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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=0,0

Latest revision as of 15:08, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:11781140..11781150,-p@chr11:11781140..11781150
-
Mm9::chr12:105433069..105433075,-p@chr12:105433069..105433075
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Mm9::chr14:58802053..58802059,-p@chr14:58802053..58802059
-
Mm9::chr3:37265803..37265817,+p7@Fgf2
Mm9::chr4:147375200..147375220,+p@chr4:147375200..147375220
+
Mm9::chr5:88385298..88385340,+p@chr5:88385298..88385340
+
Mm9::chr8:125950637..125950639,-p@chr8:125950637..125950639
-
Mm9::chr8:125951458..125951466,-p@chr8:125951458..125951466
-
Mm9::chr8:125951545..125951559,-p@chr8:125951545..125951559
-
Mm9::chr8:125951622..125951629,-p@chr8:125951622..125951629
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Mm9::chr8:125951737..125951748,-p@chr8:125951737..125951748
-
Mm9::chr8:125952002..125952012,-p@chr8:125952002..125952012
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Mm9::chr8:125952310..125952320,+p@chr8:125952310..125952320
+
Mm9::chr8:125952865..125952872,-p@chr8:125952865..125952872
-
Mm9::chr8:125952972..125952981,-p@chr8:125952972..125952981
-
Mm9::chr8:125953346..125953349,-p@chr8:125953346..125953349
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Mm9::chr8:125953495..125953499,-p@chr8:125953495..125953499
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Mm9::chr8:125956179..125956189,-p@chr8:125956179..125956189
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Mm9::chr8:125956252..125956255,-p@chr8:125956252..125956255
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Mm9::chr8:125956332..125956339,-p@chr8:125956332..125956339
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Mm9::chr8:125956453..125956462,-p@chr8:125956453..125956462
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Mm9::chr8:125956513..125956519,-p@chr8:125956513..125956519
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Mm9::chr8:125956526..125956533,-p@chr8:125956526..125956533
-


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:0045794negative regulation of cell volume0.00890264614036049
GO:0032344regulation of aldosterone metabolic process0.00890264614036049
GO:0060082eye blink reflex0.00890264614036049
GO:0004058aromatic-L-amino-acid decarboxylase activity0.00890264614036049
GO:0032196transposition0.00890264614036049
GO:0006313transposition, DNA-mediated0.00890264614036049
GO:0019228generation of action potential0.00890264614036049
GO:0060072large conductance calcium-activated potassium channel activity0.00890264614036049
GO:0032341aldosterone metabolic process0.0129482392672005
GO:0060083smooth muscle contraction involved in micturition0.0129482392672005
GO:0008212mineralocorticoid metabolic process0.0129482392672005
GO:0007423sensory organ development0.0133517743582362
GO:0046541saliva secretion0.0133517743582362
GO:0060087relaxation of vascular smooth muscle0.0133517743582362
GO:0045475locomotor rhythm0.0133517743582362
GO:0032350regulation of hormone metabolic process0.0133517743582362
GO:0035295tube development0.0136405841796192
GO:0046668regulation of retinal cell programmed cell death0.0149902338833339
GO:0006884regulation of cell volume0.0149902338833339
GO:0060073micturition0.0161813088807534
GO:0048512circadian behavior0.0161813088807534
GO:0045986negative regulation of smooth muscle contraction0.0161813088807534
GO:0043195terminal button0.0166100798772788
GO:0046666retinal cell programmed cell death0.0166100798772788
