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MCL coexpression mm9:2112: Difference between revisions

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{{MCL_coexpression_mm9
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proton-transporting ATP synthase complex;0.0335122051150373;11949!GO:0001758;retinal dehydrogenase activity;0.0335122051150373;28200!GO:0004090;carbonyl reductase (NADPH) activity;0.0335122051150373;28200!GO:0043288;apocarotenoid metabolic process;0.0335122051150373;28200!GO:0042574;retinal metabolic process;0.0335122051150373;28200!GO:0045261;proton-transporting ATP synthase complex, catalytic core F(1);0.0335122051150373;11949!GO:0033178;proton-transporting two-sector ATPase complex, catalytic domain;0.0335122051150373;11949!GO:0016101;diterpenoid metabolic process;0.043528192063967;28200!GO:0001523;retinoid metabolic process;0.043528192063967;28200!GO:0006721;terpenoid metabolic process;0.043528192063967;28200!GO:0006776;vitamin A metabolic process;0.043528192063967;28200!GO:0045259;proton-transporting ATP synthase complex;0.043528192063967;11949!GO:0006775;fat-soluble vitamin metabolic process;0.043528192063967;28200!GO:0006720;isoprenoid metabolic process;0.043528192063967;28200!GO:0016620;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor;0.043528192063967;28200!GO:0015075;ion transmembrane transporter activity;0.043528192063967;53871,11949!GO:0015985;energy coupled proton transport, down electrochemical gradient;0.043528192063967;11949!GO:0015986;ATP synthesis coupled proton transport;0.043528192063967;11949!GO:0006754;ATP biosynthetic process;0.043528192063967;11949!GO:0006753;nucleoside phosphate metabolic process;0.043528192063967;11949!GO:0046933;hydrogen ion transporting ATP synthase activity, rotational mechanism;0.043528192063967;11949!GO:0016469;proton-transporting two-sector ATPase complex;0.043528192063967;11949!GO:0046961;hydrogen ion transporting ATPase activity, rotational mechanism;0.043528192063967;11949!GO:0006811;ion transport;0.043528192063967;53871,11949!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.043528192063967;28200!GO:0022891;substrate-specific transmembrane transporter activity;0.043528192063967;53871,11949!GO:0046034;ATP metabolic process;0.043528192063967;11949!GO:0019748;secondary metabolic process;0.043528192063967;28200!GO:0044455;mitochondrial membrane part;0.043528192063967;11949!GO:0009145;purine nucleoside triphosphate biosynthetic process;0.043528192063967;11949!GO:0009206;purine ribonucleoside triphosphate biosynthetic process;0.043528192063967;11949!GO:0009201;ribonucleoside triphosphate biosynthetic process;0.043528192063967;11949!GO:0019829;cation-transporting ATPase activity;0.043528192063967;11949!GO:0009142;nucleoside triphosphate biosynthetic process;0.043528192063967;11949!GO:0009205;purine ribonucleoside triphosphate metabolic process;0.043528192063967;11949!GO:0009199;ribonucleoside triphosphate metabolic process;0.043528192063967;11949!GO:0006119;oxidative phosphorylation;0.043528192063967;11949!GO:0009144;purine nucleoside triphosphate 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|gostat_on_MCL_coexpression=GO:0005753;mitochondrial proton-transporting ATP synthase complex;0.0335122051150373;11949!GO:0001758;retinal dehydrogenase activity;0.0335122051150373;28200!GO:0004090;carbonyl reductase (NADPH) activity;0.0335122051150373;28200!GO:0043288;apocarotenoid metabolic process;0.0335122051150373;28200!GO:0042574;retinal metabolic process;0.0335122051150373;28200!GO:0045261;proton-transporting ATP synthase complex, catalytic core F(1);0.0335122051150373;11949!GO:0033178;proton-transporting two-sector ATPase complex, catalytic