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MCL coexpression mm9:528: Difference between revisions

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{{MCL_coexpression_mm9
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cytoskeleton organization and biogenesis;0.0179285596888183;53857,22210!GO:0008611;ether lipid biosynthetic process;0.0179285596888183;14712!GO:0016287;glycerone-phosphate O-acyltransferase activity;0.0179285596888183;14712!GO:0046485;ether lipid metabolic process;0.0179285596888183;14712!GO:0004083;bisphosphoglycerate phosphatase activity;0.0238929610542396;56012!GO:0004082;bisphosphoglycerate mutase activity;0.0238929610542396;56012!GO:0043034;costamere;0.0238929610542396;!GO:0005782;peroxisomal matrix;0.0238929610542396;14712!GO:0004619;phosphoglycerate mutase activity;0.0238929610542396;56012!GO:0007288;sperm axoneme assembly;0.0238929610542396;22210!GO:0035084;flagellum axoneme biogenesis;0.0238929610542396;22210!GO:0016413;O-acetyltransferase activity;0.0238929610542396;14712!GO:0007017;microtubule-based process;0.0255953936678224;53857,22210!GO:0035082;axoneme biogenesis;0.0255953936678224;22210!GO:0009296;flagellum biogenesis;0.028662129411539;22210!GO:0043064;flagellum organization and biogenesis;0.0301607463160448;22210!GO:0044265;cellular macromolecule catabolic process;0.0301607463160448;56012,22210!GO:0046504;glycerol ether biosynthetic process;0.0301607463160448;14712!GO:0045017;glycerolipid biosynthetic process;0.0301607463160448;14712!GO:0001578;microtubule bundle formation;0.0306942858054484;22210!GO:0016868;intramolecular transferase activity, phosphotransferases;0.0306942858054484;56012!GO:0009057;macromolecule catabolic 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|gostat_on_MCL_coexpression=GO:0000226;microtubule cytoskeleton organization and biogenesis;0.0179285596888183;53857,22210!GO:0008611;ether lipid biosynthetic process;0.0179285596888183;14712!GO:0016287;glycerone-phosphate O-acyltransferase activity;0.0179285596888183;14712!GO:0046485;ether lipid metabolic process;0.0179285596888183;14712!GO:0004083;bisphosphoglycerate phosphatase activity;0.0238929610542396;56012!GO:0004082;bisphosphoglycerate mutase activity;0.0238929610542396;56012!GO:0043034;costamere;0.0238929610542396;!GO:0005782;peroxisomal matrix;0.0238929610542396;14712!GO:0004619;phosphoglycerate mutase activity;0.0238929610542396;56012!GO:0007288;sperm axoneme assembly;0.0238929610542396;22210!GO:0035084;flagellum axoneme biogenesis;0.0238929610542396;22210!GO:0016413;O-acetyltransferase activity;0.0238929610542396;14712!GO:0007017;microtubule-based process;0.0255953936678224;53857,22210!GO:0035082;axoneme biogenesis;0.0255953936678224;22210!GO:0009296;flagellum biogenesis;0.028662129411539;22210!GO:0043064;flagellum organization and biogenesis;0.0301607463160448;22210!GO:0044265;cellular macromolecule catabolic process;0.0301607463160448;56012,22210!GO:0046504;glycerol ether biosynthetic process;0.0301607463160448;14712!GO:0045017;glycerolipid biosynthetic process;0.0301607463160448;14712!GO:0001578;microtubule bundle formation;0.0306942858054484;22210!GO:0016868;intramolecular transferase activity, phosphotransferases;0.0306942858054484;56012!GO:0009057;macromolecule catabolic process;0.0431722467445519;56012,22210!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007100!6.23e-07!18;UBERON:0000948!6.23e-07!18;UBERON:0005498!6.23e-07!18;UBERON:0004140!6.23e-07!18;UBERON:0009881!6.23e-07!18;UBERON:0004141!6.23e-07!18;UBERON:0003084!6.23e-07!18;UBERON:0007005!6.23e-07!18;UBERON:0004139!6.23e-07!18;UBERON:0004291!6.23e-07!18
|tfbs_overrepresentation_for_novel_motifs=0.6379,0.686627,0.589984,0.25808,0.781942,0.269875,0.915684,0.875434,0.251553,0.646925,0.308886,0.336042,0.237599,0.357027,0.419678,0,1.31449,0.377686,1.72841,0.751449,0.176628,1.17357,1.67324,0.122718,0.210021,0.381085,0.203385,0.782755,0.154744,1.83883,0.75617,0.624931,1.2318,0.702925,0.832139,0.155394,0.358314,0.332941,0.097604,0.581324,0.384293,0.76591,0.295897,0.136236,1.23768,0.695306,0.457618,0.300372,0.0394476,0.474834,0.514446,0.404841,0.321327,0.759566,0.776306,0.952972,0.163199,0.868243,0.190698,0.949048,0.606104,0.413233,0.569343,0.504093,0.372973,0.541429,0.908031,1.25063,0.60172,1.10561,0.555733,0.246154,0.178539,0.808562,0.407198,2.52588,0.702638,0.447339,0.590017,0.179738,0.247973,0.546623,0.411949,0.0636668,1.66599,1.49166,0.00381013,0.0368325,0.462057,1.41118,0.975915,0.702809,0.636995,0.127646,0.0951738,0.0848579,0.0656861,0.639644,0.457849,0.529405,0.358446,0.624668,0.742871,0.514993,1.27935,0.76508,0.569344,0.296997,0.183341,0.177945,1.17217,0.744577,0.180573,0.313258,0.982794,0.381263,1.42983,0.26114,1.31704,0.714691,0.813766,0.484912,0.995764,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,1.90193,0.726634,0.252176,0.877862,0.375176,1.0039,0.0607709,0.231086,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.280171,0.460443,1.73788,0.232952,1.2821,0.3445,1.07944,0.761071,1.0355,0.374365,0.839715,0.405736,0.440483,0.222538,0.230865,0.96517,0.697256,0.593895,0.21719,0.50503,0.367885,0.356446,0.33468,0.774798
}}

