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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=-0.

Latest revision as of 14:52, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:69828848..69828937,-p1@Acadvl
Mm9::chr11:88725823..88725841,-p2@Akap1
Mm9::chr14:21871816..21871855,+p2@Adk
Mm9::chr15:103418824..103418832,-p@chr15:103418824..103418832
-
Mm9::chr15:82184710..82184721,-p2@Ndufa6
Mm9::chr17:24563621..24563646,+p1@Eci1
Mm9::chr17:56256688..56256706,-p1@Plin5
Mm9::chr17:56257000..56257011,-p3@Plin5
Mm9::chr18:68459803..68459847,-p2@4933403F05Rik
Mm9::chr18:74938857..74938878,+p1@Acaa2
Mm9::chr19:43827414..43827491,-p1@Cox15
Mm9::chr1:167391466..167391477,+p3@Brp44
Mm9::chr1:66909828..66909833,-p4@Acadl
Mm9::chr1:66909839..66909859,-p1@Acadl
Mm9::chr1:66909874..66909889,-p2@Acadl
Mm9::chr1:66909891..66909909,-p3@Acadl
Mm9::chr2:108788925..108788937,+p1@ENSMUST00000121752
Mm9::chr2:32464505..32464553,+p5@St6galnac6
Mm9::chr2:4840050..4840084,+p2@Phyh
Mm9::chr3:153607389..153607416,-p2@Acadm
Mm9::chr3:153607425..153607478,-p1@Acadm
Mm9::chr3:33980178..33980269,-p1@Dnajc19
p1@Gm15118
Mm9::chr3:79432582..79432667,-p1@Etfdh
Mm9::chr4:137280361..137280390,+p4@Rap1gap
Mm9::chr4:15872506..15872535,-p1@Decr1
Mm9::chr4:19502286..19502363,+p1@Fam82b
Mm9::chr4:19502710..19502737,+p@chr4:19502710..19502737
+
Mm9::chr4:19502743..19502759,+p@chr4:19502743..19502759
+
Mm9::chr4:59594547..59594554,+p3@Hsdl2
Mm9::chr4:59594569..59594586,+p1@Hsdl2
Mm9::chr4:59594593..59594604,+p2@Hsdl2
Mm9::chr5:115569286..115569354,-p1@Acads
Mm9::chr5:30481496..30481526,-p1@Hadha
Mm9::chr5:30481641..30481652,-p2@Hadha
Mm9::chr5:30481783..30481851,+p1@Hadhb
p1@LOC100504946
Mm9::chr5:30481855..30481876,+p2@Hadhb
p2@LOC100504946
Mm9::chr6:57642001..57642078,-p1@Pigy
Mm9::chr6:73198627..73198689,+p1@Suclg1
Mm9::chr7:147302294..147302327,-p1@Echs1
Mm9::chr7:29610320..29610333,+p2@Ech1
Mm9::chr7:29610337..29610382,+p1@Ech1
Mm9::chr7:50699474..50699512,+p1@Etfb
Mm9::chr8:23521850..23521932,+p1@Mrps31
Mm9::chr8:3279464..3279482,-p3@Insr
Mm9::chr9:53418434..53418472,-p1@Acat1
Mm9::chr9:55359963..55360037,-p1@Etfa
Mm9::chrX:45866562..45866615,-p1@Aifm1


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:0005739mitochondrion1.65811560632517e-24
GO:0044444cytoplasmic part2.17946459373208e-15
GO:0006631fatty acid metabolic process3.82667074135426e-12
GO:0032787monocarboxylic acid metabolic process5.12862614991152e-11
GO:0005737cytoplasm1.964865736978e-10
GO:0044255cellular lipid metabolic process3.34493415359138e-10
GO:0006629lipid metabolic process1.28791363384986e-09
GO:0044429mitochondrial part1.28791363384986e-09
GO:0016491oxidoreductase activity1.29731816147466e-09
GO:0043231intracellular membrane-bound organelle2.05668062419536e-09
GO:0043227membrane-bound organelle2.05668062419536e-09
GO:0050660FAD binding1.07635838369545e-08
GO:0019752carboxylic acid metabolic process2.21887555043635e-08
GO:0006082organic acid metabolic process2.21887555043635e-08
GO:0031966mitochondrial membrane6.95686117003045e-08
GO:0017133mitochondrial electron transfer flavoprotein complex6.95686117003045e-08
GO:0045251electron transfer flavoprotein complex6.95686117003045e-08
GO:0043229intracellular organelle8.31833272040718e-08
GO:0043226organelle8.31833272040718e-08
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors9.42708710462091e-08
GO:0005740mitochondrial envelope9.98768518676619e-08
GO:0006091generation of precursor metabolites and energy1.30954445229854e-07
GO:0003995acyl-CoA dehydrogenase activity1.31583543614201e-07
GO:0006118electron transport3.00563266219292e-07
GO:0050662coenzyme binding3.19863354718234e-07
GO:0005743mitochondrial inner membrane6.94884590039665e-07