domain;0.0335122051150373;11949!GO:0016101;diterpenoid metabolic process;0.043528192063967;28200!GO:0001523;retinoid metabolic process;0.043528192063967;28200!GO:0006721;terpenoid metabolic process;0.043528192063967;28200!GO:0006776;vitamin A metabolic process;0.043528192063967;28200!GO:0045259;proton-transporting ATP synthase complex;0.043528192063967;11949!GO:0006775;fat-soluble vitamin metabolic process;0.043528192063967;28200!GO:0006720;isoprenoid metabolic process;0.043528192063967;28200!GO:0016620;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor;0.043528192063967;28200!GO:0015075;ion transmembrane transporter activity;0.043528192063967;53871,11949!GO:0015985;energy coupled proton transport, down electrochemical gradient;0.043528192063967;11949!GO:0015986;ATP synthesis coupled proton transport;0.043528192063967;11949!GO:0006754;ATP biosynthetic process;0.043528192063967;11949!GO:0006753;nucleoside phosphate metabolic process;0.043528192063967;11949!GO:0046933;hydrogen ion transporting ATP synthase activity, rotational mechanism;0.043528192063967;11949!GO:0016469;proton-transporting two-sector ATPase complex;0.043528192063967;11949!GO:0046961;hydrogen ion transporting ATPase activity, rotational mechanism;0.043528192063967;11949!GO:0006811;ion transport;0.043528192063967;53871,11949!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.043528192063967;28200!GO:0022891;substrate-specific transmembrane transporter activity;0.043528192063967;53871,11949!GO:0046034;ATP metabolic process;0.043528192063967;11949!GO:0019748;secondary metabolic process;0.043528192063967;28200!GO:0044455;mitochondrial membrane part;0.043528192063967;11949!GO:0009145;purine nucleoside triphosphate biosynthetic process;0.043528192063967;11949!GO:0009206;purine ribonucleoside triphosphate biosynthetic process;0.043528192063967;11949!GO:0009201;ribonucleoside triphosphate biosynthetic process;0.043528192063967;11949!GO:0019829;cation-transporting ATPase activity;0.043528192063967;11949!GO:0009142;nucleoside triphosphate biosynthetic process;0.043528192063967;11949!GO:0009205;purine ribonucleoside triphosphate metabolic process;0.043528192063967;11949!GO:0009199;ribonucleoside triphosphate metabolic process;0.043528192063967;11949!GO:0006119;oxidative phosphorylation;0.043528192063967;11949!GO:0009144;purine nucleoside triphosphate metabolic process;0.043528192063967;11949!GO:0015992;proton transport;0.043528192063967;11949!GO:0022857;transmembrane transporter activity;0.043528192063967;53871,11949!GO:0006752;group transfer coenzyme metabolic process;0.043528192063967;11949!GO:0009141;nucleoside triphosphate metabolic process;0.043528192063967;11949!GO:0009152;purine ribonucleotide biosynthetic process;0.043528192063967;11949!GO:0006818;hydrogen transport;0.043528192063967;11949!GO:0009260;ribonucleotide biosynthetic process;0.043528192063967;11949!GO:0006766;vitamin metabolic process;0.043528192063967;28200!GO:0022892;substrate-specific transporter activity;0.043528192063967;53871,11949!GO:0009150;purine ribonucleotide metabolic process;0.043528192063967;11949!GO:0006164;purine nucleotide biosynthetic process;0.043528192063967;11949!GO:0005739;mitochondrion;0.043528192063967;28200,11949!GO:0009259;ribonucleotide metabolic process;0.0457595193689358;11949!GO:0006163;purine nucleotide metabolic process;0.0474284687075218;11949!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!3.93e-07!47;UBERON:0007100!5.97e-07!18;UBERON:0000948!5.97e-07!18;UBERON:0005498!5.97e-07!18;UBERON:0004140!5.97e-07!18;UBERON:0009881!5.97e-07!18;UBERON:0004141!5.97e-07!18;UBERON:0003084!5.97e-07!18;UBERON:0007005!5.97e-07!18;UBERON:0004139!5.97e-07!18;UBERON:0004291!5.97e-07!18
}}

