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MCL coexpression mm9:810: Difference between revisions

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{{MCL_coexpression_mm9
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9808427,0.219476212112823,0.103395905192437,0.092873634605593,0.157166310227119,0.126206209899815,0.24141783307254,0.185112080268618,0.231644697860684,0.168343188417401,0.193442483447008,0.136847230919046,0.10266111479673,0.148982201447044,0.165781451382873,0.198305064902181,0,0.228697077840199,0.434404165395524,0,0.0449471343074757,0|gostat_on_MCL_coexpression=GO:0006732;coenzyme metabolic process;0.00158271079552393;171282,14854,29807!GO:0051186;cofactor metabolic process;0.00158271079552393;171282,14854,29807!GO:0003707;steroid hormone receptor activity;0.00385919243044701;19885,15378!GO:0004879;ligand-dependent nuclear receptor activity;0.00385919243044701;19885,15378!GO:0009108;coenzyme biosynthetic process;0.00457210022760891;14854,29807!GO:0042357;thiamin diphosphate metabolic process;0.00457210022760891;29807!GO:0004363;glutathione synthase activity;0.00457210022760891;14854!GO:0009229;thiamin diphosphate biosynthetic process;0.00457210022760891;29807!GO:0004371;glycerone kinase activity;0.00457210022760891;225913!GO:0042724;thiamin and derivative biosynthetic process;0.00457210022760891;29807!GO:0004788;thiamin diphosphokinase activity;0.00457210022760891;29807!GO:0051188;cofactor biosynthetic process;0.00516392620901728;14854,29807!GO:0006772;thiamin metabolic process;0.00670482850567052;29807!GO:0048537;mucosal-associated lymphoid tissue development;0.00670482850567052;19885!GO:0042723;thiamin and derivative metabolic process;0.00670482850567052;29807!GO:0006104;succinyl-CoA metabolic process;0.00887282225080137;171282!GO:0046459;short-chain fatty acid metabolic process;0.00887282225080137;171282!GO:0044237;cellular metabolic process;0.012659751575851;171282,14854,19885,15378,29807,225913!GO:0006750;glutathione biosynthetic process;0.0158711586352915;14854!GO:0016778;diphosphotransferase activity;0.0175881248661717;29807!GO:0043648;dicarboxylic acid metabolic process;0.0215305804242013;171282!GO:0016290;palmitoyl-CoA hydrolase activity;0.0251121303351356;171282!GO:0006637;acyl-CoA metabolic process;0.0271973565350132;171282!GO:0016291;acyl-CoA thioesterase activity;0.0271973565350132;171282!GO:0016439;tRNA-pseudouridine synthase activity;0.0280890825215545;15378!GO:0006100;tricarboxylic acid cycle intermediate metabolic process;0.0280890825215545;171282!GO:0016289;CoA hydrolase activity;0.0280890825215545;171282!GO:0005524;ATP binding;0.0280890825215545;14854,29807,225913!GO:0032559;adenyl ribonucleotide binding;0.0280890825215545;14854,29807,225913!GO:0048535;lymph node development;0.0280890825215545;19885!GO:0009982;pseudouridine synthase activity;0.0280890825215545;15378!GO:0006071;glycerol metabolic process;0.0280890825215545;225913!GO:0006749;glutathione metabolic process;0.0280890825215545;14854!GO:0030554;adenyl nucleotide binding;0.0280890825215545;14854,29807,225913!GO:0019751;polyol metabolic process;0.0286642222772942;225913!GO:0046632;alpha-beta T cell differentiation;0.0292573863030531;19885!GO:0043565;sequence-specific DNA binding;0.0319626946343949;19885,15378!GO:0033077;T cell differentiation in the thymus;0.0329789809096057;19885!GO:0016866;intramolecular transferase activity;0.0361091449643436;15378!GO:0044272;sulfur compound biosynthetic process;0.0361091449643436;14854!GO:0032553;ribonucleotide binding;0.0361091449643436;14854,29807,225913!GO:0032555;purine ribonucleotide binding;0.0361091449643436;14854,29807,225913!GO:0046631;alpha-beta T cell activation;0.0361091449643436;19885!GO:0017076;purine