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MCL coexpression mm9:221: Difference between revisions

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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=0.00792175476852989

Latest revision as of 14:54, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:82059147..82059189,-p@chr12:82059147..82059189
-
Mm9::chr12:82061512..82061523,-p@chr12:82061512..82061523
-
Mm9::chr16:22929256..22929268,+p@chr16:22929256..22929268
+
Mm9::chr16:90220992..90221016,+p1@Sod1
Mm9::chr17:57365708..57365721,-p@chr17:57365708..57365721
-
Mm9::chr18:20828476..20828546,+p@chr18:20828476..20828546
+
Mm9::chr18:20828549..20828568,+p@chr18:20828549..20828568
+
Mm9::chr18:20832199..20832222,+p@chr18:20832199..20832222
+
Mm9::chr19:38191263..38191291,-p@chr19:38191263..38191291
-
Mm9::chr19:38198540..38198549,-p@chr19:38198540..38198549
-
Mm9::chr19:38198819..38198844,-p@chr19:38198819..38198844
-
Mm9::chr1:162919603..162919613,+p@chr1:162919603..162919613
+
Mm9::chr1:173274535..173274580,-p4@Nit1
Mm9::chr1:67189510..67189524,+p@chr1:67189510..67189524
+
Mm9::chr2:103294763..103294772,-p@chr2:103294763..103294772
-
Mm9::chr2:147835009..147835033,-p@chr2:147835009..147835033
-
Mm9::chr2:172981441..172981453,+p@chr2:172981441..172981453
+
Mm9::chr2:172984371..172984389,+p@chr2:172984371..172984389
+
Mm9::chr2:84613794..84613806,-p@chr2:84613794..84613806
-
Mm9::chr4:150240662..150240682,+p@chr4:150240662..150240682
+
Mm9::chr4:49549479..49549493,-p@chr4:49549479..49549493
-
Mm9::chr5:138430969..138430981,+p@chr5:138430969..138430981
+
Mm9::chr5:138431025..138431034,+p@chr5:138431025..138431034
+
Mm9::chr5:89864602..89864613,-p@chr5:89864602..89864613
-
Mm9::chr5:89867290..89867299,-p@chr5:89867290..89867299
-
Mm9::chr5:89874342..89874353,-p@chr5:89874342..89874353
-
Mm9::chr5:89874371..89874391,-p@chr5:89874371..89874391
-
Mm9::chr5:90897694..90897705,+p@chr5:90897694..90897705
+
Mm9::chr7:147950810..147950831,+p@chr7:147950810..147950831
+
Mm9::chr7:147955104..147955113,+p@chr7:147955104..147955113
+
Mm9::chr7:147955535..147955550,+p@chr7:147955535..147955550
+
Mm9::chr7:147955946..147955959,+p@chr7:147955946..147955959
+
Mm9::chr7:147956833..147956853,+p@chr7:147956833..147956853
+
Mm9::chr7:147958929..147958960,+p@chr7:147958929..147958960
+
Mm9::chr7:147958976..147959010,+p@chr7:147958976..147959010
+
Mm9::chr9:107558460..107558474,-p@chr9:107558460..107558474
-
Mm9::chr9:107560177..107560191,-p@chr9:107560177..107560191
-
Mm9::chr9:107560202..107560217,-p@chr9:107560202..107560217
-
Mm9::chr9:46077991..46078006,+p@chr9:46077991..46078006
+
Mm9::chrM:530..533,-p@chrM:530..533
-


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:0032287myelin maintenance in the peripheral nervous system0.0107189771782449
GO:0043217myelin maintenance0.0107189771782449
GO:0050665hydrogen peroxide biosynthetic process0.0107189771782449
GO:0022011myelination in the peripheral nervous system0.0107189771782449
GO:0032292ensheathment of axons in the peripheral nervous system0.0107189771782449
GO:0042554superoxide release0.0107189771782449
GO:0060087relaxation of vascular smooth muscle0.0107189771782449
GO:0019430removal of superoxide radicals0.0107189771782449
GO:0014044Schwann cell development0.0107189771782449
GO:0004785copper, zinc superoxide dismutase activity0.0107189771782449
GO:0000303response to superoxide0.0107189771782449
GO:0001895retinal homeostasis0.0107189771782449
GO:0006590thyroid hormone generation0.0107189771782449
GO:0045986negative regulation of smooth muscle contraction0.0107189771782449
GO:0000305response to oxygen radical0.0107189771782449
GO:0048678response to axon injury0.0107189771782449
