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MCL coexpression mm9:1361: Difference between revisions

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{{MCL_coexpression_mm9
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visible light;0.028009667856003;14688!GO:0007265;Ras protein signal transduction;0.028009667856003;213498,14688!GO:0004013;adenosylhomocysteinase activity;0.028009667856003;229709!GO:0016802;trialkylsulfonium hydrolase activity;0.028009667856003;229709!GO:0009628;response to abiotic stimulus;0.028009667856003;320795,14688!GO:0007213;acetylcholine receptor signaling, muscarinic pathway;0.028009667856003;14688!GO:0006972;hyperosmotic response;0.028009667856003;320795!GO:0004839;ubiquitin activating enzyme activity;0.0306322172622778;!GO:0016801;hydrolase activity, acting on ether bonds;0.0326707847199443;229709!GO:0008641;small protein activating enzyme activity;0.0391963502129323;!GO:0006970;response to osmotic stress;0.0488628921394105;320795!GO:0007264;small GTPase mediated signal transduction;0.0488628921394105;213498,14688!GO:0030010;establishment of cell 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|ontology_enrichment_celltype=CL:0002321!1.28e-13!70;CL:0000393!1.25e-10!39;CL:0000211!1.25e-10!39;CL:0000055!4.48e-10!49;CL:0000117!1.06e-09!23;CL:0000337!1.06e-09!23;CL:0000540!6.14e-09!33;CL:0000047!6.14e-09!33;CL:0000031!6.14e-09!33;CL:0000404!6.14e-09!33;CL:0000221!1.55e-08!44;CL:0000133!1.55e-08!44;CL:0002319!2.08e-08!43
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!1.92e-19!75;UBERON:0001017!2.64e-19!73;UBERON:0000073!2.27e-18!54;UBERON:0004121!2.20e-17!95;UBERON:0000924!2.20e-17!95;UBERON:0006601!2.20e-17!95;UBERON:0001049!2.98e-17!52;UBERON:0005068!2.98e-17!52;UBERON:0006241!2.98e-17!52;UBERON:0007135!2.98e-17!52;UBERON:0000955!1.19e-14!47;UBERON:0006238!1.19e-14!47;UBERON:0002346!1.21e-14!64;UBERON:0003075!1.21e-14!64;UBERON:0007284!1.21e-14!64;UBERON:0002020!2.13e-14!34;UBERON:0010371!2.64e-14!73;UBERON:0002616!2.97e-14!46;UBERON:0003080!1.01e-12!40;UBERON:0002780!3.19e-12!39;UBERON:0001890!3.19e-12!39;UBERON:0006240!3.19e-12!39;UBERON:0003528!4.56e-12!29;UBERON:0002791!4.56e-12!29;UBERON:0001893!4.56e-12!29;UBERON:0003056!8.11e-11!49;UBERON:0011216!1.84e-08!194;UBERON:0000956!2.40e-08!21;UBERON:0001869!2.40e-08!21;UBERON:0000203!2.40e-08!21;UBERON:0002619!3.53e-08!17;UBERON:0010314!6.89e-08!92;UBERON:0000160!1.94e-07!31;UBERON:0000477!6.45e-07!244
|tfbs_overrepresentation_for_novel_motifs=1.23219,1.24447,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.594834,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.143775,0.426133,0.35122,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,1.02135,0.181062,0.558142,0.960397,0.336199,0.589948,0.364821,1.36145,0.326478,0.629145,0.303703,0.27383,0.342638,0.56353,0.0995018,0.366415,0.659176,1.30113,0.77511,0.589246,0.0835644,1.02809,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,1.36208,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,4.64017,1.156,0.599223,1.70884,0.589776,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,5.55221,0.0610418,1.02367,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,1.47187,0.769162,0.685716,0.976308,0.775372,0.160254,0.871473,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,0.585058,0.435642,1.09461,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,1.87959,0.53982,0.858327,0.862623,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,1.5739,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,1.38743,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,1.25623,0.348692,1.03315,6.0079,1.10596,0.287383,0.678689,1.18867,0.71546,0.983048,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,1.28815
}}

Latest revision as of 16:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:37781865..37781924,-p1@Gcap14
Mm9::chr3:107499380..107499492,-p1@Ahcyl1
Mm9::chr3:87421463..87421535,+p1@Arhgef11
Mm9::chr4:154865462..154865520,+p1@Gnb1
Mm9::chr7:104937295..104937344,+p5@Pak1
Mm9::chrX:20240024..20240035,+p3@Uba1


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:0007603phototransduction, visible light0.028009667856003
GO:0007265Ras protein signal transduction0.028009667856003
GO:0004013adenosylhomocysteinase activity0.028009667856003
GO:0016802trialkylsulfonium hydrolase activity0.028009667856003
GO:0009628response to abiotic stimulus0.028009667856003
GO:0007213acetylcholine receptor signaling, muscarinic pathway0.028009667856003
GO:0006972hyperosmotic response0.028009667856003
GO:0004839ubiquitin activating enzyme activity0.0306322172622778
GO:0016801hydrolase activity, acting on ether bonds0.0326707847199443
GO:0008641small protein activating enzyme activity0.0391963502129323
GO:0006970response to osmotic stress0.0488628921394105
GO:0007264small GTPase mediated signal transduction0.0488628921394105
GO:0030010establishment of cell polarity0.0489685997794773



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 system1.92e-1975
central nervous system2.64e-1973
regional part of nervous system2.27e-1854
ectoderm-derived structure2.20e-1795
ectoderm2.20e-1795
presumptive ectoderm2.20e-1795
neural tube2.98e-1752
neural rod2.98e-1752
future spinal cord2.98e-1752
neural keel2.98e-1752
brain1.19e-1447
future brain1.19e-1447
neurectoderm1.21e-1464
neural plate1.21e-1464
presumptive neural plate1.21e-1464
gray matter2.13e-1434
ecto-epithelium2.64e-1473
regional part of brain2.97e-1446
anterior neural tube1.01e-1240
regional part of forebrain3.19e-1239
forebrain3.19e-1239
future forebrain3.19e-1239
brain grey matter4.56e-1229
regional part of telencephalon4.56e-1229
telencephalon4.56e-1229
pre-chordal neural plate8.11e-1149
organ system subdivision1.84e-08194
cerebral cortex2.40e-0821
cerebral hemisphere2.40e-0821
pallium2.40e-0821
regional part of cerebral cortex3.53e-0817
structure with developmental contribution from neural crest6.89e-0892
intestine1.94e-0731
anatomical cluster6.45e-07244


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)
MA0003.12.22936
MA0004.10.536396
MA0006.11.68531
MA0007.10.52077
MA0009.10.987341
MA0014.16.06782
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.969171
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.17.06521
MA0074.10.638014
MA0076.11.04996
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.111145
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.11.0169
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.822296
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.11.2655
MA0140.10.625902
MA0141.11.07584
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.761789
MA0146.11.89206
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.25.87618
MA0138.20.788113
MA0002.21.27678
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.76177
MA0065.20.763394
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.11.33283
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.13.21072
MA0163.11.03138
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.23.78002
MA0102.21.7182
MA0258.10.290587
MA0259.11.5079
MA0442.10
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