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{{MCL_coexpression_mm9
{
|coexpression_dpi_cluster_scores_mean=0.0100418328292688

Latest revision as of 15:36, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:71018347..71018381,-p5@Epb4.9
Mm9::chr17:28145497..28145525,-p1@ENSMUST00000156965
Mm9::chr6:17257254..17257270,+p9@Cav1
Mm9::chr6:17257272..17257287,+p10@Cav1
Mm9::chr6:17257659..17257744,+p1@Cav1
Mm9::chr6:17257746..17257750,+p14@Cav1
Mm9::chr6:17257878..17257893,+p7@Cav1
Mm9::chr6:17257899..17257921,+p4@Cav1
Mm9::chr6:17257943..17257959,+p8@Cav1
Mm9::chr6:17289478..17289493,+p@chr6:17289478..17289493
+
Mm9::chr7:16535631..16535670,-p@chr7:16535631..16535670
-
Mm9::chrX:96085769..96085827,-p2@Ophn1


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:0033483gas homeostasis0.006299989005677
GO:0052547regulation of peptidase activity0.006299989005677
GO:0030857negative regulation of epithelial cell differentiation0.006299989005677
GO:0045908negative regulation of vasodilation0.006299989005677
GO:0033484nitric oxide homeostasis0.006299989005677
GO:0042312regulation of vasodilation0.006299989005677
GO:0030036actin cytoskeleton organization and biogenesis0.006299989005677
GO:0030029actin filament-based process0.006299989005677
GO:0045907positive regulation of vasoconstriction0.006299989005677
GO:0048552regulation of metalloenzyme activity0.006299989005677
GO:0045019negative regulation of nitric oxide biosynthetic process0.006299989005677
GO:0048554positive regulation of metalloenzyme activity0.006299989005677
GO:0008047enzyme activator activity0.00642131613139922
GO:0046426negative regulation of JAK-STAT cascade0.00704309866806752
GO:0001937negative regulation of endothelial cell proliferation0.00704309866806752
GO:0060056mammary gland involution0.00704309866806752
GO:0003779actin binding0.00704309866806752
GO:0043409negative regulation of MAPKKK cascade0.0104982558724032
GO:0009892negative regulation of metabolic process0.0108361950797176
GO:0001936regulation of endothelial cell proliferation0.0108361950797176
GO:0008092cytoskeletal protein binding0.0108361950797176
GO:0019217regulation of fatty acid metabolic process0.0115011763969493
GO:0030856regulation of epithelial cell differentiation0.0115011763969493
GO:0001935endothelial cell proliferation0.0116269258240364
GO:0016599caveolar membrane0.0116269258240364
GO:0019229regulation of vasoconstriction0.0116269258240364
GO:0005901caveola0.0117265153474903
GO:0045428regulation of nitric oxide biosynthetic process0.0117265153474903
GO:0000188inactivation of MAPK activity0.0117265153474903
GO:0019915sequestering of lipid0.0125944559437872
GO:0007010cytoskeleton organization and biogenesis0.0131029077561029
GO:0016504protease activator activity0.013737900740806
GO:0000299integral to membrane of membrane fraction0.013737900740806
GO:0016043cellular component organization and biogenesis0.013749311394344
GO:0046425regulation of JAK-STAT cascade0.0140315153656317
GO:0042311vasodilation0.0140692156112715
GO:0042310vasoconstriction0.0140692156112715
GO:0046209nitric oxide metabolic process0.0140692156112715
GO:0043407negative regulation of MAP kinase activity0.0140692156112715
GO:0042632cholesterol homeostasis0.0140692156112715
GO:0006809nitric oxide biosynthetic process0.0140692156112715
GO:0006940regulation of smooth muscle contraction0.0140692156112715
GO:0055088lipid homeostasis0.0140692156112715
GO:0051899membrane depolarization0.0140692156112715
GO:0055092sterol homeostasis0.0140692156112715
GO:0043408regulation of MAPKKK cascade0.0140692156112715
GO:0051016barbed-end actin filament capping0.0140692156112715
GO:0030835negative regulation of actin filament depolymerization0.0140692156112715
GO:0006641triacylglycerol metabolic process0.0140692156112715
GO:0051693actin filament capping0.0140692156112715