GO:0045932negative regulation of muscle contraction0.0107189771782449
GO:0016721oxidoreductase activity, acting on superoxide radicals as acceptor0.0107189771782449
GO:0004784superoxide dismutase activity0.0107189771782449
GO:0006807nitrogen compound metabolic process0.0107189771782449
GO:0006309DNA fragmentation during apoptosis0.0107189771782449
GO:0060122inner ear receptor stereocilium organization and biogenesis0.0107189771782449
GO:0060088auditory receptor cell stereocilium organization and biogenesis0.0107189771782449
GO:0002093auditory receptor cell morphogenesis0.0107189771782449
GO:0014037Schwann cell differentiation0.0107189771782449
GO:0002262myeloid cell homeostasis0.0107189771782449
GO:0060119inner ear receptor cell development0.0107189771782449
GO:0019841retinol binding0.0107189771782449
GO:0006921cell structure disassembly during apoptosis0.0107189771782449
GO:0060117auditory receptor cell development0.0107189771782449
GO:0060052neurofilament cytoskeleton organization and biogenesis0.0107189771782449
GO:0046716muscle maintenance0.0107189771782449
GO:0030262apoptotic nuclear changes0.0107189771782449
GO:0042743hydrogen peroxide metabolic process0.0107189771782449
GO:0045471response to ethanol0.0107189771782449
GO:0042542response to hydrogen peroxide0.0107189771782449
GO:0042403thyroid hormone metabolic process0.0107189771782449
GO:0016918retinal binding0.0107189771782449
GO:0021782glial cell development0.0107189771782449
GO:0007009plasma membrane organization and biogenesis0.0107189771782449
GO:0019840isoprenoid binding0.0129603531713899
GO:0005501retinoid binding0.0129603531713899
GO:0006308DNA catabolic process0.0129603531713899
GO:0042311vasodilation0.013639344489914
GO:0006801superoxide metabolic process0.0142880540346329
GO:0000302response to reactive oxygen species0.0149084567094372
GO:0045104intermediate filament cytoskeleton organization and biogenesis0.0151793935216803
GO:0006940regulation of smooth muscle contraction0.0151793935216803
GO:0001541ovarian follicle development0.0157434300619522
GO:0006749glutathione metabolic process0.0162848112175334
GO:0006302double-strand break repair0.0164816990927163
GO:0045103intermediate filament-based process0.0164816990927163
GO:0007566embryo implantation0.0166865981119955
GO:0022411cellular component disassembly0.0166865981119955
GO:0007422peripheral nervous system development0.0166865981119955
GO:0043524negative regulation of neuron apoptosis0.0166865981119955
GO:0042491auditory receptor cell differentiation0.0166865981119955
GO:0006879cellular iron ion homeostasis0.0166865981119955
GO:0055072iron ion homeostasis0.0166865981119955
GO:0001894tissue homeostasis0.0166865981119955
GO:0006997nuclear organization and biogenesis0.0166865981119955
GO:0006939smooth muscle contraction0.0166865981119955
GO:0048871multicellular organismal homeostasis0.0166865981119955
GO:0001776leukocyte homeostasis0.0166865981119955
GO:0042552myelination0.0166865981119955
GO:0060113inner ear receptor cell differentiation0.0166865981119955
GO:0048872homeostasis of number of cells0.0166865981119955
GO:0007568aging0.0166865981119955
GO:0007272ensheathment of neurons0.0166865981119955
GO:0051241negative regulation of multicellular organismal process0.0166865981119955
GO:0008366axon ensheathment0.0166865981119955
GO:0010033response to organic substance0.0166865981119955
GO:0006800oxygen and reactive oxygen species metabolic process0.0166865981119955
GO:0022601menstrual cycle phase0.0166865981119955
GO:0042493response to drug0.0166865981119955
GO:0009408response to heat0.0166865981119955
GO:0022602menstrual cycle process0.0166865981119955
GO:0006937regulation of muscle contraction0.0175405363270691
