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MCL coexpression mm9:282: Difference between revisions

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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-

Latest revision as of 15:01, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79605103..79605149,+p1@Atp5d
Mm9::chr10:93661772..93661788,+p1@Ndufa12
Mm9::chr11:4604306..4604333,-p1@Gm6293
p1@Uqcr10
Mm9::chr11:4604337..4604354,-p2@Gm6293
p2@Uqcr10
Mm9::chr12:103213893..103213956,-p@chr12:103213893..103213956
-
Mm9::chr12:113205165..113205228,-p1@2010107E04Rik
Mm9::chr15:35867911..35867933,-p1@Cox6c
p1@Gm6265
Mm9::chr15:82184655..82184691,-p1@Ndufa6
Mm9::chr16:31948518..31948628,-p1@0610012G03Rik
Mm9::chr16:91931799..91931863,-p1@Atp5o
p1@LOC100047429
Mm9::chr17:56857182..56857242,+p1@Gm4943
p1@Ndufa11
Mm9::chr2:73749342..73749365,-p1@Atp5g3
Mm9::chr4:115747627..115747654,-p1@Uqcrh
Mm9::chr4:138686900..138686936,-p1@Minos1
Mm9::chr5:108863378..108863389,-p2@Atp5k
Mm9::chr5:108863392..108863428,-p1@Atp5k
Mm9::chr5:145952403..145952417,-p1@Atp5j2
Mm9::chr5:145952418..145952434,-p2@Atp5j2
Mm9::chr5:145952435..145952441,-p3@Atp5j2
Mm9::chr6:38484833..38484872,+p1@1110001J03Rik
Mm9::chr6:39542568..39542587,+p2@Ndufb2
Mm9::chr6:39542589..39542616,+p1@Ndufb2
Mm9::chr7:104548559..104548625,+p1@LOC635087
p1@LOC675851
p1@Ndufc2
Mm9::chr7:31411098..31411141,-p1@Cox6b1
Mm9::chr7:31411146..31411158,-p2@Cox6b1
Mm9::chr8:123192165..123192168,+p3@Cox4i1
Mm9::chr8:123192181..123192199,+p1@Cox4i1
Mm9::chr9:57369041..57369121,+p1@Cox5a
Mm9::chr9:79607484..79607552,-p1@Cox7a2
Mm9::chrX:103211038..103211098,+p1@Cox7b


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:0015078hydrogen ion transmembrane transporter activity1.05733629719142e-22
GO:0015077monovalent inorganic cation transmembrane transporter activity1.05733629719142e-22
GO:0022890inorganic cation transmembrane transporter activity3.54830758606969e-21
GO:0005739mitochondrion9.86692785967779e-19
GO:0006091generation of precursor metabolites and energy2.4288803476115e-15
GO:0008324cation transmembrane transporter activity7.5024477992368e-15
GO:0015075ion transmembrane transporter activity1.87677659765519e-13
GO:0004129cytochrome-c oxidase activity1.87677659765519e-13
GO:0016676oxidoreductase activity, acting on heme group of donors, oxygen as acceptor1.87677659765519e-13
GO:0015002heme-copper terminal oxidase activity1.87677659765519e-13
GO:0016675oxidoreductase activity, acting on heme group of donors1.87677659765519e-13
GO:0022891substrate-specific transmembrane transporter activity8.03203548082412e-13
GO:0005743mitochondrial inner membrane1.79294810501441e-12
GO:0019866organelle inner membrane2.36125922112985e-12
GO:0031966mitochondrial membrane3.19913423151459e-12
GO:0022857transmembrane transporter activity3.45313822500132e-12
GO:0005740mitochondrial envelope5.69069868358036e-12
GO:0022892substrate-specific transporter activity9.04729830375329e-12
GO:0044429mitochondrial part2.24664088917973e-11
GO:0045259proton-transporting ATP synthase complex2.47998723586563e-11
GO:0044444cytoplasmic part4.04478104000245e-11
GO:0016491oxidoreductase activity4.14035824222607e-11
GO:0031975envelope8.25689641937836e-11
GO:0031967organelle envelope8.25689641937836e-11
