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MCL coexpression mm9:1342: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0008113;peptide-methionine-(S)-S-oxide reductase activity;0.00591667350134873;110265!GO:0016671;oxidoreductase activity, acting on sulfur group of donors, disulfide as acceptor;0.0118314019548379;110265!GO:0016667;oxidoreductase activity, acting on sulfur group of donors;0.0197125197651981;110265!
|ontology_enrichment_celltype=CL:0000221!7.55e-15!44;CL:0000133!7.55e-15!44;CL:0002319!1.07e-14!43;CL:0000540!2.84e-14!33;CL:0000047!2.84e-14!33;CL:0000031!2.84e-14!33;CL:0000404!2.84e-14!33;CL:0000117!7.50e-14!23;CL:0000337!7.50e-14!23;CL:0000055!1.64e-10!49;CL:0000393!1.44e-09!39;CL:0000211!1.44e-09!39
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!3.70e-31!73;UBERON:0001016!4.43e-30!75;UBERON:0004121!1.18e-28!95;UBERON:0000924!1.18e-28!95;UBERON:0006601!1.18e-28!95;UBERON:0000073!6.13e-26!54;UBERON:0002346!4.39e-25!64;UBERON:0003075!4.39e-25!64;UBERON:0007284!4.39e-25!64;UBERON:0010371!1.98e-24!73;UBERON:0001049!2.27e-24!52;UBERON:0005068!2.27e-24!52;UBERON:0006241!2.27e-24!52;UBERON:0007135!2.27e-24!52;UBERON:0000955!3.60e-22!47;UBERON:0006238!3.60e-22!47;UBERON:0002616!1.88e-21!46;UBERON:0002020!3.25e-20!34;UBERON:0003056!2.71e-19!49;UBERON:0003080!5.59e-19!40;UBERON:0002780!2.05e-18!39;UBERON:0001890!2.05e-18!39;UBERON:0006240!2.05e-18!39;UBERON:0003528!5.18e-18!29;UBERON:0002791!5.18e-18!29;UBERON:0001893!5.18e-18!29;UBERON:0010314!1.85e-16!92;UBERON:0000956!2.79e-13!21;UBERON:0001869!2.79e-13!21;UBERON:0000203!2.79e-13!21;UBERON:0002619!1.65e-10!17;UBERON:0000922!1.61e-07!320;UBERON:0000468!1.76e-07!333
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,1.32583,0.916672,0.550971,0.645383,0.691572,0.7141,1.00112,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.143775,0.426133,0.713088,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,0.336199,1.11492,0.364821,0.607065,0.326478,0.629145,0.303703,2.94766,0.342638,0.56353,0.0995018,0.366415,0.659176,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.742129,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.740068,1.156,1.13013,0.57254,1.11463,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,1.17421,0.220054,0.534643,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.685716,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,1.09461,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.247162,0.53982,0.858327,0.862623,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,1.67297,1.06946,0.52828,1.2285,0.679647,1.35909,2.32117,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.183562,0.667976,1.10596,0.783181,0.678689,1.18867,1.70209,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,1.28815
}}

Latest revision as of 16:46, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:36819193..36819217,+p@chr13:36819193..36819217
+
Mm9::chr13:43711319..43711360,+p1@Rnf182
Mm9::chr13:43711367..43711385,+p2@Rnf182
Mm9::chr13:43711396..43711413,+p3@Rnf182
Mm9::chr14:65035972..65035999,-p6@Msra
Mm9::chr14:65036638..65036670,-p@chr14:65036638..65036670
-


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:0008113peptide-methionine-(S)-S-oxide reductase activity0.00591667350134873
GO:0016671oxidoreductase activity, acting on sulfur group of donors, disulfide as acceptor0.0118314019548379
GO:0016667oxidoreductase activity, acting on sulfur group of donors0.0197125197651981



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
central nervous system3.70e-3173
nervous system4.43e-3075
ectoderm-derived structure1.18e-2895
ectoderm1.18e-2895
presumptive ectoderm1.18e-2895
regional part of nervous system6.13e-2654
neurectoderm4.39e-2564
neural plate4.39e-2564
presumptive neural plate4.39e-2564
ecto-epithelium1.98e-2473
neural tube2.27e-2452
neural rod2.27e-2452
future spinal cord2.27e-2452
neural keel2.27e-2452
brain3.60e-2247
future brain3.60e-2247
regional part of brain1.88e-2146
gray matter3.25e-2034
pre-chordal neural plate2.71e-1949
anterior neural tube5.59e-1940
regional part of forebrain2.05e-1839
forebrain2.05e-1839
future forebrain2.05e-1839
brain grey matter5.18e-1829
regional part of telencephalon5.18e-1829
telencephalon5.18e-1829
structure with developmental contribution from neural crest1.85e-1692
cerebral cortex2.79e-1321
cerebral hemisphere2.79e-1321
pallium2.79e-1321
regional part of cerebral cortex1.65e-1017
embryo1.61e-07320
multi-cellular organism1.76e-07333


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)
MA0003.10.276983
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.12867
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.11.12834
MA0043.11.08567
MA0046.11.02391
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.212634
MA0056.10
MA0057.11.43735
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.11.79596
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.12.57164
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.11.2824
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.11.16221
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.10.0392287
MA0147.10.858298
MA0148.11.3627
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.525037
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
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
MA0162.11.08528
MA0163.10.664494
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.22.11904
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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