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MCL coexpression mm9:2959: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0017000;antibiotic biosynthetic process;0.0153365824918586;!GO:0016999;antibiotic metabolic process;0.0153365824918586;!GO:0017144;drug metabolic process;0.0153365824918586;!GO:0007632;visual behavior;0.0341393564777385;18574!GO:0008542;visual learning;0.0341393564777385;18574!GO:0004114;3',5'-cyclic-nucleotide phosphodiesterase activity;0.0341393564777385;18574!GO:0004112;cyclic-nucleotide phosphodiesterase activity;0.0341393564777385;18574!GO:0007612;learning;0.047803038389033;18574!GO:0005089;Rho guanyl-nucleotide exchange factor activity;0.047803038389033;207212!GO:0035023;regulation of Rho protein signal transduction;0.047803038389033;207212!GO:0005088;Ras guanyl-nucleotide exchange factor activity;0.047803038389033;207212!GO:0008081;phosphoric diester hydrolase activity;0.047803038389033;18574!GO:0007611;learning and/or memory;0.047803038389033;18574!GO:0009416;response to light stimulus;0.047803038389033;18574!GO:0007266;Rho protein signal transduction;0.0488756573929596;207212!
|ontology_enrichment_celltype=CL:0000117!2.44e-13!23;CL:0000337!2.44e-13!23;CL:0000221!1.10e-10!44;CL:0000133!1.10e-10!44;CL:0002319!1.20e-10!43;CL:0000540!1.55e-10!33;CL:0000047!1.55e-10!33;CL:0000031!1.55e-10!33;CL:0000404!1.55e-10!33;CL:0000055!5.79e-07!49
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002346!3.23e-28!64;UBERON:0003075!3.23e-28!64;UBERON:0007284!3.23e-28!64;UBERON:0001017!6.19e-27!73;UBERON:0001016!1.21e-26!75;UBERON:0000073!9.45e-26!54;UBERON:0004121!1.54e-24!95;UBERON:0000924!1.54e-24!95;UBERON:0006601!1.54e-24!95;UBERON:0001049!3.56e-24!52;UBERON:0005068!3.56e-24!52;UBERON:0006241!3.56e-24!52;UBERON:0007135!3.56e-24!52;UBERON:0003056!3.60e-23!49;UBERON:0010371!3.63e-23!73;UBERON:0000955!1.65e-20!47;UBERON:0006238!1.65e-20!47;UBERON:0002616!8.07e-20!46;UBERON:0003080!2.44e-18!40;UBERON:0002780!1.03e-17!39;UBERON:0001890!1.03e-17!39;UBERON:0006240!1.03e-17!39;UBERON:0002020!2.82e-17!34;UBERON:0010314!1.40e-15!92;UBERON:0003528!9.70e-14!29;UBERON:0002791!9.70e-14!29;UBERON:0001893!9.70e-14!29;UBERON:0000956!9.05e-09!21;UBERON:0001869!9.05e-09!21;UBERON:0000203!9.05e-09!21;UBERON:0002619!4.86e-08!17
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,1.05917,1.47967,0.872889,2.37023,0.902078,0.536514,1.24975,0.582863,0.831295,0.261619,0.610669,0.922882,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,2.1742,1.44925,1.882,1.83166,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,8.73829,1.69956,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,1.31639,0.509215,0.464141,1.26539,1.05692,0.928366,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,1.63106,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.79445,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,2.45536,0.38417,4.69532,1.39822,1.28513,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,1.95046
}}

Latest revision as of 19:21, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:103333594..103333648,+p2@Pde1b
Mm9::chr7:108043087..108043098,-p8@Arhgef17
Mm9::chr8:121970938..121971035,+p1@Necab2


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:0017000antibiotic biosynthetic process0.0153365824918586
GO:0016999antibiotic metabolic process0.0153365824918586
GO:0017144drug metabolic process0.0153365824918586
GO:0007632visual behavior0.0341393564777385
GO:0008542visual learning0.0341393564777385
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.0341393564777385
GO:0004112cyclic-nucleotide phosphodiesterase activity0.0341393564777385
GO:0007612learning0.047803038389033
GO:0005089Rho guanyl-nucleotide exchange factor activity0.047803038389033
GO:0035023regulation of Rho protein signal transduction0.047803038389033
GO:0005088Ras guanyl-nucleotide exchange factor activity0.047803038389033
GO:0008081phosphoric diester hydrolase activity0.047803038389033
GO:0007611learning and/or memory0.047803038389033
GO:0009416response to light stimulus0.047803038389033
GO:0007266Rho protein signal transduction0.0488756573929596



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
CNS neuron (sensu Vertebrata)2.44e-1323
neuroblast (sensu Vertebrata)2.44e-1323
ectodermal cell1.10e-1044
neurectodermal cell1.10e-1044
neural cell1.20e-1043
neuron1.55e-1033
neuronal stem cell1.55e-1033
neuroblast1.55e-1033
electrically signaling cell1.55e-1033
non-terminally differentiated cell5.79e-0749

Uber Anatomy
Ontology termp-valuen
neurectoderm3.23e-2864
neural plate3.23e-2864
presumptive neural plate3.23e-2864
central nervous system6.19e-2773
nervous system1.21e-2675
regional part of nervous system9.45e-2654
ectoderm-derived structure1.54e-2495
ectoderm1.54e-2495
presumptive ectoderm1.54e-2495
neural tube3.56e-2452
neural rod3.56e-2452
future spinal cord3.56e-2452
neural keel3.56e-2452
pre-chordal neural plate3.60e-2349
ecto-epithelium3.63e-2373
brain1.65e-2047
future brain1.65e-2047
regional part of brain8.07e-2046
anterior neural tube2.44e-1840
regional part of forebrain1.03e-1739
forebrain1.03e-1739
future forebrain1.03e-1739
gray matter2.82e-1734
structure with developmental contribution from neural crest1.40e-1592
brain grey matter9.70e-1429
regional part of telencephalon9.70e-1429
telencephalon9.70e-1429
cerebral cortex9.05e-0921
cerebral hemisphere9.05e-0921
pallium9.05e-0921
regional part of cerebral cortex4.86e-0817


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)
MA0003.13.77865
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.11.93445
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
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
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.896032
MA0058.11.65098
MA0059.11.68104
MA0060.10.502699
MA0061.11.33581
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.13.60195
MA0074.10.911576
MA0076.10.657929
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
MA0105.12.75918
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.11.46662
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
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.10.292366
MA0146.10.900029
MA0147.11.37022
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.22.07301
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.21.21648
MA0047.20.962424
MA0112.20.794478
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.925147
MA0155.11.52001
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.17.41514
MA0163.11.48428
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.26.70315
MA0102.22.01714
MA0258.10.520639
MA0259.11.34197
MA0442.10
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