GO:0042490mechanoreceptor differentiation0.0175405363270691
GO:0035150regulation of tube size0.0175405363270691
GO:0050880regulation of blood vessel size0.0175405363270691
GO:0003018vascular process in circulatory system0.0175405363270691
GO:0043523regulation of neuron apoptosis0.0175405363270691
GO:0008585female gonad development0.0177164895652743
GO:0000187activation of MAPK activity0.0177164895652743
GO:0046660female sex differentiation0.0177164895652743
GO:0046545development of primary female sexual characteristics0.0177164895652743
GO:0001508regulation of action potential0.0180007112873751
GO:0051402neuron apoptosis0.0180753989237622
GO:0010001glial cell differentiation0.0180753989237622
GO:0042698menstrual cycle0.0184729230284163
GO:0008217regulation of blood pressure0.0184729230284163
GO:0007565female pregnancy0.0184729230284163
GO:0042063gliogenesis0.0184729230284163
GO:0043406positive regulation of MAP kinase activity0.0184729230284163
GO:0003015heart process0.0194126521668794
GO:0060047heart contraction0.0194126521668794
GO:0006979response to oxidative stress0.0196501810043307
GO:0009266response to temperature stimulus0.019882863913751
GO:0005496steroid binding0.020110846275557
GO:0008632apoptotic program0.0207567600192747
GO:0008406gonad development0.021389824937823
GO:0040014regulation of multicellular organism growth0.0215963087660436
GO:0048608reproductive structure development0.0217898213156336
GO:0005507copper ion binding0.0217898213156336
GO:0042472inner ear morphogenesis0.0217898213156336
GO:0045137development of primary sexual characteristics0.0231800685237416
GO:0042471ear morphogenesis0.0233228395653605
GO:0006790sulfur metabolic process0.0233228395653605
GO:0043405regulation of MAP kinase activity0.0233228395653605
GO:0035264multicellular organism growth0.0234966471543257
GO:0048839inner ear development0.026614254532153
GO:0048609reproductive process in a multicellular organism0.026614254532153
GO:0032504multicellular organism reproduction0.026614254532153
GO:0006576biogenic amine metabolic process0.0267529476252007
GO:0007548sex differentiation0.0268892090938311
GO:0043583ear development0.0277504102388111
GO:0042445hormone metabolic process0.0292932526269463
GO:0045860positive regulation of protein kinase activity0.0292932526269463
GO:0003012muscle system process0.0292932526269463
GO:0006936muscle contraction0.0292932526269463
GO:0003006reproductive developmental process0.030098302471113
GO:0006575amino acid derivative metabolic process0.030199078496392
GO:0033674positive regulation of kinase activity0.0302981913730126
GO:0051347positive regulation of transferase activity0.0303956810186028
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0304915860835648
GO:0007605sensory perception of sound0.0309203563178191
GO:0008015blood circulation0.0311866791041741
GO:0003013circulatory system process0.0311866791041741
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0311866791041741
GO:0050954sensory perception of mechanical stimulus0.0315966940632543
GO:0055066di-, tri-valent inorganic cation homeostasis0.0316788577864999
GO:0030003cellular cation homeostasis0.033354623183995
GO:0019842vitamin binding0.0334221975041883
GO:0055080cation homeostasis0.0338028119167185
GO:0000165MAPKKK cascade0.0370205692594804
GO:0005179hormone activity0.0370205692594804
GO:0045859regulation of protein kinase activity0.0392058207943284
GO:0043549regulation of kinase activity0.0404450888437307
GO:0043085positive regulation of catalytic activity0.0407601450841903
GO:0051338regulation of transferase activity0.0407708495992517
GO:0006873cellular ion homeostasis0.043424470701464
GO:0055082cellular chemical homeostasis0.043424470701464
GO:0035239tube morphogenesis0.043424470701464