GO:0019866organelle inner membrane8.41320618852152e-07
GO:0031090organelle membrane8.41320618852152e-07
GO:0031975envelope9.4794313635429e-07
GO:0031967organelle envelope9.4794313635429e-07
GO:0048037cofactor binding2.34431853847999e-06
GO:0016408C-acyltransferase activity6.04619670303629e-06
GO:0044424intracellular part9.81965099562373e-06
GO:0016649oxidoreductase activity, acting on the CH-NH group of donors, quinone or similar compound as acceptor2.23136533387483e-05
GO:0004174electron-transferring-flavoprotein dehydrogenase activity2.23136533387483e-05
GO:0005622intracellular2.23136533387483e-05
GO:0019395fatty acid oxidation3.57827918294243e-05
GO:0003988acetyl-CoA C-acyltransferase activity6.3051334652743e-05
GO:0004300enoyl-CoA hydratase activity0.000119679395567415
GO:0003985acetyl-CoA C-acetyltransferase activity0.000119679395567415
GO:0016453C-acetyltransferase activity0.000194408750444265
GO:0009055electron carrier activity0.000473241497485848
GO:0005759mitochondrial matrix0.000596910453837229
GO:0031980mitochondrial lumen0.000596910453837229
GO:0006635fatty acid beta-oxidation0.00137074076337276
GO:0016645oxidoreductase activity, acting on the CH-NH group of donors0.00323241232455029
GO:0044446intracellular organelle part0.00323241232455029
GO:0044422organelle part0.00326303287681961
GO:0004466long-chain-acyl-CoA dehydrogenase activity0.00930571099858341
GO:0004001adenosine kinase activity0.00930571099858341
GO:0009054electron acceptor activity0.00930571099858341
GO:0000506glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex0.00930571099858341
GO:0016508long-chain-enoyl-CoA hydratase activity0.00930571099858341
GO:0004085butyryl-CoA dehydrogenase activity0.00930571099858341
GO:0048244phytanoyl-CoA dioxygenase activity0.00930571099858341
GO:0016509long-chain-3-hydroxyacyl-CoA dehydrogenase activity0.00930571099858341
GO:0044238primary metabolic process0.0134292477774332
GO:0008415acyltransferase activity0.0134292477774332
GO:0019867outer membrane0.0134292477774332
GO:0016747transferase activity, transferring groups other than amino-acyl groups0.0134921306993982
GO:0016836hydro-lyase activity0.0146278648282746
GO:0016746transferase activity, transferring acyl groups0.0146278648282746
GO:0017076purine nucleotide binding0.0152679599825912
GO:0004776succinate-CoA ligase (GDP-forming) activity0.0155438834799722
GO:0001561fatty acid alpha-oxidation0.0155438834799722
GO:0001665alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity0.0155438834799722
GO:00086702,4-dienoyl-CoA reductase (NADPH) activity0.0155438834799722
GO:0016407acetyltransferase activity0.0170747080902416
GO:0030554adenyl nucleotide binding0.0170747080902416
GO:0044464cell part0.0170747080902416
GO:0005623cell0.0170747080902416
GO:0016835carbon-oxygen lyase activity0.0179611104752788
GO:0001574ganglioside biosynthetic process0.0202722378490755
GO:0043174nucleoside salvage0.0202722378490755
GO:0004774succinate-CoA ligase activity0.0202722378490755
GO:0006166purine ribonucleoside salvage0.0202722378490755
GO:0043101purine salvage0.0202722378490755
GO:0046467membrane lipid biosynthetic process0.0244534639900949
GO:0000166nucleotide binding0.02536204098249
GO:0046128purine ribonucleoside metabolic process0.02536204098249
GO:0009437carnitine metabolic process0.02536204098249
GO:0043094metabolic compound salvage0.02536204098249
GO:0005498sterol carrier activity0.030560194247214
GO:0042278purine nucleoside metabolic process0.030560194247214
GO:0006688glycosphingolipid biosynthetic process0.030560194247214
GO:0044237cellular metabolic process0.0319559371146957
GO:0042579microbody0.0319559371146957
GO:0005777peroxisome0.0319559371146957