GO:0019216regulation of lipid metabolic process0.0140692156112715
GO:0065008regulation of biological quality0.0141602239531468
GO:0030834regulation of actin filament depolymerization0.0141602239531468
GO:0051260protein homooligomerization0.0141602239531468
GO:0030042actin filament depolymerization0.0141602239531468
GO:0001666response to hypoxia0.0141602239531468
GO:0030879mammary gland development0.0145734667951733
GO:0006639acylglycerol metabolic process0.0156225056388434
GO:0046486glycerolipid metabolic process0.0157301330214369
GO:0006638neutral lipid metabolic process0.0157301330214369
GO:0006939smooth muscle contraction0.0158307499795965
GO:0006662glycerol ether metabolic process0.0158307499795965
GO:0007259JAK-STAT cascade0.0159795788235808
GO:0051241negative regulation of multicellular organismal process0.0159795788235808
GO:0001570vasculogenesis0.0159795788235808
GO:0051259protein oligomerization0.0159795788235808
GO:0008064regulation of actin polymerization and/or depolymerization0.0159795788235808
GO:0009890negative regulation of biosynthetic process0.0159795788235808
GO:0051261protein depolymerization0.0159795788235808
GO:0032535regulation of cellular component size0.0159795788235808
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0159795788235808
GO:0030832regulation of actin filament length0.0159795788235808
GO:0006937regulation of muscle contraction0.0159795788235808
GO:0051129negative regulation of cellular component organization and biogenesis0.0159795788235808
GO:0045121lipid raft0.0159795788235808
GO:0003018vascular process in circulatory system0.0159795788235808
GO:0035150regulation of tube size0.0159795788235808
GO:0051493regulation of cytoskeleton organization and biogenesis0.0159795788235808
GO:0033043regulation of organelle organization and biogenesis0.0159795788235808
GO:0050880regulation of blood vessel size0.0159795788235808
GO:0048471perinuclear region of cytoplasm0.0159795788235808
GO:0048523negative regulation of cellular process0.0159795788235808
GO:0030855epithelial cell differentiation0.0159795788235808
GO:0006469negative regulation of protein kinase activity0.0159795788235808
GO:0033673negative regulation of kinase activity0.0159795788235808
GO:0051348negative regulation of transferase activity0.0166693735062763
GO:0008154actin polymerization and/or depolymerization0.0173431207786081
GO:0048519negative regulation of biological process0.0175818613596208
GO:0042391regulation of membrane potential0.0177991051732299
GO:0005938cell cortex0.0194749469217216
GO:0043086negative regulation of catalytic activity0.0194749469217216
GO:0051128regulation of cellular component organization and biogenesis0.0221237649373292
GO:0006874cellular calcium ion homeostasis0.0239057884286992
GO:0043405regulation of MAP kinase activity0.0240510247413231
GO:0055074calcium ion homeostasis0.0241931599858816
GO:0006996organelle organization and biogenesis0.0249903506627886
GO:0006875cellular metal ion homeostasis0.0256294601944308
GO:0055065metal ion homeostasis0.0258698153636066
GO:0051248negative regulation of protein metabolic process0.0258698153636066
GO:0048732gland development0.0278617492606456
GO:0044271nitrogen compound biosynthetic process0.0283283464028833
GO:0003012muscle system process0.030325157929097
GO:0006936muscle contraction0.030325157929097
GO:0045596negative regulation of cell differentiation0.0307538950754711
GO:0009968negative regulation of signal transduction0.0322439760883674
GO:0007519skeletal muscle development0.03277731045783
GO:0008015blood circulation0.03277731045783
GO:0003013circulatory system process0.03277731045783
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.03277731045783
GO:0055066di-, tri-valent inorganic cation homeostasis0.0334994817972183
GO:0006816calcium ion transport0.0345952572881161