nucleotide binding;0.039258165142745;14854,29807,225913!GO:0006767;water-soluble vitamin metabolic process;0.0433610996112219;29807!GO:0006629;lipid metabolic process;0.0464976064349754;171282,15378!GO:0005496;steroid 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|gostat_on_MCL_coexpression=GO:0006732;coenzyme metabolic process;0.00158271079552393;171282,14854,29807!GO:0051186;cofactor metabolic process;0.00158271079552393;171282,14854,29807!GO:0003707;steroid hormone receptor activity;0.00385919243044701;19885,15378!GO:0004879;ligand-dependent nuclear receptor activity;0.00385919243044701;19885,15378!GO:0009108;coenzyme biosynthetic process;0.00457210022760891;14854,29807!GO:0042357;thiamin diphosphate metabolic process;0.00457210022760891;29807!GO:0004363;glutathione synthase activity;0.00457210022760891;14854!GO:0009229;thiamin diphosphate biosynthetic process;0.00457210022760891;29807!GO:0004371;glycerone kinase activity;0.00457210022760891;225913!GO:0042724;thiamin and derivative biosynthetic process;0.00457210022760891;29807!GO:0004788;thiamin diphosphokinase activity;0.00457210022760891;29807!GO:0051188;cofactor biosynthetic process;0.00516392620901728;14854,29807!GO:0006772;thiamin metabolic process;0.00670482850567052;29807!GO:0048537;mucosal-associated lymphoid tissue development;0.00670482850567052;19885!GO:0042723;thiamin and derivative metabolic process;0.00670482850567052;29807!GO:0006104;succinyl-CoA metabolic process;0.00887282225080137;171282!GO:0046459;short-chain fatty acid metabolic process;0.00887282225080137;171282!GO:0044237;cellular metabolic process;0.012659751575851;171282,14854,19885,15378,29807,225913!GO:0006750;glutathione biosynthetic process;0.0158711586352915;14854!GO:0016778;diphosphotransferase activity;0.0175881248661717;29807!GO:0043648;dicarboxylic acid metabolic process;0.0215305804242013;171282!GO:0016290;palmitoyl-CoA hydrolase activity;0.0251121303351356;171282!GO:0006637;acyl-CoA metabolic process;0.0271973565350132;171282!GO:0016291;acyl-CoA thioesterase activity;0.0271973565350132;171282!GO:0016439;tRNA-pseudouridine synthase activity;0.0280890825215545;15378!GO:0006100;tricarboxylic acid cycle intermediate metabolic process;0.0280890825215545;171282!GO:0016289;CoA hydrolase activity;0.0280890825215545;171282!GO:0005524;ATP binding;0.0280890825215545;14854,29807,225913!GO:0032559;adenyl ribonucleotide binding;0.0280890825215545;14854,29807,225913!GO:0048535;lymph node development;0.0280890825215545;19885!GO:0009982;pseudouridine synthase activity;0.0280890825215545;15378!GO:0006071;glycerol metabolic process;0.0280890825215545;225913!GO:0006749;glutathione metabolic process;0.0280890825215545;14854!GO:0030554;adenyl nucleotide binding;0.0280890825215545;14854,29807,225913!GO:0019751;polyol metabolic process;0.0286642222772942;225913!GO:0046632;alpha-beta T cell differentiation;0.0292573863030531;19885!GO:0043565;sequence-specific DNA binding;0.0319626946343949;19885,15378!GO:0033077;T cell differentiation in the thymus;0.0329789809096057;19885!GO:0016866;intramolecular transferase activity;0.0361091449643436;15378!GO:0044272;sulfur compound biosynthetic process;0.0361091449643436;14854!GO:0032553;ribonucleotide binding;0.0361091449643436;14854,29807,225913!GO:0032555;purine ribonucleotide binding;0.0361091449643436;14854,29807,225913!GO:0046631;alpha-beta T cell activation;0.0361091449643436;19885!GO:0017076;purine nucleotide binding;0.039258165142745;14854,29807,225913!GO:0006767;water-soluble vitamin metabolic process;0.0433610996112219;29807!GO:0006629;lipid metabolic process;0.0464976064349754;171282,15378!GO:0005496;steroid binding;0.0499772616505179;15378!
}}