GO:0006309DNA fragmentation during apoptosis0.0399021080604241
GO:0016405CoA-ligase activity0.0399021080604241
GO:0009119ribonucleoside metabolic process0.0399021080604241
GO:0009409response to cold0.0436488458499015
GO:0001573ganglioside metabolic process0.0436488458499015
GO:0009247glycolipid biosynthetic process0.0436488458499015
GO:0006921cell structure disassembly during apoptosis0.0436488458499015
GO:0042594response to starvation0.0480556462130121
GO:0030262apoptotic nuclear changes0.0480556462130121



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 tube4.09e-1447
digestive tract diverticulum1.05e-0823
sac1.05e-0823
exocrine gland1.26e-0825
exocrine system1.26e-0825
mesenchyme1.70e-0861
entire embryonic mesenchyme1.70e-0861
liver1.71e-0822
epithelial sac1.71e-0822
digestive gland1.71e-0822
epithelium of foregut-midgut junction1.71e-0822
anatomical boundary1.71e-0822
hepatobiliary system1.71e-0822
foregut-midgut junction1.71e-0822
hepatic diverticulum1.71e-0822
liver primordium1.71e-0822
septum transversum1.71e-0822
liver bud1.71e-0822
primary circulatory organ2.85e-0718
heart2.85e-0718
primitive heart tube2.85e-0718
primary heart field2.85e-0718
anterior lateral plate mesoderm2.85e-0718
heart tube2.85e-0718
heart primordium2.85e-0718
cardiac mesoderm2.85e-0718
cardiogenic plate2.85e-0718
heart rudiment2.85e-0718
intestine2.97e-0731
abdomen element3.91e-0749
abdominal segment element3.91e-0749
abdominal segment of trunk3.91e-0749
abdomen3.91e-0749
trunk mesenchyme4.48e-0745
cardiovascular system5.49e-0723
circulatory system5.49e-0723


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)
MA0003.13.09904
MA0004.10.297268
MA0006.10.773056
MA0007.10.508139
MA0009.11.25924
MA0014.13.3391
MA0017.10.904366
MA0019.10.130554
MA0024.10.609961
MA0025.10.417226
MA0027.11.75175
MA0028.11.12708
MA0029.10.576747
MA0030.10.202852
MA0031.10.180639
MA0038.10.0780356
MA0040.10.250394
MA0041.10.604556
MA0042.10.168388
MA0043.10.310854
MA0046.10.266754
MA0048.10.503721
MA0050.11.01176
MA0051.10.0817759
MA0052.10.255985
MA0055.10.128873
MA0056.10
MA0057.10.127289
MA0058.10.320209
MA0059.10.871419
MA0060.10.612966
MA0061.10.543316
MA0063.10
MA0066.11.92091
MA0067.10.509729
MA0068.10.218342
MA0069.10.256221
MA0070.10.696297
MA0071.10.648023
MA0072.10.243673
MA0073.10.0170189
MA0074.10.472995
MA0076.10.45657
MA0077.10.229013
MA0078.10.096354
MA0081.10.398476
MA0083.10.310264
MA0084.10.803542
MA0087.10.278783
MA0088.11.29463
MA0089.10
MA0090.10.243754
MA0091.10.0337713
MA0092.10.0989774
MA0093.10.380004
MA0095.10
MA0098.10
MA0100.10.0558545
MA0101.10.187027
MA0103.10.118811
MA0105.11.8412
MA0106.10.0999571
MA0107.10.414802
MA0108.20.142919
MA0109.10
MA0111.10.109224
MA0113.10.29406
MA0114.12.43956
MA0115.10.312936
MA0116.10.527003
MA0117.10.289199
MA0119.10.367636
MA0122.10.303728
MA0124.10.464833
MA0125.10.404137
MA0130.10
MA0131.12.54893
MA0132.10
MA0133.10
MA0135.10.338295
MA0136.10.067305
MA0139.10.873628
MA0140.10.0558148
MA0141.13.27321
MA0142.10.171883
MA0143.10.0944901
MA0144.10.00215559
MA0145.10.797966
MA0146.11.6615
MA0147.10.844635
MA0148.10.324184
MA0149.10.0164376
MA0062.20.191828
MA0035.20.057452
MA0039.27.38815
MA0138.20.391841
MA0002.20.0183197
MA0137.20.13719
MA0104.21.281
MA0047.20.0777193
MA0112.23.2383
MA0065.21.97094
MA0150.10.0269329
MA0151.10
MA0152.10.267919
MA0153.10.351062
MA0154.10.350845
MA0155.11.96142
MA0156.10.126796
MA0157.10.153179
MA0158.10
MA0159.10.263263
MA0160.10.329275
MA0161.10
MA0162.11.57197
MA0163.12.78597
MA0164.10.238634
MA0080.20.0397196
MA0018.20.0712081
MA0099.20.383444
MA0079.20.72171
MA0102.20.852517
MA0258.10.686336
MA0259.11.05613
MA0442.10
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