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MCL coexpression mm9:1749: Difference between revisions

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{{MCL_coexpression_mm9
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complex;0.00793838039950046;71954!GO:0051882;mitochondrial depolarization;0.00793838039950046;14629!GO:0051900;regulation of mitochondrial depolarization;0.00793838039950046;14629!GO:0017109;glutamate-cysteine ligase complex;0.00793838039950046;14629!GO:0004357;glutamate-cysteine ligase activity;0.00793838039950046;14629!GO:0031400;negative regulation of protein modification process;0.00793838039950046;14629!GO:0031397;negative regulation of protein ubiquitination;0.00793838039950046;14629!GO:0032436;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;0.00793838039950046;14629!GO:0045732;positive regulation of protein catabolic process;0.00793838039950046;14629!GO:0046685;response to arsenic;0.00793838039950046;14629!GO:0019852;L-ascorbic acid metabolic process;0.00793838039950046;14629!GO:0051881;regulation of mitochondrial membrane potential;0.00793838039950046;14629!GO:0032434;regulation of proteasomal ubiquitin-dependent protein catabolic process;0.00793838039950046;14629!GO:0042826;histone deacetylase binding;0.00917248567671488;71954!GO:0009896;positive regulation of catabolic process;0.00917248567671488;14629!GO:0031396;regulation of protein ubiquitination;0.0107481232450235;14629!GO:0031399;regulation of protein modification process;0.0114637225623367;14629!GO:0006750;glutathione biosynthetic process;0.0114637225623367;14629!GO:0042176;regulation of protein catabolic process;0.0199024952786521;14629!GO:0010035;response to inorganic substance;0.0203103648031622;14629!GO:0043161;proteasomal ubiquitin-dependent protein catabolic process;0.0203103648031622;14629!GO:0009894;regulation of catabolic process;0.0203103648031622;14629!GO:0009410;response to xenobiotic stimulus;0.0209199939838632;14629!GO:0051899;membrane depolarization;0.0243383954177021;14629!GO:0006749;glutathione metabolic process;0.026109373956511;14629!GO:0000118;histone deacetylase complex;0.0290619734447417;71954!GO:0005769;early 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|gostat_on_MCL_coexpression=GO:0016580;Sin3 complex;0.00793838039950046;71954!GO:0051882;mitochondrial depolarization;0.00793838039950046;14629!GO:0051900;regulation of mitochondrial depolarization;0.00793838039950046;14629!GO:0017109;glutamate-cysteine ligase complex;0.00793838039950046;14629!GO:0004357;glutamate-cysteine ligase activity;0.00793838039950046;14629!GO:0031400;negative regulation of protein modification process;0.00793838039950046;14629!GO:0031397;negative regulation of protein ubiquitination;0.00793838039950046;14629!GO:0032436;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;0.00793838039950046;14629!GO:0045732;positive regulation of protein catabolic process;0.00793838039950046;14629!GO:0046685;response to arsenic;0.00793838039950046;14629!GO:0019852;L-ascorbic acid metabolic process;0.00793838039950046;14629!GO:0051881;regulation of mitochondrial membrane potential;0.00793838039950046;14629!GO:0032434;regulation of proteasomal ubiquitin-dependent protein catabolic process;0.00793838039950046;14629!GO:0042826;histone deacetylase binding;0.00917248567671488;71954!GO:0009896;positive regulation of catabolic process;0.00917248567671488;14629!GO:0031396;regulation of protein ubiquitination;0.0107481232450235;14629!GO:0031399;regulation of protein modification process;0.0114637225623367;14629!GO:0006750;glutathione biosynthetic process;0.0114637225623367;14629!GO:0042176;regulation of protein catabolic process;0.0199024952786521;14629!GO:0010035;response to inorganic substance;0.0203103648031622;14629!GO:0043161;proteasomal ubiquitin-dependent protein catabolic process;0.0203103648031622;14629!GO:0009894;regulation of catabolic process;0.0203103648031622;14629!GO:0009410;response to xenobiotic stimulus;0.0209199939838632;14629!GO:0051899;membrane depolarization;0.0243383954177021;14629!GO:0006749;glutathione metabolic process;0.026109373956511;14629!GO:0000118;histone deacetylase complex;0.0290619734447417;71954!GO:0005769;early endosome;0.0292552720323949;22320!GO:0044272;sulfur compound biosynthetic process;0.0355521467343833;14629!GO:0016567;protein ubiquitination;0.0445874032465923;14629!GO:0006767;water-soluble vitamin metabolic process;0.0445874032465923;14629!GO:0042391;regulation of membrane potential;0.0464568016525159;14629!GO:0032446;protein modification by small protein conjugation;0.0482077793142717;14629!
|ontology_enrichment_celltype=CL:0000066!9.04e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004119!3.20e-16!118;UBERON:0000925!3.20e-16!118;UBERON:0006595!3.20e-16!118;UBERON:0005177!3.62e-16!79;UBERON:0001007!1.29e-15!116;UBERON:0001555!1.29e-15!116;UBERON:0007026!1.29e-15!116;UBERON:0009569!2.16e-15!66;UBERON:0002100!7.63e-15!90;UBERON:0004921!1.54e-14!114;UBERON:0005172!4.54e-12!49;UBERON:0005173!4.54e-12!49;UBERON:0002417!4.54e-12!49;UBERON:0000916!4.54e-12!49;UBERON:0002365!1.20e-11!25;UBERON:0002330!1.20e-11!25;UBERON:0000466!1.25e-11!79;UBERON:0009854!4.31e-11!23;UBERON:0009856!4.31e-11!23;UBERON:0002107!8.29e-11!22;UBERON:0007499!8.29e-11!22;UBERON:0006925!8.29e-11!22;UBERON:0009497!8.29e-11!22;UBERON:0000015!8.29e-11!22;UBERON:0002423!8.29e-11!22;UBERON:0006235!8.29e-11!22;UBERON:0008835!8.29e-11!22;UBERON:0003894!8.29e-11!22;UBERON:0004161!8.29e-11!22;UBERON:0008836!8.29e-11!22;UBERON:0004923!1.00e-09!24;UBERON:0000160!4.04e-09!31;UBERON:0000344!4.92e-09!15;UBERON:0005409!5.14e-09!47;UBERON:0003104!1.09e-08!61;UBERON:0009142!1.09e-08!61;UBERON:0005256!2.29e-08!45;UBERON:0005911!3.51e-08!69;UBERON:0001242!7.87e-08!13;UBERON:0000060!7.87e-08!13;UBERON:0001262!7.87e-08!13;UBERON:0004786!7.87e-08!13
}}