GO:0005746mitochondrial respiratory chain2.26330566003301e-10
GO:0006754ATP biosynthetic process7.71766825778342e-10
GO:0006753nucleoside phosphate metabolic process7.71766825778342e-10
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism7.71766825778342e-10
GO:0006118electron transport8.05556299087337e-10
GO:0016469proton-transporting two-sector ATPase complex8.05556299087337e-10
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism8.05556299087337e-10
GO:0046034ATP metabolic process1.14142287713848e-09
GO:0031090organelle membrane1.14142287713848e-09
GO:0044455mitochondrial membrane part1.82288624436117e-09
GO:0009145purine nucleoside triphosphate biosynthetic process1.88343627958062e-09
GO:0009206purine ribonucleoside triphosphate biosynthetic process1.88343627958062e-09
GO:0009201ribonucleoside triphosphate biosynthetic process1.88343627958062e-09
GO:0019829cation-transporting ATPase activity2.29993136824492e-09
GO:0009142nucleoside triphosphate biosynthetic process2.50016271453906e-09
GO:0009205purine ribonucleoside triphosphate metabolic process2.71317565922131e-09
GO:0009199ribonucleoside triphosphate metabolic process2.93949786269354e-09
GO:0006119oxidative phosphorylation3.10572142613345e-09
GO:0009144purine nucleoside triphosphate metabolic process3.10572142613345e-09
GO:0015992proton transport3.70374928605004e-09
GO:0006752group transfer coenzyme metabolic process3.98878846161067e-09
GO:0009141nucleoside triphosphate metabolic process4.70792313813386e-09
GO:0009152purine ribonucleotide biosynthetic process5.04803559962466e-09
GO:0006818hydrogen transport5.40620743321387e-09
GO:0009260ribonucleotide biosynthetic process6.86453453459934e-09
GO:0009150purine ribonucleotide metabolic process8.60754032332113e-09
GO:0006164purine nucleotide biosynthetic process9.13697633655863e-09
GO:0009259ribonucleotide metabolic process1.30947163954274e-08
GO:0006163purine nucleotide metabolic process1.70623179333128e-08
GO:0042625ATPase activity, coupled to transmembrane movement of ions2.65334621531328e-08
GO:0009108coenzyme biosynthetic process2.94886131388546e-08
GO:0015985energy coupled proton transport, down electrochemical gradient4.44895075053608e-08
GO:0015986ATP synthesis coupled proton transport4.44895075053608e-08
GO:0051188cofactor biosynthetic process5.8450139263461e-08
GO:0005737cytoplasm8.7239609072799e-08
GO:0043492ATPase activity, coupled to movement of substances1.38094086905866e-07
GO:0042626ATPase activity, coupled to transmembrane movement of substances1.38094086905866e-07
GO:0016820hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances1.41908810414275e-07
GO:0009165nucleotide biosynthetic process1.79897586450396e-07
GO:0015399primary active transmembrane transporter activity2.21809094621284e-07
GO:0015405P-P-bond-hydrolysis-driven transmembrane transporter activity2.21809094621284e-07
GO:0045263proton-transporting ATP synthase complex, coupling factor F(o)3.48517249543282e-07
GO:0033177proton-transporting two-sector ATPase complex, proton-transporting domain3.48517249543282e-07
GO:0006732coenzyme metabolic process6.26132608600419e-07
GO:0009117nucleotide metabolic process1.17448947152925e-06
GO:0051186cofactor metabolic process1.3606977549702e-06
