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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_mean=-0.

Latest revision as of 15:25, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:29032970..29033027,+p2@Echdc1
Mm9::chr12:85791894..85791968,-p1@Aldh6a1
Mm9::chr13:100785517..100785602,-p1@Mccc2
Mm9::chr14:122933527..122933589,+p1@Pcca
Mm9::chr14:17075823..17075858,-p1@Oxsm
Mm9::chr17:41071625..41071700,+p1@Mut
Mm9::chr17:59152687..59152766,-p1@Nudt12
Mm9::chr1:9538130..9538182,+p1@Adhfe1
Mm9::chr2:103325295..103325315,-p2@Cat
Mm9::chr3:116216012..116216062,+p1@Dbt
Mm9::chr6:13019879..13019895,+p2@Tmem106b
Mm9::chr6:52590297..52590380,-p1@Hibadh
Mm9::chr7:138554147..138554240,+p1@Acadsb
Mm9::chr9:100935276..100935286,-p1@Pccb


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:0005739mitochondrion6.27523475493706e-07
GO:0016421CoA carboxylase activity6.99466227946502e-07
GO:0016885ligase activity, forming carbon-carbon bonds8.15675020897826e-07
GO:0004658propionyl-CoA carboxylase activity2.66318474284288e-05
GO:0044444cytoplasmic part0.000348096818503853
GO:0019752carboxylic acid metabolic process0.000401318676234845
GO:0006082organic acid metabolic process0.000401318676234845
GO:0032787monocarboxylic acid metabolic process0.000401318676234845
GO:0050662coenzyme binding0.00187420164834863
GO:0006631fatty acid metabolic process0.00437035419185468
GO:0048037cofactor binding0.00458679476633284
GO:0006767water-soluble vitamin metabolic process0.00647224500148516
GO:0043754dihydrolipoyllysine-residue (2-methylpropanoyl)transferase activity0.00712211691228839
GO:0050093methanol dehydrogenase activity0.00712211691228839
GO:00084423-hydroxyisobutyrate dehydrogenase activity0.00712211691228839
GO:0006768biotin metabolic process0.00712211691228839
GO:0004494methylmalonyl-CoA mutase activity0.00712211691228839
GO:0016937short-branched-chain-acyl-CoA dehydrogenase activity0.00712211691228839
GO:0004491methylmalonate-semialdehyde dehydrogenase (acylating) activity0.00712211691228839
GO:0006573valine metabolic process0.00712211691228839
GO:0000210NAD+ diphosphatase activity0.00712211691228839
GO:0006766vitamin metabolic process0.00891888207802721
GO:0006633fatty acid biosynthetic process0.00996741276421327
GO:0005737cytoplasm0.00996741276421327
GO:0046394carboxylic acid biosynthetic process0.00996741276421327
GO:0016053organic acid biosynthetic process0.00996741276421327
GO:0009343biotin carboxylase complex0.00996741276421327
GO:0004485methylcrotonoyl-CoA carboxylase activity0.00996741276421327
GO:0009317acetyl-CoA carboxylase complex0.00996741276421327
GO:00043153-oxoacyl-[acyl-carrier-protein] synthase activity0.00996741276421327
GO:0016874ligase activity0.0108751984293086
GO:0016491oxidoreductase activity0.0128106815241885
GO:0004075biotin carboxylase activity0.0128106815241885
GO:0004616phosphogluconate dehydrogenase (decarboxylating) activity0.0128106815241885
GO:0003989acetyl-CoA carboxylase activity0.0128106815241885
GO:0019842vitamin binding0.0154437815892189
GO:0009374biotin binding0.0160294455529876
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0160294455529876
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0173664581883205
GO:0031406carboxylic acid binding0.0173664581883205
GO:0031419cobalamin binding0.0173664581883205
GO:0004312fatty-acid synthase activity0.0173664581883205
GO:0031405lipoic acid binding0.0173664581883205
GO:0009081branched chain family amino acid metabolic process0.0232159235755607
GO:0004551nucleotide diphosphatase activity0.0232159235755607
GO:0006098pentose-phosphate shunt0.0249314317801191
GO:0006740NADPH regeneration0.0249314317801191
GO:0044255cellular lipid metabolic process0.0249314317801191
GO:0008415acyltransferase activity0.0286860817617896
GO:0016747transferase activity, transferring groups other than amino-acyl groups0.0287585165101509
GO:0043231intracellular membrane-bound organelle0.028983523454345
GO:0043227membrane-bound organelle0.028983523454345
GO:0016746transferase activity, transferring acyl groups0.0293142905754877
GO:0050897cobalt ion binding0.0303585470970815
GO:0051186cofactor metabolic process0.0310630974510198
GO:0006629lipid metabolic process0.0314364698181849
GO:0006739NADP metabolic process0.0365655058362674
GO:0003995acyl-CoA dehydrogenase activity0.041039433488073
GO:0008610lipid biosynthetic process0.045193925620091