GO:0030003cellular cation homeostasis0.0345952572881161
GO:0051093negative regulation of developmental process0.0345952572881161
GO:0055080cation homeostasis0.0352516481138001
GO:0005515protein binding0.0352516481138001
GO:0051336regulation of hydrolase activity0.0353110778694542
GO:0051240positive regulation of multicellular organismal process0.0375581357212475
GO:0008285negative regulation of cell proliferation0.0375581357212475
GO:0000165MAPKKK cascade0.0375581357212475
GO:0048771tissue remodeling0.0378576733827624
GO:0014706striated muscle development0.0378576733827624
GO:0002009morphogenesis of an epithelium0.0378576733827624
GO:0006461protein complex assembly0.0381562639468962
GO:0045859regulation of protein kinase activity0.0384499058216531
GO:0043549regulation of kinase activity0.0395773064087564
GO:0015674di-, tri-valent inorganic cation transport0.0395773064087564
GO:0043085positive regulation of catalytic activity0.0395773064087564
GO:0051338regulation of transferase activity0.0395773064087564
GO:0055082cellular chemical homeostasis0.0421181734176855
GO:0006873cellular ion homeostasis0.0421181734176855
GO:0035239tube morphogenesis0.0423645627375206
GO:0005096GTPase activator activity0.0428887853344136
GO:0045595regulation of cell differentiation0.0431253665652444
GO:0009889regulation of biosynthetic process0.0433582941140103
GO:0006631fatty acid metabolic process0.0444132124674194
GO:0007517muscle development0.0452719842466176
GO:0050801ion homeostasis0.0452719842466176
GO:0010324membrane invagination0.0452719842466176
GO:0006897endocytosis0.0452719842466176
GO:0048514blood vessel morphogenesis0.0462736517263243



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 bud3.29e-0817
cardiovascular system1.53e-0723
circulatory system1.53e-0723
lung6.07e-0714
respiratory tube6.07e-0714
respiration organ6.07e-0714
pair of lungs6.07e-0714
lung primordium6.07e-0714
lung bud6.07e-0714
epithelial fold9.14e-0720


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)
MA0003.10.829197
MA0004.10.303605
MA0006.10.16569
MA0007.10.790701
MA0009.10.709264
MA0014.10.0136923
MA0017.11.04297
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.173587
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.10.432665
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.168666
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.89968
MA0056.10
MA0057.10.151898
MA0058.10.223242
MA0059.10.658541
MA0060.10.108526
MA0061.10.805149
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.10.361347
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.10.00478565
MA0074.10.390075
MA0076.10.200996
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.0983922
MA0089.10
MA0090.10.753315
MA0091.10.315003
MA0092.10.753925
MA0093.10.179936
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.675688
MA0103.11.07649
MA0105.10.846872
MA0106.10.478503
MA0107.10.555009
MA0108.20.557195
MA0109.10
MA0111.10.78079
MA0113.10.452439
MA0114.10.797973
MA0115.10.805567
MA0116.11.52988
MA0117.10.774259
MA0119.11.25662
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.14.16003
MA0140.10.379562
MA0141.10.210047
MA0142.10.604892
MA0143.10.467531
MA0144.10.129525
MA0145.10.0257706
MA0146.10.142424
MA0147.10.138228
MA0148.10.317692
MA0149.10.245177
MA0062.20.0662974
MA0035.20.383789
MA0039.20.382143
MA0138.20.523978
MA0002.20.0901987
MA0137.20.207733
MA0104.20.099275
MA0047.20.431964
MA0112.20.025769
MA0065.20.265926
MA0150.10.790482
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.11.03999
MA0155.11.71283
MA0156.10.200311
MA0157.10.574484
MA0158.10
MA0159.10.876351
MA0160.10.320315
MA0161.10
MA0162.10.0257461
MA0163.10.069011
MA0164.13.78388
MA0080.20.190316
MA0018.20.417217
MA0099.20.518072
MA0079.20.0563048
MA0102.21.42135
MA0258.10.376353
MA0259.10.408856
MA0442.10
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