p@chrM:4458..4469
-
Mm9::chrM:4578..4619,-p@chrM:4578..4619
-
Mm9::chrM:4666..4678,+p@chrM:4666..4678
+
Mm9::chrM:4756..4799,-p@chrM:4756..4799
-
Mm9::chrM:5400..5413,+p5@uc009vey.1
Mm9::chrM:5756..5799,+p2@uc009vey.1
Mm9::chrM:5803..5815,+p3@uc009vey.1
Mm9::chrM:5858..5875,-p@chrM:5858..5875
-
Mm9::chrM:5995..6020,+p@chrM:5995..6020
+
Mm9::chrM:6223..6252,-p@chrM:6223..6252
-
Mm9::chrM:6343..6355,+p@chrM:6343..6355
+
Mm9::chrM:6394..6410,-p@chrM:6394..6410
-
Mm9::chrM:732..741,-p@chrM:732..741
-
Mm9::chrM:747..752,-p@chrM:747..752
-
Mm9::chrM:761..788,-p@chrM:761..788
-
Mm9::chrM:847..854,-p@chrM:847..854
-
Mm9::chrM:872..884,-p@chrM:872..884
-


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:0043492ATPase activity, coupled to movement of substances0.000261983846171992
GO:0042626ATPase activity, coupled to transmembrane movement of substances0.000261983846171992
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances0.000261983846171992
GO:0015399primary active transmembrane transporter activity0.000261983846171992
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity0.000261983846171992
GO:0022890inorganic cation transmembrane transporter activity0.000261983846171992
GO:0042623ATPase activity, coupled0.00113551783422043
GO:0016887ATPase activity0.00143225804776179
GO:0022857transmembrane transporter activity0.00143225804776179
GO:0019829cation-transporting ATPase activity0.00196826326539344
GO:0022804active transmembrane transporter activity0.00196826326539344
GO:0017111nucleoside-triphosphatase activity0.00382345223712324
GO:0042625ATPase activity, coupled to transmembrane movement of ions0.00382345223712324
GO:0008324cation transmembrane transporter activity0.00382345223712324
GO:0006812cation transport0.00382345223712324
GO:0016462pyrophosphatase activity0.00382345223712324
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.00382345223712324
GO:0016817hydrolase activity, acting on acid anhydrides0.00382345223712324
GO:0008281sulfonylurea receptor activity0.00382345223712324
GO:0015078hydrogen ion transmembrane transporter activity0.00402197291278715
GO:0015077monovalent inorganic cation transmembrane transporter activity0.00426228829950633
GO:0044444cytoplasmic part0.00682722862485371
GO:0015075ion transmembrane transporter activity0.00694111304843444
GO:0006811ion transport0.00916983564024917
GO:0022891substrate-specific transmembrane transporter activity0.00964404751801714
GO:0016787hydrolase activity0.015556254694115
GO:0045261proton-transporting ATP synthase complex, catalytic core F(1)0.015556254694115
GO:0045822negative regulation of heart contraction0.015556254694115
GO:0022892substrate-specific transporter activity0.0158781682819606
GO:0005743mitochondrial inner membrane0.0158781682819606
GO:0005739mitochondrion0.0158781682819606
GO:0033178proton-transporting two-sector ATPase complex, catalytic domain0.0158781682819606
GO:0019866organelle inner membrane0.0163316586477871
GO:0005388calcium-transporting ATPase activity0.0163316586477871
GO:0015085calcium ion transmembrane transporter activity0.0163316586477871
GO:0031966mitochondrial membrane0.0163316586477871
GO:0006810transport0.0170374105095469
GO:0051607defense response to virus0.0171866913912484
GO:0005740mitochondrial envelope0.0174298880022101
GO:0051234establishment of localization0.0174298880022101
GO:0015672monovalent inorganic cation transport0.0181365385753757
GO:0016681oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor0.0181365385753757
GO:0008121ubiquinol-cytochrome-c reductase activity0.0181365385753757
GO:0016679oxidoreductase activity, acting on diphenols and related substances as donors0.0181365385753757
GO:0002026regulation of the force of heart contraction0.0205627534392368
GO:0044429mitochondrial part0.0205627534392368
GO:0051179localization0.0234035705418116
GO:0005524ATP binding0.0241959533458616
GO:0032559adenyl ribonucleotide binding0.0245317249527846
GO:0006984ER-nuclear signaling pathway0.0249284428697
GO:0045259proton-transporting ATP synthase complex0.0249284428697
GO:0031975envelope0.0249284428697
GO:0031967organelle envelope0.0249284428697
GO:0030554adenyl nucleotide binding0.0255460380134302
GO:0030001metal ion transport0.025798276506608
GO:0006091generation of precursor metabolites and energy0.0279310251649472
GO:0016529sarcoplasmic reticulum0.0304914112504821
GO:0005746mitochondrial respiratory chain0.034348616802724
GO:0016528sarcoplasm0.034348616802724
GO:0005737cytoplasm0.034404236229464
GO:0051241negative regulation of multicellular organismal process0.034404236229464
GO:0032553ribonucleotide binding0.0345042940770394
GO:0032555purine ribonucleotide binding0.0345042940770394
GO:0015985energy coupled proton transport, down electrochemical gradient0.0345042940770394
GO:0015986ATP synthesis coupled proton transport0.0345042940770394
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.0350728759100535
GO:0006937regulation of muscle contraction0.0356241901384143