Latest revision as of 15:55, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:85379338..85379385,+p1@Acot4
Mm9::chr18:61879449..61879487,-p@chr18:61879449..61879487
-
Mm9::chr19:10678794..10678805,-p4@Dak
Mm9::chr2:155418444..155418506,-p1@Gss
Mm9::chr2:163367451..163367464,-p1@0610008F07Rik
Mm9::chr2:163372869..163372882,+p3@Hnf4a
Mm9::chr2:163372884..163372904,+p1@Hnf4a
Mm9::chr3:94176733..94176794,+p1@Rorc
Mm9::chr6:43616157..43616223,-p1@Tpk1


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:0006732coenzyme metabolic process0.00158271079552393
GO:0051186cofactor metabolic process0.00158271079552393
GO:0003707steroid hormone receptor activity0.00385919243044701
GO:0004879ligand-dependent nuclear receptor activity0.00385919243044701
GO:0009108coenzyme biosynthetic process0.00457210022760891
GO:0042357thiamin diphosphate metabolic process0.00457210022760891
GO:0004363glutathione synthase activity0.00457210022760891
GO:0009229thiamin diphosphate biosynthetic process0.00457210022760891
GO:0004371glycerone kinase activity0.00457210022760891
GO:0042724thiamin and derivative biosynthetic process0.00457210022760891
GO:0004788thiamin diphosphokinase activity0.00457210022760891
GO:0051188cofactor biosynthetic process0.00516392620901728
GO:0006772thiamin metabolic process0.00670482850567052
GO:0048537mucosal-associated lymphoid tissue development0.00670482850567052
GO:0042723thiamin and derivative metabolic process0.00670482850567052
GO:0006104succinyl-CoA metabolic process0.00887282225080137
GO:0046459short-chain fatty acid metabolic process0.00887282225080137
GO:0044237cellular metabolic process0.012659751575851
GO:0006750glutathione biosynthetic process0.0158711586352915
GO:0016778diphosphotransferase activity0.0175881248661717
GO:0043648dicarboxylic acid metabolic process0.0215305804242013
GO:0016290palmitoyl-CoA hydrolase activity0.0251121303351356
GO:0006637acyl-CoA metabolic process0.0271973565350132
GO:0016291acyl-CoA thioesterase activity0.0271973565350132
GO:0016439tRNA-pseudouridine synthase activity0.0280890825215545
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.0280890825215545
GO:0016289CoA hydrolase activity0.0280890825215545
GO:0005524ATP binding0.0280890825215545
GO:0032559adenyl ribonucleotide binding0.0280890825215545
GO:0048535lymph node development0.0280890825215545
GO:0009982pseudouridine synthase activity0.0280890825215545
GO:0006071glycerol metabolic process0.0280890825215545
GO:0006749glutathione metabolic process0.0280890825215545
GO:0030554adenyl nucleotide binding0.0280890825215545
GO:0019751polyol metabolic process0.0286642222772942
GO:0046632alpha-beta T cell differentiation0.0292573863030531
GO:0043565sequence-specific DNA binding0.0319626946343949
GO:0033077T cell differentiation in the thymus0.0329789809096057
GO:0016866intramolecular transferase activity0.0361091449643436
GO:0044272sulfur compound biosynthetic process0.0361091449643436
GO:0032553ribonucleotide binding0.0361091449643436
GO:0032555purine ribonucleotide binding0.0361091449643436
GO:0046631alpha-beta T cell activation0.0361091449643436
GO:0017076purine nucleotide binding0.039258165142745
GO:0006767water-soluble vitamin metabolic process0.0433610996112219
GO:0006629lipid metabolic process0.0464976064349754
GO:0005496steroid binding0.0499772616505179



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
intestinal epithelial cell7.14e-089
epithelial cell of alimentary canal7.14e-089
epithelial cell3.99e-0725

Uber Anatomy
Ontology termp-valuen
intestine1.10e-1931
gastrointestinal system1.88e-1747
digestive tract diverticulum1.91e-1523
sac1.91e-1523
endoderm-derived structure3.23e-15118
endoderm3.23e-15118
presumptive endoderm3.23e-15118
liver6.08e-1522
epithelial sac6.08e-1522
digestive gland6.08e-1522
epithelium of foregut-midgut junction6.08e-1522
anatomical boundary6.08e-1522
hepatobiliary system6.08e-1522
foregut-midgut junction6.08e-1522
hepatic diverticulum6.08e-1522
liver primordium6.08e-1522
septum transversum6.08e-1522
liver bud6.08e-1522
digestive system1.02e-14116
digestive tract1.02e-14116
primitive gut1.02e-14116
subdivision of digestive tract1.20e-13114
exocrine gland6.13e-1325
exocrine system6.13e-1325
abdomen element4.66e-1249
abdominal segment element4.66e-1249
abdominal segment of trunk4.66e-1249
abdomen4.66e-1249
mucosa5.39e-1215
intestinal mucosa9.85e-1113
anatomical wall9.85e-1113
wall of intestine9.85e-1113
gastrointestinal system mucosa9.85e-1113
epithelium of mucosa7.14e-089
gastrointestinal system epithelium7.14e-089
intestinal epithelium7.14e-089
mesenchyme8.03e-0861
entire embryonic mesenchyme8.03e-0861
organ component layer9.82e-0824
subdivision of trunk1.28e-0766
gut epithelium4.68e-0755


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)
MA0003.10.170768
MA0004.10.394951
MA0006.10.238555
MA0007.10.991467
MA0009.10.82278
MA0014.10.433479
MA0017.10.726051
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.11.5585
MA0042.11.51496
MA0043.10.918718
MA0046.11.99676
MA0048.10.589612
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.692644
MA0056.10
MA0057.10.258928
MA0058.10.823526
MA0059.11.53319
MA0060.10.169058
MA0061.10.194456
MA0063.10
MA0066.11.29967
MA0067.11.16502
MA0068.10.954794
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.662187
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.897217
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.11.5772
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.95209
MA0093.10.709711
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.11.37229
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.12.71067
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.442138
MA0146.10.148686
MA0147.10.593505
MA0148.10.410398
MA0149.10.330018
MA0062.20.113962
MA0035.20.482026
MA0039.21.08337
MA0138.20.630612
MA0002.20.447007
MA0137.20.287486
MA0104.20.926067
MA0047.20.533516
MA0112.20.0543294
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.581988
MA0155.10.0631765
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.614411
MA0160.10.413266
MA0161.10
MA0162.10.0672805
MA0163.11.95739
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.23.31089
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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