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MCL coexpression mm9:3011: Difference between revisions

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{{MCL_coexpression_mm9
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activity;0.00635494561255974;29858!GO:0019307;mannose biosynthetic process;0.00635494561255974;29858!GO:0017176;phosphatidylinositol N-acetylglucosaminyltransferase activity;0.00847279656663992;14755!GO:0016868;intramolecular transferase activity, phosphotransferases;0.0118662327192853;29858!GO:0006013;mannose metabolic process;0.0118662327192853;29858!GO:0009059;macromolecule biosynthetic process;0.0118662327192853;14755,29858!GO:0046489;phosphoinositide biosynthetic process;0.0127001419728853;14755!GO:0006506;GPI anchor biosynthetic process;0.0127001419728853;14755!GO:0006505;GPI anchor metabolic process;0.0127001419728853;14755!GO:0019319;hexose biosynthetic process;0.0127001419728853;29858!GO:0046165;alcohol biosynthetic process;0.0127001419728853;29858!GO:0046364;monosaccharide biosynthetic process;0.0127001419728853;29858!GO:0016866;intramolecular transferase activity;0.0127001419728853;29858!GO:0008375;acetylglucosaminyltransferase 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|gostat_on_MCL_coexpression=GO:0004615;phosphomannomutase activity;0.00635494561255974;29858!GO:0019307;mannose biosynthetic process;0.00635494561255974;29858!GO:0017176;phosphatidylinositol N-acetylglucosaminyltransferase activity;0.00847279656663992;14755!GO:0016868;intramolecular transferase activity, phosphotransferases;0.0118662327192853;29858!GO:0006013;mannose metabolic process;0.0118662327192853;29858!GO:0009059;macromolecule biosynthetic process;0.0118662327192853;14755,29858!GO:0046489;phosphoinositide biosynthetic process;0.0127001419728853;14755!GO:0006506;GPI anchor biosynthetic process;0.0127001419728853;14755!GO:0006505;GPI anchor metabolic process;0.0127001419728853;14755!GO:0019319;hexose biosynthetic process;0.0127001419728853;29858!GO:0046165;alcohol biosynthetic process;0.0127001419728853;29858!GO:0046364;monosaccharide biosynthetic process;0.0127001419728853;29858!GO:0016866;intramolecular transferase activity;0.0127001419728853;29858!GO:0008375;acetylglucosaminyltransferase activity;0.0127001419728853;14755!GO:0046474;glycerophospholipid biosynthetic process;0.0127001419728853;14755!GO:0009058;biosynthetic process;0.0140788124567925;14755,29858!GO:0006497;protein amino acid lipidation;0.0155164378682723;14755!GO:0030384;phosphoinositide metabolic process;0.0155164378682723;14755!GO:0042158;lipoprotein biosynthetic process;0.0157007492328778;14755!GO:0042157;lipoprotein metabolic process;0.0167282449499493;14755!GO:0008654;phospholipid biosynthetic process;0.0167282449499493;14755!GO:0006650;glycerophospholipid metabolic process;0.0167282449499493;14755!GO:0046467;membrane lipid biosynthetic process;0.0198555935392707;14755!GO:0016051;carbohydrate biosynthetic process;0.0208742371195118;29858!GO:0008194;UDP-glycosyltransferase activity;0.0218107067656773;14755!GO:0006644;phospholipid metabolic process;0.0282642874915134;14755!GO:0019318;hexose metabolic process;0.0294755794378617;29858!GO:0005996;monosaccharide metabolic process;0.0294755794378617;29858!GO:0016758;transferase activity, transferring hexosyl groups;0.0294755794378617;14755!GO:0006643;membrane lipid metabolic process;0.0310316901515955;14755!GO:0016853;isomerase activity;0.0310316901515955;29858!GO:0016757;transferase activity, transferring glycosyl groups;0.0451561517912396;14755!GO:0008610;lipid biosynthetic process;0.0451561517912396;14755!GO:0044262;cellular carbohydrate metabolic process;0.0458003654367581;29858!GO:0006066;alcohol metabolic process;0.0458003654367581;29858!
|ontology_enrichment_celltype=CL:0000055!4.92e-19!49;CL:0002319!4.78e-17!43;CL:0000221!1.11e-16!44;CL:0000133!1.11e-16!44;CL:0000393!6.17e-14!39;CL:0000211!6.17e-14!39;CL:0000540!4.58e-12!33;CL:0000047!4.58e-12!33;CL:0000031!4.58e-12!33;CL:0000404!4.58e-12!33;CL:0000117!4.28e-10!23;CL:0000337!4.28e-10!23;CL:0002321!2.62e-09!70
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!8.35e-29!75;UBERON:0001017!3.06e-28!73;UBERON:0004121!2.32e-27!95;UBERON:0000924!2.32e-27!95;UBERON:0006601!2.32e-27!95;UBERON:0002346!1.93e-21!64;UBERON:0003075!1.93e-21!64;UBERON:0007284!1.93e-21!64;UBERON:0000073!1.21e-20!54;UBERON:0001049!3.15e-19!52;UBERON:0005068!3.15e-19!52;UBERON:0006241!3.15e-19!52;UBERON:0007135!3.15e-19!52;UBERON:0010371!8.58e-19!73;UBERON:0000955!7.51e-17!47;UBERON:0006238!7.51e-17!47;UBERON:0002020!7.99e-17!34;UBERON:0010314!2.16e-16!92;UBERON:0002616!2.42e-16!46;UBERON:0003528!1.45e-14!29;UBERON:0002791!1.45e-14!29;UBERON:0001893!1.45e-14!29;UBERON:0003056!2.00e-14!49;UBERON:0003080!3.63e-13!40;UBERON:0002780!1.19e-12!39;UBERON:0001890!1.19e-12!39;UBERON:0006240!1.19e-12!39;UBERON:0000956!1.93e-11!21;UBERON:0001869!1.93e-11!21;UBERON:0000203!1.93e-11!21;UBERON:0002619!3.31e-10!17;UBERON:0002021!1.28e-07!10;UBERON:0000411!1.28e-07!10;UBERON:0001950!1.28e-07!10;UBERON:0003076!5.15e-07!12;UBERON:0003057!5.15e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,1.17946,0.479531,0.235304,0.870507,0.906098,1.18012,0.933025,0.608226,0,1.14208,0.578045,1.98772,0.876292,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,1.05917,0.608816,0.444545,0.563758,0.902078,0.536514,1.24975,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.663409,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,1.07031,0.402065,0.411601,1.04436,1.20986,0.684144,1.19917,1.16055,1.00151,0.459035,1.32978,1.62246,0.195254,0.380977,1.06194,2.07346,3.54973,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.833542
}}