GO:0045932negative regulation of muscle contraction0.0166100798772788
GO:0006519amino acid and derivative metabolic process0.0166100798772788
GO:0019218regulation of steroid metabolic process0.0166100798772788
GO:0045766positive regulation of angiogenesis0.0166100798772788
GO:0003964RNA-directed DNA polymerase activity0.0166100798772788
GO:0007622rhythmic behavior0.0166100798772788
GO:0060004reflex0.0169448824132453
GO:0007267cell-cell signaling0.0169448824132453
GO:0009308amine metabolic process0.0169448824132453
GO:0021940positive regulation of granule cell precursor proliferation0.0169448824132453
GO:0019031viral envelope0.0169448824132453
GO:0033267axon part0.0169448824132453
GO:0021936regulation of granule cell precursor proliferation0.0169448824132453
GO:0006807nitrogen compound metabolic process0.0169448824132453
GO:0042423catecholamine biosynthetic process0.0169448824132453
GO:0021930granule cell precursor proliferation0.0169448824132453
GO:0021534cell proliferation in hindbrain0.0169448824132453
GO:0021924cell proliferation in the external granule layer0.0169448824132453
GO:0000186activation of MAPKK activity0.0173953161140378
GO:0015269calcium-activated potassium channel activity0.0173953161140378
GO:0007589fluid secretion0.0173953161140378
GO:0010092specification of organ identity0.0181096647399395
GO:0022600digestive system process0.0181096647399395
GO:0022839ion gated channel activity0.0181096647399395
GO:0001759induction of an organ0.0181096647399395
GO:0031128induction0.0181096647399395
GO:0042311vasodilation0.0181096647399395
GO:0044423virion part0.0181096647399395
GO:0045168cell-cell signaling during cell fate commitment0.0181096647399395
GO:0005227calcium activated cation channel activity0.0181096647399395
GO:0003014renal system process0.0181096647399395
GO:0050679positive regulation of epithelial cell proliferation0.0190551599685365
GO:0019752carboxylic acid metabolic process0.0195566751615055
GO:0006082organic acid metabolic process0.0195566751615055
GO:0006940regulation of smooth muscle contraction0.0204943845685066
GO:0004190aspartic-type endopeptidase activity0.021336517097799
GO:0019216regulation of lipid metabolic process0.0217935754465432
GO:0005104fibroblast growth factor receptor binding0.0217935754465432
GO:0051260protein homooligomerization0.0233310614519163
GO:0001666response to hypoxia0.0233310614519163
GO:0007628adult walking behavior0.0240640544446906
GO:0042491auditory receptor cell differentiation0.0247746585682556
GO:0042401biogenic amine biosynthetic process0.0250894075588815
GO:0050678regulation of epithelial cell proliferation0.0250894075588815
GO:0016831carboxy-lyase activity0.025930627077134
GO:0006939smooth muscle contraction0.025930627077134
GO:0001934positive regulation of protein amino acid phosphorylation0.025930627077134
GO:0033240positive regulation of amine metabolic process0.025930627077134
GO:0045764positive regulation of amino acid metabolic process0.025930627077134
GO:0060113inner ear receptor cell differentiation0.025930627077134
GO:0042398amino acid derivative biosynthetic process0.0259944882515241
GO:0051241negative regulation of multicellular organismal process0.0259944882515241
GO:0018958phenol metabolic process0.0259944882515241
GO:0007623circadian rhythm0.0259944882515241
GO:0006584catecholamine metabolic process0.0259944882515241
GO:0051259protein oligomerization0.0259944882515241
GO:0045765regulation of angiogenesis0.0259944882515241
GO:0032147activation of protein kinase activity0.0259944882515241
GO:0050673epithelial cell proliferation0.0265351635456519