Latest revision as of 17:26, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:186706870..186706910,-p1@C130074G19Rik
Mm9::chr5:117566094..117566106,-p5@Suds3
Mm9::chr6:72340615..72340633,-p2@Vamp8
Mm9::chr7:134614869..134614882,+p6@Prr14
Mm9::chr9:77602333..77602348,+p1@Gclc


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:0016580Sin3 complex0.00793838039950046
GO:0051882mitochondrial depolarization0.00793838039950046
GO:0051900regulation of mitochondrial depolarization0.00793838039950046
GO:0017109glutamate-cysteine ligase complex0.00793838039950046
GO:0004357glutamate-cysteine ligase activity0.00793838039950046
GO:0031400negative regulation of protein modification process0.00793838039950046
GO:0031397negative regulation of protein ubiquitination0.00793838039950046
GO:0032436positive regulation of proteasomal ubiquitin-dependent protein catabolic process0.00793838039950046
GO:0045732positive regulation of protein catabolic process0.00793838039950046
GO:0046685response to arsenic0.00793838039950046
GO:0019852L-ascorbic acid metabolic process0.00793838039950046
GO:0051881regulation of mitochondrial membrane potential0.00793838039950046
GO:0032434regulation of proteasomal ubiquitin-dependent protein catabolic process0.00793838039950046
GO:0042826histone deacetylase binding0.00917248567671488
GO:0009896positive regulation of catabolic process0.00917248567671488
GO:0031396regulation of protein ubiquitination0.0107481232450235
GO:0031399regulation of protein modification process0.0114637225623367
GO:0006750glutathione biosynthetic process0.0114637225623367
GO:0042176regulation of protein catabolic process0.0199024952786521
GO:0010035response to inorganic substance0.0203103648031622
GO:0043161proteasomal ubiquitin-dependent protein catabolic process0.0203103648031622
GO:0009894regulation of catabolic process0.0203103648031622
GO:0009410response to xenobiotic stimulus0.0209199939838632
GO:0051899membrane depolarization0.0243383954177021
GO:0006749glutathione metabolic process0.026109373956511
GO:0000118histone deacetylase complex0.0290619734447417
GO:0005769early endosome0.0292552720323949
GO:0044272sulfur compound biosynthetic process0.0355521467343833
GO:0016567protein ubiquitination0.0445874032465923
GO:0006767water-soluble vitamin metabolic process0.0445874032465923
GO:0042391regulation of membrane potential0.0464568016525159
GO:0032446protein modification by small protein conjugation0.0482077793142717



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
epithelial cell9.04e-0725

Uber Anatomy
Ontology termp-valuen
endoderm-derived structure3.20e-16118
endoderm3.20e-16118
presumptive endoderm3.20e-16118
trunk region element3.62e-1679
digestive system1.29e-15116
digestive tract1.29e-15116
primitive gut1.29e-15116
subdivision of trunk2.16e-1566
trunk7.63e-1590
subdivision of digestive tract1.54e-14114
abdomen element4.54e-1249
abdominal segment element4.54e-1249
abdominal segment of trunk4.54e-1249
abdomen4.54e-1249
exocrine gland1.20e-1125
exocrine system1.20e-1125
immaterial anatomical entity1.25e-1179
digestive tract diverticulum4.31e-1123
sac4.31e-1123
liver8.29e-1122
epithelial sac8.29e-1122
digestive gland8.29e-1122
epithelium of foregut-midgut junction8.29e-1122
anatomical boundary8.29e-1122
hepatobiliary system8.29e-1122
foregut-midgut junction8.29e-1122
hepatic diverticulum8.29e-1122
liver primordium8.29e-1122
septum transversum8.29e-1122
liver bud8.29e-1122
organ component layer1.00e-0924
intestine4.04e-0931
mucosa4.92e-0915
gastrointestinal system5.14e-0947
mesenchyme1.09e-0861
entire embryonic mesenchyme1.09e-0861
trunk mesenchyme2.29e-0845
endo-epithelium3.51e-0869
intestinal mucosa7.87e-0813
anatomical wall7.87e-0813
wall of intestine7.87e-0813
gastrointestinal system mucosa7.87e-0813


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)
MA0003.10.6678
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.736185
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.0851423
MA0056.10
MA0057.11.68574
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.11.74609
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.148348
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.949408
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.11.45902
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.476962
MA0146.10.822925
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.21.30506
MA0035.20.700704
MA0039.22.26967
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.929207
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.11.11105
MA0155.10.515751
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.11.35147
MA0163.10.497328
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.24.18591
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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