Latest revision as of 15:27, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:51814250..51814277,-p3@Ube2b
Mm9::chr11:5703272..5703283,+p@chr11:5703272..5703283
+
Mm9::chr11:5703322..5703350,-p@chr11:5703322..5703350
-
Mm9::chr11:5703561..5703572,-p@chr11:5703561..5703572
-
Mm9::chr12:112216830..112216853,-p4@Ankrd9
Mm9::chr16:8470856..8470900,+p1@Mettl22
Mm9::chr19:18745302..18745339,+p1@2410127L17Rik
Mm9::chr3:33919005..33919032,+p1@Fxr1
Mm9::chr3:87710813..87710831,+p5@Hdgf
Mm9::chr6:121160730..121160737,+p4@Tuba8
Mm9::chr6:121160789..121160804,+p3@Tuba8
Mm9::chr6:121160809..121160831,+p1@Tuba8
Mm9::chr8:127386932..127386989,+p1@Gnpat
Mm9::chr8:87339523..87339533,-p@chr8:87339523..87339533
-


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:0000226microtubule cytoskeleton organization and biogenesis0.0179285596888183
GO:0008611ether lipid biosynthetic process0.0179285596888183
GO:0016287glycerone-phosphate O-acyltransferase activity0.0179285596888183
GO:0046485ether lipid metabolic process0.0179285596888183
GO:0004083bisphosphoglycerate phosphatase activity0.0238929610542396
GO:0004082bisphosphoglycerate mutase activity0.0238929610542396
GO:0043034costamere0.0238929610542396
GO:0005782peroxisomal matrix0.0238929610542396
GO:0004619phosphoglycerate mutase activity0.0238929610542396
GO:0007288sperm axoneme assembly0.0238929610542396
GO:0035084flagellum axoneme biogenesis0.0238929610542396
GO:0016413O-acetyltransferase activity0.0238929610542396
GO:0007017microtubule-based process0.0255953936678224
GO:0035082axoneme biogenesis0.0255953936678224
GO:0009296flagellum biogenesis0.028662129411539
GO:0043064flagellum organization and biogenesis0.0301607463160448
GO:0044265cellular macromolecule catabolic process0.0301607463160448
GO:0046504glycerol ether biosynthetic process0.0301607463160448
GO:0045017glycerolipid biosynthetic process0.0301607463160448
GO:0001578microtubule bundle formation0.0306942858054484
GO:0016868intramolecular transferase activity, phosphotransferases0.0306942858054484
GO:0009057macromolecule catabolic process0.0431722467445519



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
primary circulatory organ6.23e-0718
heart6.23e-0718
primitive heart tube6.23e-0718
primary heart field6.23e-0718
anterior lateral plate mesoderm6.23e-0718
heart tube6.23e-0718
heart primordium6.23e-0718
cardiac mesoderm6.23e-0718
cardiogenic plate6.23e-0718
heart rudiment6.23e-0718


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)
MA0003.12.00246
MA0004.12.84615
MA0006.10.817804
MA0007.10.689082
MA0009.10.649874
MA0014.11.6016
MA0017.10.458117
MA0019.10.480432
MA0024.10.608636
MA0025.12.02771
MA0027.12.275
MA0028.10.430035
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.381016
MA0040.10.661716
MA0041.10.198922
MA0042.10.189008
MA0043.11.75687
MA0046.10.683926
MA0048.12.15231
MA0050.10.789929
MA0051.11.00935
MA0052.10.669354
MA0055.11.58259
MA0056.10
MA0057.11.56086
MA0058.13.089
MA0059.11.68775
MA0060.10.279564
MA0061.10.0995825
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.271058
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.10.627909
MA0074.10.340281
MA0076.10.491745
MA0077.10.632005
MA0078.11.07325
MA0081.10.605506
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.171343
MA0089.10
MA0090.10.231074
MA0091.10.269175
MA0092.10.231323
MA0093.13.47148
MA0095.10
MA0098.10
MA0100.10.879972
MA0101.10.199903
MA0103.10.477056
MA0105.10.385363
MA0106.11.91018
MA0107.10.153373
MA0108.20.50131
MA0109.10
MA0111.10.679612
MA0113.10.400008
MA0114.10.323836
MA0115.10.744589
MA0116.11.91953
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
MA0139.10.499924
MA0140.10.330266
MA0141.10.511953
MA0142.10.547747
MA0143.10.414534
MA0144.12.24304
MA0145.10.370377
MA0146.12.21874
MA0147.13.00648
MA0148.10.271704
MA0149.10.204102
MA0062.20.706083
MA0035.20.33429
MA0039.20.439375
MA0138.20.469076
MA0002.20.235791
MA0137.20.506794
MA0104.22.52199
MA0047.20.380343
MA0112.21.27607
MA0065.20.190247
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.118426
MA0155.10.22104
MA0156.10.163042
MA0157.10.518122
MA0158.10
MA0159.10.365914
MA0160.10.274172
MA0161.10
MA0162.12.05444
MA0163.13.65841
MA0164.10.357779
MA0080.20.153997
MA0018.21.708
MA0099.20.463355
MA0079.25.88685
MA0102.21.35579
MA0258.10.626814
MA0259.11.12445
MA0442.10
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