GO:0050885neuromuscular process controlling balance0.027062826715482
GO:0006937regulation of muscle contraction0.0271343841043562
GO:0042490mechanoreceptor differentiation0.0271343841043562
GO:0035150regulation of tube size0.0271343841043562
GO:0050880regulation of blood vessel size0.0271343841043562
GO:0003018vascular process in circulatory system0.0271343841043562
GO:0010001glial cell differentiation0.0296503924151127
GO:0016830carbon-carbon lyase activity0.0296503924151127
GO:0007586digestion0.0308666142778457
GO:0042063gliogenesis0.0310544238753382
GO:0008344adult locomotory behavior0.0310544238753382
GO:0030902hindbrain development0.0310544238753382
GO:0042391regulation of membrane potential0.0310544238753382
GO:0048592eye morphogenesis0.0314634567007677
GO:0030170pyridoxal phosphate binding0.0329704769089509
GO:0045597positive regulation of cell differentiation0.0329704769089509
GO:0050905neuromuscular process0.0333476121965123
GO:0016324apical plasma membrane0.0344167751500116
GO:0033238regulation of amine metabolic process0.0354616015674823
GO:0001932regulation of protein amino acid phosphorylation0.0354616015674823
GO:0006521regulation of amino acid metabolic process0.0354616015674823
GO:0008076voltage-gated potassium channel complex0.0364687924247634
GO:0042325regulation of phosphorylation0.0367629008567103
GO:0051174regulation of phosphorus metabolic process0.0367629008567103
GO:0019220regulation of phosphate metabolic process0.0367629008567103
GO:0044238primary metabolic process0.0375257099524355
GO:0009309amine biosynthetic process0.0375257099524355
GO:0008201heparin binding0.0375257099524355
GO:0048519negative regulation of biological process0.0375257099524355
GO:0044237cellular metabolic process0.0375257099524355
GO:0030534adult behavior0.0379220605897542
GO:0030424axon0.0382054290145383
GO:0030324lung development0.0390914509679259
GO:0030323respiratory tube development0.0393596825726832
GO:0044463cell projection part0.040817260730519
GO:0051094positive regulation of developmental process0.0409692666526285
GO:0050878regulation of body fluid levels0.0409692666526285
GO:0048839inner ear development0.0409692666526285
GO:0006576biogenic amine metabolic process0.0417875351795504
GO:0006310DNA recombination0.0419106468578885
GO:0005539glycosaminoglycan binding0.0419106468578885
GO:0048469cell maturation0.0419106468578885
GO:0043583ear development0.0423585509541974
GO:0044271nitrogen compound biosynthetic process0.0423585509541974
GO:0045177apical part of cell0.0425771180631387
GO:0042445hormone metabolic process0.0438181956187094
GO:0030247polysaccharide binding0.0438181956187094
GO:0045860positive regulation of protein kinase activity0.0438181956187094
GO:0003012muscle system process0.0438181956187094
GO:0006936muscle contraction0.0438181956187094
GO:0005249voltage-gated potassium channel activity0.0438181956187094
GO:0001871pattern binding0.0442068707507138
GO:0004519endonuclease activity0.0442068707507138
GO:0006575amino acid derivative metabolic process0.0449093739861729
GO:0033674positive regulation of kinase activity0.0450926938268783
GO:0051347positive regulation of transferase activity0.0452732925550205
GO:0021700developmental maturation0.045952462281696
GO:0007605sensory perception of sound0.046124155030082
GO:0048468cell development0.0463028947904052
GO:0009653anatomical structure morphogenesis0.0463028947904052
GO:0008015blood circulation0.0463028947904052
GO:0003013circulatory system process0.0463028947904052
GO:0050954sensory perception of mechanical stimulus0.0469461488761132
GO:0045165cell fate commitment0.0480569921767356
