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MCL coexpression mm9:947: Difference between revisions

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{{MCL_coexpression_mm9
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dehydrogenase activity;9.92756832831844e-09;66916,104130,67184,17991!GO:0008137;NADH dehydrogenase (ubiquinone) activity;9.92756832831844e-09;66916,104130,67184,17991!GO:0050136;NADH dehydrogenase (quinone) activity;9.92756832831844e-09;66916,104130,67184,17991!GO:0016655;oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor;9.92756832831844e-09;66916,104130,67184,17991!GO:0016651;oxidoreductase activity, acting on NADH or NADPH;2.69754622110827e-08;66916,104130,67184,17991!GO:0009055;electron carrier activity;4.22632194422487e-07;66916,104130,67184,17991!GO:0005739;mitochondrion;1.53363318564445e-05;66916,104130,67184,68499,17991!GO:0005743;mitochondrial inner membrane;0.000246676531560567;66916,67184,17991!GO:0016491;oxidoreductase activity;0.000246676531560567;66916,104130,67184,17991!GO:0019866;organelle inner membrane;0.000246676531560567;66916,67184,17991!GO:0031966;mitochondrial membrane;0.000253537101248045;66916,67184,17991!GO:0005740;mitochondrial envelope;0.000292830429940016;66916,67184,17991!GO:0044429;mitochondrial part;0.000441221674244483;66916,67184,17991!GO:0031975;envelope;0.000635323993806063;66916,67184,17991!GO:0031967;organelle envelope;0.000635323993806063;66916,67184,17991!GO:0031090;organelle membrane;0.00158077024502968;66916,67184,17991!GO:0044444;cytoplasmic part;0.00231874999342916;66916,104130,67184,68499,17991!GO:0045271;respiratory chain complex I;0.00666739374011737;17991!GO:0030964;NADH dehydrogenase complex (quinone);0.00666739374011737;17991!GO:0005747;mitochondrial respiratory chain complex I;0.00666739374011737;17991!GO:0005746;mitochondrial respiratory chain;0.0250280328214345;17991!GO:0005737;cytoplasm;0.0250280328214345;66916,104130,67184,68499,17991!GO:0044455;mitochondrial membrane part;0.0362587023427898;17991!GO:0043231;intracellular membrane-bound 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|gostat_on_MCL_coexpression=GO:0003954;NADH dehydrogenase activity;9.92756832831844e-09;66916,104130,67184,17991!GO:0008137;NADH dehydrogenase (ubiquinone) activity;9.92756832831844e-09;66916,104130,67184,17991!GO:0050136;NADH dehydrogenase (quinone) activity;9.92756832831844e-09;66916,104130,67184,17991!GO:0016655;oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor;9.92756832831844e-09;66916,104130,67184,17991!GO:0016651;oxidoreductase activity, acting on NADH or NADPH;2.69754622110827e-08;66916,104130,67184,17991!GO:0009055;electron carrier activity;4.22632194422487e-07;66916,104130,67184,17991!GO:0005739;mitochondrion;1.53363318564445e-05;66916,104130,67184,68499,17991!GO:0005743;mitochondrial inner membrane;0.000246676531560567;66916,67184,17991!GO:0016491;oxidoreductase activity;0.000246676531560567;66916,104130,67184,17991!GO:0019866;organelle inner membrane;0.000246676531560567;66916,67184,17991!GO:0031966;mitochondrial membrane;0.000253537101248045;66916,67184,17991!GO:0005740;mitochondrial envelope;0.000292830429940016;66916,67184,17991!GO:0044429;mitochondrial part;0.000441221674244483;66916,67184,17991!GO:0031975;envelope;0.000635323993806063;66916,67184,17991!GO:0031967;organelle envelope;0.000635323993806063;66916,67184,17991!GO:0031090;organelle membrane;0.00158077024502968;66916,67184,17991!GO:0044444;cytoplasmic part;0.00231874999342916;66916,104130,67184,68499,17991!GO:0045271;respiratory chain complex I;0.00666739374011737;17991!GO:0030964;NADH dehydrogenase complex (quinone);0.00666739374011737;17991!GO:0005747;mitochondrial respiratory chain complex I;0.00666739374011737;17991!GO:0005746;mitochondrial respiratory chain;0.0250280328214345;17991!GO:0005737;cytoplasm;0.0250280328214345;66916,104130,67184,68499,17991!GO:0044455;mitochondrial membrane part;0.0362587023427898;17991!GO:0043231;intracellular membrane-bound organelle;0.0454890527855033;66916,104130,67184,68499,17991!GO:0043227;membrane-bound organelle;0.0454890527855033;66916,104130,67184,68499,17991!
}}

Latest revision as of 16:09, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:54691582..54691628,+p1@Higd2a
Mm9::chr17:31657078..31657114,+p2@Ndufv3
Mm9::chr17:31657115..31657156,+p1@Ndufv3
Mm9::chr18:36904172..36904207,-p1@Ndufa2
Mm9::chr6:83059065..83059108,+p1@Mrpl53
Mm9::chr8:72425531..72425556,-p@chr8:72425531..72425556
-
Mm9::chr8:86090623..86090714,+p1@Ndufb7
Mm9::chrX:20194388..20194415,-p1@Ndufb11