Latest revision as of 19:26, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:81791248..81791276,-p2@Pmm1
Mm9::chr15:81791281..81791302,-p1@Pmm1
Mm9::chr7:35015332..35015343,-p3@Gpi1


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:0004615phosphomannomutase activity0.00635494561255974
GO:0019307mannose biosynthetic process0.00635494561255974
GO:0017176phosphatidylinositol N-acetylglucosaminyltransferase activity0.00847279656663992
GO:0016868intramolecular transferase activity, phosphotransferases0.0118662327192853
GO:0006013mannose metabolic process0.0118662327192853
GO:0009059macromolecule biosynthetic process0.0118662327192853
GO:0046489phosphoinositide biosynthetic process0.0127001419728853
GO:0006506GPI anchor biosynthetic process0.0127001419728853
GO:0006505GPI anchor metabolic process0.0127001419728853
GO:0019319hexose biosynthetic process0.0127001419728853
GO:0046165alcohol biosynthetic process0.0127001419728853
GO:0046364monosaccharide biosynthetic process0.0127001419728853
GO:0016866intramolecular transferase activity0.0127001419728853
GO:0008375acetylglucosaminyltransferase activity0.0127001419728853
GO:0046474glycerophospholipid biosynthetic process0.0127001419728853
GO:0009058biosynthetic process0.0140788124567925
GO:0006497protein amino acid lipidation0.0155164378682723
GO:0030384phosphoinositide metabolic process0.0155164378682723
GO:0042158lipoprotein biosynthetic process0.0157007492328778
GO:0042157lipoprotein metabolic process0.0167282449499493
GO:0008654phospholipid biosynthetic process0.0167282449499493
GO:0006650glycerophospholipid metabolic process0.0167282449499493
GO:0046467membrane lipid biosynthetic process0.0198555935392707
GO:0016051carbohydrate biosynthetic process0.0208742371195118
GO:0008194UDP-glycosyltransferase activity0.0218107067656773
GO:0006644phospholipid metabolic process0.0282642874915134
GO:0019318hexose metabolic process0.0294755794378617
GO:0005996monosaccharide metabolic process0.0294755794378617
GO:0016758transferase activity, transferring hexosyl groups0.0294755794378617
GO:0006643membrane lipid metabolic process0.0310316901515955
GO:0016853isomerase activity0.0310316901515955
GO:0016757transferase activity, transferring glycosyl groups0.0451561517912396
GO:0008610lipid biosynthetic process0.0451561517912396
GO:0044262cellular carbohydrate metabolic process0.0458003654367581
GO:0006066alcohol metabolic process0.0458003654367581



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>

Uber Anatomy
Ontology termp-valuen
nervous system8.35e-2975
central nervous system3.06e-2873
ectoderm-derived structure2.32e-2795
ectoderm2.32e-2795
presumptive ectoderm2.32e-2795
neurectoderm1.93e-2164
neural plate1.93e-2164
presumptive neural plate1.93e-2164
regional part of nervous system1.21e-2054
neural tube3.15e-1952
neural rod3.15e-1952
future spinal cord3.15e-1952
neural keel3.15e-1952
ecto-epithelium8.58e-1973
brain7.51e-1747
future brain7.51e-1747
gray matter7.99e-1734
structure with developmental contribution from neural crest2.16e-1692
regional part of brain2.42e-1646
brain grey matter1.45e-1429
regional part of telencephalon1.45e-1429
telencephalon1.45e-1429
pre-chordal neural plate2.00e-1449
anterior neural tube3.63e-1340
regional part of forebrain1.19e-1239
forebrain1.19e-1239
future forebrain1.19e-1239
cerebral cortex1.93e-1121
cerebral hemisphere1.93e-1121
pallium1.93e-1121
regional part of cerebral cortex3.31e-1017
occipital lobe1.28e-0710
visual cortex1.28e-0710
neocortex1.28e-0710
posterior neural tube5.15e-0712
chordal neural plate5.15e-0712


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)
MA0003.11.87396
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.11.33691
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.11.49373
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.932001
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.14.16062
MA0074.12.10566
MA0076.11.58243
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.766354
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.11.3296
MA0115.11.38041
MA0116.12.49617
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.12.03543
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.11.44606
MA0146.12.77996
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.26.10909
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.21.21648
MA0047.20.962424
MA0112.20.29236
MA0065.20.79573
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.11.53682
MA0163.13.6249
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.27.3104
MA0102.22.01714
MA0258.10.520639
MA0259.11.34197
MA0442.10
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