GO:0017076purine nucleotide binding0.0356539037701388
GO:0031090organelle membrane0.0356539037701388
GO:0006754ATP biosynthetic process0.0356539037701388
GO:0008016regulation of heart contraction0.0356539037701388
GO:0006753nucleoside phosphate metabolic process0.0356539037701388
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.0356539037701388
GO:0016469proton-transporting two-sector ATPase complex0.0356622251257868
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.0356622251257868
GO:0046034ATP metabolic process0.0380308442694986
GO:0046872metal ion binding0.0386396994300299
GO:0003015heart process0.0386834730076833
GO:0044455mitochondrial membrane part0.0386834730076833
GO:0060047heart contraction0.0386834730076833
GO:0043167ion binding0.0386834730076833
GO:0009145purine nucleoside triphosphate biosynthetic process0.0386834730076833
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.0386834730076833
GO:0009201ribonucleoside triphosphate biosynthetic process0.0386834730076833
GO:0009142nucleoside triphosphate biosynthetic process0.0397338313523514
GO:0031072heat shock protein binding0.0397338313523514
GO:0000166nucleotide binding0.0397338313523514
GO:0009615response to virus0.0397338313523514
GO:0009205purine ribonucleoside triphosphate metabolic process0.0397338313523514
GO:0009199ribonucleoside triphosphate metabolic process0.0399961135745742
GO:0006119oxidative phosphorylation0.0399961135745742
GO:0009144purine nucleoside triphosphate metabolic process0.0399961135745742
GO:0015992proton transport0.0411063997127163
GO:0006752group transfer coenzyme metabolic process0.0414307661811456
GO:0009141nucleoside triphosphate metabolic process0.042501333781138
GO:0009152purine ribonucleotide biosynthetic process0.042660028059148
GO:0006818hydrogen transport0.042660028059148
GO:0051082unfolded protein binding0.042660028059148
GO:0006874cellular calcium ion homeostasis0.0429513261419073
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0430894060987638
GO:0009260ribonucleotide biosynthetic process0.0430894060987638
GO:0055074calcium ion homeostasis0.0430894060987638
GO:0009150purine ribonucleotide metabolic process0.0447512556476065
GO:0006164purine nucleotide biosynthetic process0.0448313313920833
GO:0006875cellular metal ion homeostasis0.0448313313920833
GO:0030017sarcomere0.0448313313920833
GO:0055065metal ion homeostasis0.0457456490522219
GO:0044449contractile fiber part0.0459822841835844
GO:0009259ribonucleotide metabolic process0.0462143975165351
GO:0006163purine nucleotide metabolic process0.0483845809800927
GO:0030016myofibril0.0485899872175221
GO:0043292contractile fiber0.0494267785038611



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)
MA0003.10
MA0004.10.000113815
MA0006.14.50139e-07
MA0007.17.91436e-05
MA0009.10.0332518
MA0014.10
MA0017.11.38882e-06
MA0019.10.0070307
MA0024.10.0243869
MA0025.10.112484
MA0027.11.27344
MA0028.17.10733e-07
MA0029.10.0206395
MA0030.10.0217275
MA0031.10.0162748
MA0038.10.00172518
MA0040.10.948421
MA0041.10.237592
MA0042.10.202258
MA0043.10.0594714
MA0046.10.369888
MA0048.18.10402e-12
MA0050.10.00225801
MA0051.10.0127417
MA0052.10.0380511
MA0055.14.82164e-17
MA0056.10
MA0057.11.95382e-12
MA0058.17.71782e-06
MA0059.11.15233e-05
MA0060.15.93165e-09
MA0061.16.23503e-07
MA0063.10
MA0066.10.00146164
MA0067.10.168725
MA0068.13.67647e-09
MA0069.10.0381337
MA0070.10.601714
MA0071.10.00955853
MA0072.10.0338673
MA0073.10
MA0074.10.00597934
MA0076.12.90458e-06
MA0077.10.0291972
MA0078.10.00309721
MA0081.12.33209e-05
MA0083.10.0592182
MA0084.10.389496
MA0087.10.176117
MA0088.19.03575e-14
MA0089.10
MA0090.14.8236e-05
MA0091.10.00628658
MA0092.10.000491385
MA0093.11.00787e-06
MA0095.10
MA0098.10
MA0100.10.000667479
MA0101.10.000171657
MA0103.12.12132e-06
MA0105.14.25942e-10
MA0106.10.0204187
MA0107.10.000152329
MA0108.20.0089207
MA0109.10
MA0111.10.000678687
MA0113.10.00235077
MA0114.15.50748e-07
MA0115.10.0603699
MA0116.14.45992e-07
MA0117.10.0504915
MA0119.10.000174506
MA0122.10.0564431
MA0124.10.140394
MA0125.10.10523
MA0130.10
MA0131.10.00669352
MA0132.10
MA0133.10
MA0135.10.0717833
MA0136.10.0011368
MA0139.11.4073e-08
MA0140.10.000666116
MA0141.15.4901e-05
MA0142.10.0674733
MA0143.10.0179177
MA0144.13.25461e-05
MA0145.12.65582e-10
MA0146.10
MA0147.17.31385e-08
MA0148.10.00663778
MA0149.11.80341e-05
MA0062.22.81582e-11
MA0035.20.00538304
MA0039.20
MA0138.20.00613288
MA0002.21.83165e-07
MA0137.23.95936e-06
MA0104.22.3022e-09
MA0047.20.00170565
MA0112.24.24661e-12
MA0065.23.83079e-13
MA0150.17.8922e-05
MA0151.10
MA0152.10.0112967
MA0153.10.268164
MA0154.19.14241e-11
MA0155.13.01357e-12
MA0156.12.81239e-06
MA0157.10.0106833
MA0158.10
MA0159.11.23225e-07
MA0160.10.00017664
MA0161.10
MA0162.10
MA0163.10
MA0164.10.00114344
MA0080.21.72907e-06
MA0018.20.00133342
MA0099.20.00571341
MA0079.20
MA0102.20.430603
MA0258.12.61195e-07
MA0259.17.04293e-07
MA0442.10
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