GO:0001654eye development0.0496252425198387
GO:0019842vitamin binding0.0497620568061787
GO:0016779nucleotidyltransferase activity0.049896969746898



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
bone marrow cell6.64e-383
mesenchymal stem cell of the bone marrow6.64e-383
central nervous system macrophage3.19e-252
microglial cell3.19e-252
cardiocyte5.00e-183
striated muscle cell5.00e-183
cardiac muscle cell5.00e-183
cardiac muscle myoblast5.00e-183
monopoietic cell3.67e-134
myeloid leukocyte3.67e-134
phagocyte3.67e-134
monocyte3.67e-134
macrophage3.67e-134
tissue-resident macrophage3.67e-134
macrophage dendritic cell progenitor3.67e-134
monoblast3.67e-134
promonocyte3.67e-134
muscle precursor cell1.61e-096
contractile cell1.61e-096
muscle cell1.61e-096
myoblast1.61e-096
stuff accumulating cell4.19e-096
mesodermal cell2.72e-087
defensive cell6.16e-087
granulocyte monocyte progenitor cell6.16e-087
oligodendrocyte precursor cell4.66e-078
connective tissue cell5.09e-0746
mesenchymal cell5.09e-0746
somatic stem cell7.08e-0791
multi fate stem cell7.08e-0791

Uber Anatomy
Ontology termp-valuen
bone marrow1.31e-1916
musculoskeletal system2.74e-1932
bone element2.25e-1422
skeletal element2.25e-1422
skeletal system2.25e-1422
lateral plate mesoderm3.43e-0787
hematopoietic system3.59e-0745
blood island3.59e-0745
connective tissue5.09e-0746
hemolymphoid system9.79e-0748
immune system9.79e-0748


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)
MA0003.10.0379965
MA0004.10.135415
MA0006.10.0509523
MA0007.10.126548
MA0009.10.467692
MA0014.11.63329e-05
MA0017.10.222109
MA0019.15.21568
MA0024.10.430047
MA0025.10.677312
MA0027.12.06014
MA0028.10.055063
MA0029.10.411611
MA0030.10.417163
MA0031.10.387282
MA0038.10.231663
MA0040.10.478574
MA0041.10.0931678
MA0042.10.0865208
MA0043.10.552986
MA0046.10.499059
MA0048.10.0277501
MA0050.10.481243
MA0051.10.238165
MA0052.10.485607
MA0055.10.168072
MA0056.10
MA0057.10.0707752
MA0058.10.0831725
MA0059.10.0892761
MA0060.10.483231
MA0061.10.31638
MA0063.10
MA0066.10.223752
MA0067.10.78096
MA0068.10.00423247
MA0069.10.485904
MA0070.10.477443
MA0071.10.479923
MA0072.10.470071
MA0073.10.00822401
MA0074.11.71791
MA0076.10.0701228
MA0077.10.451332
MA0078.10.726633
MA0081.10.101252
MA0083.10.552276
MA0084.11.09535
MA0087.10.513946
MA0088.10.171701
MA0089.10
MA0090.10.115519
MA0091.10.143375
MA0092.10.115696
MA0093.10.212413
MA0095.10
MA0098.10
MA0100.12.37452
MA0101.11.07479
MA0103.10.235667
MA0105.10.27408
MA0106.11.35881
MA0107.10.493454
MA0108.20.334189
MA0109.10
MA0111.11.27377
MA0113.10.247414
MA0114.10.899025
MA0115.10.555491
MA0116.10.0508724
MA0117.10.526724
MA0119.10.0941347
MA0122.10.544387
MA0124.10.731064
MA0125.11.59167
MA0130.10
MA0131.10.312378
MA0132.10
MA0133.10
MA0135.10.585739
MA0136.10.2124
MA0139.10.078666
MA0140.10.190563
MA0141.10.0753473
MA0142.10.375247
MA0143.10.259584
MA0144.10.912796
MA0145.10.0410716
MA0146.10.0429011
MA0147.10.0375422
MA0148.10.145271
MA0149.10.0966891
MA0062.20.0515767
MA0035.21.07381
MA0039.20.00990489
MA0138.20.306125
MA0002.20.655962
MA0137.20.257328
MA0104.20.0212101
MA0047.20.231108
MA0112.20.0996805
MA0065.20.333255
MA0150.10.794087
MA0151.10
MA0152.11.21903
MA0153.10.600798
MA0154.10.520245
MA0155.10.016317
MA0156.10.0697319
MA0157.10.348973
MA0158.10
MA0159.10.0409628
MA0160.10.147126
MA0161.10
MA0162.10.0110162
MA0163.11.3446
MA0164.10.212655
MA0080.20.229013
MA0018.20.219518
MA0099.20.301184
MA0079.26.42975e-11
MA0102.21.14642
MA0258.10.284909
MA0259.10.0340942
MA0442.10
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