Latest revision as of 18:01, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:56097590..56097604,+p3@Dhrs4
Mm9::chr18:34569069..34569112,+p1@Pkd2l2
Mm9::chr2:10001781..10001793,-p3@Atp5c1
Mm9::chr2:102913921..102913945,+p2@Apip


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:0005753mitochondrial proton-transporting ATP synthase complex0.0335122051150373
GO:0001758retinal dehydrogenase activity0.0335122051150373
GO:0004090carbonyl reductase (NADPH) activity0.0335122051150373
GO:0043288apocarotenoid metabolic process0.0335122051150373
GO:0042574retinal metabolic process0.0335122051150373
GO:0045261proton-transporting ATP synthase complex, catalytic core F(1)0.0335122051150373
GO:0033178proton-transporting two-sector ATPase complex, catalytic domain0.0335122051150373
GO:0016101diterpenoid metabolic process0.043528192063967
GO:0001523retinoid metabolic process0.043528192063967
GO:0006721terpenoid metabolic process0.043528192063967
GO:0006776vitamin A metabolic process0.043528192063967
GO:0045259proton-transporting ATP synthase complex0.043528192063967
GO:0006775fat-soluble vitamin metabolic process0.043528192063967
GO:0006720isoprenoid metabolic process0.043528192063967
GO:0016620oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor0.043528192063967
GO:0015075ion transmembrane transporter activity0.043528192063967
GO:0015985energy coupled proton transport, down electrochemical gradient0.043528192063967
GO:0015986ATP synthesis coupled proton transport0.043528192063967
GO:0006754ATP biosynthetic process0.043528192063967
GO:0006753nucleoside phosphate metabolic process0.043528192063967
GO:0046933hydrogen ion transporting ATP synthase activity, rotational mechanism0.043528192063967
GO:0016469proton-transporting two-sector ATPase complex0.043528192063967
GO:0046961hydrogen ion transporting ATPase activity, rotational mechanism0.043528192063967
GO:0006811ion transport0.043528192063967
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.043528192063967
GO:0022891substrate-specific transmembrane transporter activity0.043528192063967
GO:0046034ATP metabolic process0.043528192063967
GO:0019748secondary metabolic process0.043528192063967
GO:0044455mitochondrial membrane part0.043528192063967
GO:0009145purine nucleoside triphosphate biosynthetic process0.043528192063967
GO:0009206purine ribonucleoside triphosphate biosynthetic process0.043528192063967
GO:0009201ribonucleoside triphosphate biosynthetic process0.043528192063967
GO:0019829cation-transporting ATPase activity0.043528192063967
GO:0009142nucleoside triphosphate biosynthetic process0.043528192063967
GO:0009205purine ribonucleoside triphosphate metabolic process0.043528192063967
GO:0009199ribonucleoside triphosphate metabolic process0.043528192063967
GO:0006119oxidative phosphorylation0.043528192063967
GO:0009144purine nucleoside triphosphate metabolic process0.043528192063967
GO:0015992proton transport0.043528192063967
GO:0022857transmembrane transporter activity0.043528192063967
GO:0006752group transfer coenzyme metabolic process0.043528192063967
GO:0009141nucleoside triphosphate metabolic process0.043528192063967
GO:0009152purine ribonucleotide biosynthetic process0.043528192063967
GO:0006818hydrogen transport0.043528192063967
GO:0009260ribonucleotide biosynthetic process0.043528192063967
GO:0006766vitamin metabolic process0.043528192063967
GO:0022892substrate-specific transporter activity0.043528192063967
GO:0009150purine ribonucleotide metabolic process0.043528192063967
GO:0006164purine nucleotide biosynthetic process0.043528192063967
GO:0005739mitochondrion0.043528192063967
GO:0009259ribonucleotide metabolic process0.0457595193689358
GO:0006163purine nucleotide metabolic process0.0474284687075218



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
epithelial tube3.93e-0747
primary circulatory organ5.97e-0718
heart5.97e-0718
primitive heart tube5.97e-0718
primary heart field5.97e-0718
anterior lateral plate mesoderm5.97e-0718
heart tube5.97e-0718
heart primordium5.97e-0718
cardiac mesoderm5.97e-0718
cardiogenic plate5.97e-0718
heart rudiment5.97e-0718


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)
MA0003.10.600426
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.276754
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.11.35097
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.396346
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0140887
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.11.14526
MA0146.10.647546
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.238019
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.346529
MA0163.10.0996272
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.0553806
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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