GO:0043231intracellular membrane-bound organelle1.43698032170725e-06
GO:0043227membrane-bound organelle1.44178994678713e-06
GO:0055086nucleobase, nucleoside and nucleotide metabolic process1.56499460731309e-06
GO:0042623ATPase activity, coupled3.20782411227553e-06
GO:0045277respiratory chain complex IV5.12142662743087e-06
GO:0005751mitochondrial respiratory chain complex IV5.12142662743087e-06
GO:0016887ATPase activity6.38709978841597e-06
GO:0015672monovalent inorganic cation transport9.85818446189381e-06
GO:0009055electron carrier activity1.3099532405824e-05
GO:0022804active transmembrane transporter activity1.53804529191378e-05
GO:0043229intracellular organelle1.56591431738442e-05
GO:0043226organelle1.56802140393725e-05
GO:0050136NADH dehydrogenase (quinone) activity1.85878917188007e-05
GO:0008137NADH dehydrogenase (ubiquinone) activity1.85878917188007e-05
GO:0003954NADH dehydrogenase activity1.85878917188007e-05
GO:0016655oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor2.22593648814792e-05
GO:0045261proton-transporting ATP synthase complex, catalytic core F(1)2.23327021135196e-05
GO:0033178proton-transporting two-sector ATPase complex, catalytic domain3.0893555504857e-05
GO:0016651oxidoreductase activity, acting on NADH or NADPH5.29021266596043e-05
GO:0017111nucleoside-triphosphatase activity7.30249867802728e-05
GO:0006812cation transport8.28326688719e-05
GO:0016462pyrophosphatase activity9.07913750686655e-05
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides9.25249537390662e-05
GO:0016817hydrolase activity, acting on acid anhydrides9.25249537390662e-05
GO:0044446intracellular organelle part0.000118210290136629
GO:0044422organelle part0.000120296055700488
GO:0016020membrane0.000222191969850013
GO:0044424intracellular part0.000311841004108929
GO:0008553hydrogen-exporting ATPase activity, phosphorylative mechanism0.000357569312107896
GO:0016310phosphorylation0.000419934088670099
GO:0043234protein complex0.000462971162058658
GO:0006811ion transport0.000509175039586427
GO:0005622intracellular0.000510439505774936
GO:0006793phosphorus metabolic process0.000868157074691329
GO:0006796phosphate metabolic process0.000868157074691329
GO:0044249cellular biosynthetic process0.00119791353739778
GO:0032991macromolecular complex0.00179250151765528
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.00206099288275178
GO:0004450isocitrate dehydrogenase (NADP+) activity0.00403514912425858
GO:0006097glyoxylate cycle0.00403514912425858
GO:0009058biosynthetic process0.00440211700390514
GO:0006122mitochondrial electron transport, ubiquinol to cytochrome c0.00523506662048088
GO:0046487glyoxylate metabolic process0.00523506662048088
GO:0004448isocitrate dehydrogenase activity0.00906907335524909
GO:0016681oxidoreductase activity, acting on diphenols and related substances as donors, cytochrome as acceptor0.0138616711060358
GO:0008121ubiquinol-cytochrome-c reductase activity0.0138616711060358
GO:0016679oxidoreductase activity, acting on diphenols and related substances as donors0.0138616711060358
GO:0006081aldehyde metabolic process0.0149871073464189
GO:0006810transport0.0175507520279265
GO:0042775organelle ATP synthesis coupled electron transport0.0183974721949875
GO:0044425membrane part0.0185690319330983
GO:0051234establishment of localization0.0194144269875745