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:0003954NADH dehydrogenase activity9.92756832831844e-09
GO:0008137NADH dehydrogenase (ubiquinone) activity9.92756832831844e-09
GO:0050136NADH dehydrogenase (quinone) activity9.92756832831844e-09
GO:0016655oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor9.92756832831844e-09
GO:0016651oxidoreductase activity, acting on NADH or NADPH2.69754622110827e-08
GO:0009055electron carrier activity4.22632194422487e-07
GO:0005739mitochondrion1.53363318564445e-05
GO:0005743mitochondrial inner membrane0.000246676531560567
GO:0016491oxidoreductase activity0.000246676531560567
GO:0019866organelle inner membrane0.000246676531560567
GO:0031966mitochondrial membrane0.000253537101248045
GO:0005740mitochondrial envelope0.000292830429940016
GO:0044429mitochondrial part0.000441221674244483
GO:0031975envelope0.000635323993806063
GO:0031967organelle envelope0.000635323993806063
GO:0031090organelle membrane0.00158077024502968
GO:0044444cytoplasmic part0.00231874999342916
GO:0045271respiratory chain complex I0.00666739374011737
GO:0030964NADH dehydrogenase complex (quinone)0.00666739374011737
GO:0005747mitochondrial respiratory chain complex I0.00666739374011737
GO:0005746mitochondrial respiratory chain0.0250280328214345
GO:0005737cytoplasm0.0250280328214345
GO:0044455mitochondrial membrane part0.0362587023427898
GO:0043231intracellular membrane-bound organelle0.0454890527855033
GO:0043227membrane-bound organelle0.0454890527855033



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
embryonic cell2.39e-0770

Uber Anatomy
Ontology termp-valuen
primary circulatory organ3.79e-0918
heart3.79e-0918
primitive heart tube3.79e-0918
primary heart field3.79e-0918
anterior lateral plate mesoderm3.79e-0918
heart tube3.79e-0918
heart primordium3.79e-0918
cardiac mesoderm3.79e-0918
cardiogenic plate3.79e-0918
heart rudiment3.79e-0918
cardiovascular system1.51e-0723
circulatory system1.51e-0723
epithelial tube3.02e-0747
compound organ6.26e-0743


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)
MA0003.10.127295
MA0004.10.434673
MA0006.10.747445
MA0007.11.07722
MA0009.10.870101
MA0014.10.548455
MA0017.10.296816
MA0019.10.688051
MA0024.10.826339
MA0025.11.10341
MA0027.12.51754
MA0028.12.15675
MA0029.10.804619
MA0030.10.811181
MA0031.10.775627
MA0038.10.577528
MA0040.10.882616
MA0041.10.360875
MA0042.10.348174
MA0043.10.966833
MA0046.10.906029
MA0048.10.335404
MA0050.10.472794
MA0051.10.586414
MA0052.10.890676
MA0055.10.117901
MA0056.10
MA0057.10.0935008
MA0058.10.341628
MA0059.10.353484
MA0060.11.08928
MA0061.10.224905
MA0063.10
MA0066.10.566617
MA0067.11.21448
MA0068.10.319589
MA0069.10.891016
MA0070.10.881319
MA0071.11.18945
MA0072.13.35076
MA0073.10.0449725
MA0074.10.531046
MA0076.11.52758
MA0077.10.851175
MA0078.10.61926
MA0081.10.375851
MA0083.10.96604
MA0084.11.54225
MA0087.10.922929
MA0088.10.853781
MA0089.10
MA0090.10.401197
MA0091.10.447561
MA0092.10.401504
MA0093.10.289361
MA0095.10
MA0098.10
MA0100.10.519598
MA0101.10.362124
MA0103.10.307078
MA0105.10.41549
MA0106.10.626997
MA0107.10.301222
MA0108.20.710846
MA0109.10
MA0111.11.06639
MA0113.10.598933
MA0114.10.222763
MA0115.10.969632
MA0116.10.747001
MA0117.10.937363
MA0119.10.362692
MA0122.10.957212
MA0124.11.16127
MA0125.11.0872
MA0130.10
MA0131.11.63575
MA0132.10
MA0133.10
MA0135.11.00325
MA0136.10.550755
MA0139.10.977634
MA0140.10.519484
MA0141.10.325895
MA0142.10.761136
MA0143.10.615203
MA0144.10.225588
MA0145.10.0701568
MA0146.10.946874
MA0147.10.236889
MA0148.10.450593
MA0149.10.367458
MA0062.22.64619
MA0035.20.524137
MA0039.20.812684
MA0138.20.675599
MA0002.20.172399
MA0137.20.32312
MA0104.20.18504
MA0047.20.576767
MA0112.21.87605
MA0065.20.528619
MA0150.10.419883
MA0151.10
MA0152.10.576873
MA0153.11.01988
MA0154.11.12269
MA0155.10.275377
MA0156.10.843735
MA0157.10.729116
MA0158.10
MA0159.10.688775
MA0160.11.14982
MA0161.10
MA0162.10.230918
MA0163.10.408151
MA0164.10.551114
MA0080.20.302064
MA0018.20.560731
MA0099.20.669311
MA0079.20.431684
MA0102.21.59466
MA0258.11.78339
MA0259.10.227035
MA0442.10
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