GO:0040008regulation of growth0.043424470701464
GO:0043066negative regulation of apoptosis0.043424470701464
GO:0043069negative regulation of programmed cell death0.0437031775315356
GO:0006732coenzyme metabolic process0.0456875550042585
GO:0050801ion homeostasis0.0470448710507012
GO:0007517muscle development0.0470448710507012
GO:0009628response to abiotic stimulus0.0472911694927452



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
metabolising cell1.72e-125
endopolyploid cell1.72e-125
parenchymal cell1.72e-125
polyploid cell1.72e-125
hepatocyte1.72e-125

Uber Anatomy
Ontology termp-valuen
liver2.90e-3922
epithelial sac2.90e-3922
digestive gland2.90e-3922
epithelium of foregut-midgut junction2.90e-3922
anatomical boundary2.90e-3922
hepatobiliary system2.90e-3922
foregut-midgut junction2.90e-3922
hepatic diverticulum2.90e-3922
liver primordium2.90e-3922
septum transversum2.90e-3922
liver bud2.90e-3922
digestive tract diverticulum2.02e-3723
sac2.02e-3723
exocrine gland3.52e-3425
exocrine system3.52e-3425
trunk mesenchyme1.38e-1745
epithelial tube1.06e-1647
abdomen element6.87e-1649
abdominal segment element6.87e-1649
abdominal segment of trunk6.87e-1649
abdomen6.87e-1649
gut epithelium8.30e-1455
endocrine gland2.17e-1260
mesenchyme3.90e-1261
entire embryonic mesenchyme3.90e-1261
gland3.43e-1165
foregut4.74e-1180
unilaminar epithelium5.66e-1166
subdivision of trunk5.66e-1166
endo-epithelium2.34e-1069
endocrine system8.59e-1072
immaterial anatomical entity1.21e-0879
trunk region element1.21e-0879
trunk3.37e-0790


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)
MA0003.17.43491e-06
MA0004.10.175855
MA0006.10.0482011
MA0007.10.36842
MA0009.10.784333
MA0014.14.56514e-05
MA0017.10.166299
MA0019.10.165823
MA0024.10.256408
MA0025.10.472823
MA0027.11.82121
MA0028.10.0108633
MA0029.10.677139
MA0030.10.687705
MA0031.10.630961
MA0038.10.342732
MA0040.10.29711
MA0041.10.108468
MA0042.10.243023
MA0043.10.361422
MA0046.10.314603
MA0048.10.00704414
MA0050.10.216098
MA0051.10.109661
MA0052.10.303096
MA0055.10.0155406
MA0056.10
MA0057.10.0824798
MA0058.10.0213244
MA0059.10.251616
MA0060.10.248105
MA0061.10.324757
MA0063.10
MA0066.11.11704
MA0067.10.568484
MA0068.10.0180147
MA0069.10.303349
MA0070.10.29615
MA0071.10.470038
MA0072.10.289901
MA0073.10.000355255
MA0074.10.0834867
MA0076.10.192105
MA0077.10.274126
MA0078.10.398814
MA0081.10.12094
MA0083.10.360799
MA0084.10.868194
MA0087.10.32742
MA0088.10.273988
MA0089.10
MA0090.10.333785
MA0091.10.0506469
MA0092.10.14376
MA0093.10.0581493
MA0095.10
MA0098.10
MA0100.10.269978
MA0101.10.496168
MA0103.10.35556
MA0105.10.184981
MA0106.10.130893
MA0107.10.172402
MA0108.20.531039
MA0109.10
MA0111.10.156488
MA0113.10.747569
MA0114.10.0259019
MA0115.10.363622
MA0116.10.133148
MA0117.10.33849
MA0119.10.79786
MA0122.10.353887
MA0124.10.522168
MA0125.10.459209
MA0130.10
MA0131.10.163115
MA0132.10
MA0133.10
MA0135.10.390343
MA0136.10.638017
MA0139.10.473556
MA0140.10.0784504
MA0141.10.660564
MA0142.10.211884
MA0143.10.393238
MA0144.10.76648
MA0145.10.00643914
MA0146.10.00140485
MA0147.10.0315369
MA0148.10.192241
MA0149.16.53777
MA0062.20.0509634
MA0035.20.275446
MA0039.27.03395e-05
MA0138.20.158423
MA0002.20.698114
MA0137.20.204103
MA0104.20.013958
MA0047.20.341736
MA0112.20.0399458
MA0065.20.787205
MA0150.10.161196
MA0151.10
MA0152.10.696832
MA0153.10.403751
MA0154.10.409013
MA0155.10.0263581
MA0156.11.28221
MA0157.10.558733
MA0158.10
MA0159.10.0356292
MA0160.10.195348
MA0161.10
MA0162.11.37996e-05
MA0163.10.0375029
MA0164.10.308781
MA0080.21.20909
MA0018.20.0971053
MA0099.20.469638
MA0079.24.37043e-10
MA0102.20.917775
MA0258.10.683745
MA0259.10.083201
MA0442.10
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