GO:0042773ATP synthesis coupled electron transport0.0203241207026174
GO:0006099tricarboxylic acid cycle0.0283744543440641
GO:0046356acetyl-CoA catabolic process0.0293074506563158
GO:0009060aerobic respiration0.03022462737763
GO:0051179localization0.0326273468132348
GO:0009109coenzyme catabolic process0.0331418405798954
GO:0045333cellular respiration0.0340040252329686
GO:0051187cofactor catabolic process0.0359605109405213
GO:0006084acetyl-CoA metabolic process0.0378832626877978
GO:0016787hydrolase activity0.040075716893728



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
primary circulatory organ3.84e-0918
heart3.84e-0918
primitive heart tube3.84e-0918
primary heart field3.84e-0918
anterior lateral plate mesoderm3.84e-0918
heart tube3.84e-0918
heart primordium3.84e-0918
cardiac mesoderm3.84e-0918
cardiogenic plate3.84e-0918
heart rudiment3.84e-0918
compound organ3.86e-0843
mucosa5.00e-0815
intestine2.34e-0731
intestinal mucosa4.35e-0713
anatomical wall4.35e-0713
wall of intestine4.35e-0713
gastrointestinal system mucosa4.35e-0713
cardiovascular system6.25e-0723
circulatory system6.25e-0723


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)
MA0003.10.677571
MA0004.10.0858689
MA0006.11.56211
MA0007.10.079003
MA0009.10.377631
MA0014.12.88405
MA0017.10.309289
MA0019.10.238713
MA0024.10.90728
MA0025.10.57681
MA0027.11.94532
MA0028.15.14174
MA0029.10.325591
MA0030.10.330711
MA0031.10.303242
MA0038.10.164914
MA0040.10.387805
MA0041.11.17584
MA0042.10.0492946
MA0043.10.457929
MA0046.10.407017
MA0048.10.275931
MA0050.10.341753
MA0051.10.508508
MA0052.10.394392
MA0055.10.151382
MA0056.10
MA0057.10.0247426
MA0058.10.0469235
MA0059.10.0512607
MA0060.10.283235
MA0061.10.180685
MA0063.10
MA0066.10.47816
MA0067.10.677115
MA0068.10.00730072
MA0069.10.39467
MA0070.10.386747
MA0071.10.694637
MA0072.10.379853
MA0073.11.88906e-05
MA0074.10.136938
MA0076.14.23721
MA0077.10.36238
MA0078.10.559895
MA0081.10.473128
MA0083.10.457256
MA0084.10.985399
MA0087.10.421024
MA0088.14.46117
MA0089.10
MA0090.10.247654
MA0091.10.092107
MA0092.10.248035
MA0093.10.0301253
MA0095.10
MA0098.10
MA0100.10.130363
MA0101.10.443304
MA0103.10.329394
MA0105.10.253333
MA0106.10.196768
MA0107.10.135394
MA0108.20.255046
MA0109.10
MA0111.10.560888
MA0113.10.527946
MA0114.10.177231
MA0115.10.460306
MA0116.11.1449
MA0117.10.433078
MA0119.10.201463
MA0122.10.449781
MA0124.10.628716
MA0125.10.562419
MA0130.10
MA0131.10.663769
MA0132.10
MA0133.10
MA0135.10.489063
MA0136.10.148556
MA0139.10.599004
MA0140.10.130298
MA0141.13.06922
MA0142.10.292245
MA0143.10.188991
MA0144.11.24405
MA0145.10.144964
MA0146.10.462627
MA0147.10.200453
MA0148.10.0936023
MA0149.10.0566148
MA0062.23.2503
MA0035.20.132954
MA0039.20.585693
MA0138.20.650745
MA0002.20.390259
MA0137.22.45742
MA0104.20.437378
MA0047.20.493658
MA0112.20.375285
MA0065.20.145939
MA0150.10.0789524
MA0151.10
MA0152.10.493821
MA0153.10.503426
MA0154.10.268349
MA0155.10.0168571
MA0156.10.148468
MA0157.10.26838
MA0158.10
MA0159.10.216399
MA0160.11.08345
MA0161.10
MA0162.10.0280361
MA0163.10.193343
MA0164.10.890114
MA0080.20.319523
MA0018.21.46511
MA0099.20.22555
MA0079.22.43739e-06
MA0102.21.03585
MA0258.10.157835
MA0259.11.25397
MA0442.10
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