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 tube1.96e-1147
trunk region element5.93e-1179
exocrine gland9.27e-1025
exocrine system9.27e-1025
mesenchyme3.07e-0961
entire embryonic mesenchyme3.07e-0961
trunk4.49e-0990
abdomen element9.84e-0949
abdominal segment element9.84e-0949
abdominal segment of trunk9.84e-0949
abdomen9.84e-0949
digestive tract diverticulum1.99e-0823
sac1.99e-0823
liver2.21e-0822
epithelial sac2.21e-0822
digestive gland2.21e-0822
epithelium of foregut-midgut junction2.21e-0822
anatomical boundary2.21e-0822
hepatobiliary system2.21e-0822
foregut-midgut junction2.21e-0822
hepatic diverticulum2.21e-0822
liver primordium2.21e-0822
septum transversum2.21e-0822
liver bud2.21e-0822
multi-cellular organism2.88e-08333
anatomical conduit8.92e-08122
subdivision of trunk1.06e-0766
trunk mesenchyme1.58e-0745
tissue4.88e-07349


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)
MA0003.10.178528
MA0004.10.258473
MA0006.10.817804
MA0007.10.689082
MA0009.10.649874
MA0014.10.232005
MA0017.10.458117
MA0019.10.480432
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.11.97836
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.198922
MA0042.10.189008
MA0043.10.74191
MA0046.10.683926
MA0048.10.534002
MA0050.10.290354
MA0051.10.388883
MA0052.10.669354
MA0055.10.14835
MA0056.10
MA0057.10.489127
MA0058.10.183941
MA0059.10.19314
MA0060.15.59556
MA0061.10.0995825
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.112041
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.19.79163e-05
MA0074.10.340281
MA0076.11.51892
MA0077.10.632005
MA0078.10.418168
MA0081.10.210747
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.0649199
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.10.231323
MA0093.10.144649
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.10.199903
MA0103.10.477056
MA0105.11.5005
MA0106.10.425111
MA0107.10.46624
MA0108.20.50131
MA0109.10
MA0111.10.242308
MA0113.10.400008
MA0114.10.323836
MA0115.10.744589
MA0116.10.411741
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.10.476296
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.0649474
MA0140.10.330266
MA0141.10.511953
MA0142.10.547747
MA0143.10.414534
MA0144.10.674112
MA0145.10.189432
MA0146.10.0854135
MA0147.10.709361
MA0148.10.271704
MA0149.10.204102
MA0062.21.53832
MA0035.20.33429
MA0039.21.15989
MA0138.20.469076
MA0002.20.0664561
MA0137.20.506794
MA0104.20.547442
MA0047.20.380343
MA0112.20.370361
MA0065.20.371748
MA0150.10.688872
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.837005
MA0155.10.423059
MA0156.10.949678
MA0157.10.518122
MA0158.10
MA0159.10.114033
MA0160.10.753068
MA0161.10
MA0162.10.767982
MA0163.10.0112325
MA0164.10.357779
MA0080.20.153997
MA0018.20.366212
MA0099.20.463355
MA0079.20.357641
MA0102.21.35579
MA0258.10.626814
MA0259.10.678628
MA0442.10
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