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MCL coexpression mm9:1354: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000117!3.05e-11!23;CL:0000337!3.05e-11!23;CL:0000393!5.62e-11!39;CL:0000211!5.62e-11!39;CL:0000540!2.46e-10!33;CL:0000047!2.46e-10!33;CL:0000031!2.46e-10!33;CL:0000404!2.46e-10!33;CL:0000055!4.07e-09!49;CL:0000221!2.45e-08!44;CL:0000133!2.45e-08!44;CL:0002319!2.48e-08!43
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!2.32e-22!73;UBERON:0000073!6.83e-22!54;UBERON:0001016!7.85e-22!75;UBERON:0001049!3.63e-20!52;UBERON:0005068!3.63e-20!52;UBERON:0006241!3.63e-20!52;UBERON:0007135!3.63e-20!52;UBERON:0004121!6.48e-20!95;UBERON:0000924!6.48e-20!95;UBERON:0006601!6.48e-20!95;UBERON:0002346!3.79e-19!64;UBERON:0003075!3.79e-19!64;UBERON:0007284!3.79e-19!64;UBERON:0010371!2.15e-18!73;UBERON:0000955!4.63e-18!47;UBERON:0006238!4.63e-18!47;UBERON:0002616!1.93e-17!46;UBERON:0003080!1.03e-15!40;UBERON:0002020!1.16e-15!34;UBERON:0010314!1.35e-15!92;UBERON:0003056!2.52e-15!49;UBERON:0002780!3.20e-15!39;UBERON:0001890!3.20e-15!39;UBERON:0006240!3.20e-15!39;UBERON:0003528!2.54e-13!29;UBERON:0002791!2.54e-13!29;UBERON:0001893!2.54e-13!29;UBERON:0000025!6.70e-10!114;UBERON:0000956!8.25e-10!21;UBERON:0001869!8.25e-10!21;UBERON:0000203!8.25e-10!21;UBERON:0004111!1.33e-09!122;UBERON:0000468!1.68e-09!333;UBERON:0002619!3.70e-08!17;UBERON:0002021!1.49e-07!10;UBERON:0000411!1.49e-07!10;UBERON:0001950!1.49e-07!10;UBERON:0000922!5.63e-07!320
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,0.464605,0.535892,0.346849,0.550971,0.645383,0.691572,0.7141,2.6668,2.48703,0.632897,1.28144,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.143775,0.426133,1.17476,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,2.70623,0.534301,0.558142,0.960397,0.892985,0.589948,0.956447,0.335531,0.326478,1.52228,0.303703,0.752287,0.342638,0.56353,0.0995018,0.366415,3.077,0.524258,0.77511,1.43855,0.0835644,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,1.93338,1.62226,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,3.84327,1.156,1.7706,0.57254,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,4.08047,0.479018,1.62034,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,2.2472,0.281222,0.244935,0.976308,1.826,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,0.585058,3.94462,1.92,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.528609,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,1.30967,1.2285,0.679647,1.35909,0.106956,1.25097,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.540361,4.35794,1.10596,2.18636,0.678689,2.66878,0.71546,0.376898,0.48935,2.16235,1.31911,1.03816,0.926663,1.21135,0.82857,0.671017,0.325308,0.63125,2.24139
}}

Latest revision as of 16:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:119498621..119498667,-p1@Uggt2
Mm9::chr15:77137003..77137037,-p4@Rbfox2
Mm9::chr15:77137042..77137081,-p3@Rbfox2
Mm9::chr2:106814540..106814579,-p1@2700007P21Rik
Mm9::chr6:124706496..124706545,-p4@Atn1
Mm9::chr6:124706717..124706786,-p1@Atn1


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:0009404toxin metabolic process0.00136963786774777
GO:0050827toxin receptor binding0.00136963786774777
GO:0009636response to toxin0.0173487463248051
GO:0019748secondary metabolic process0.029447214156577
GO:0003714transcription corepressor activity0.03067988823755



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 system2.32e-2273
regional part of nervous system6.83e-2254
nervous system7.85e-2275
neural tube3.63e-2052
neural rod3.63e-2052
future spinal cord3.63e-2052
neural keel3.63e-2052
ectoderm-derived structure6.48e-2095
ectoderm6.48e-2095
presumptive ectoderm6.48e-2095
neurectoderm3.79e-1964
neural plate3.79e-1964
presumptive neural plate3.79e-1964
ecto-epithelium2.15e-1873
brain4.63e-1847
future brain4.63e-1847
regional part of brain1.93e-1746
anterior neural tube1.03e-1540
gray matter1.16e-1534
structure with developmental contribution from neural crest1.35e-1592
pre-chordal neural plate2.52e-1549
regional part of forebrain3.20e-1539
forebrain3.20e-1539
future forebrain3.20e-1539
brain grey matter2.54e-1329
regional part of telencephalon2.54e-1329
telencephalon2.54e-1329
tube6.70e-10114
cerebral cortex8.25e-1021
cerebral hemisphere8.25e-1021
pallium8.25e-1021
anatomical conduit1.33e-09122
multi-cellular organism1.68e-09333
regional part of cerebral cortex3.70e-0817
occipital lobe1.49e-0710
visual cortex1.49e-0710
neocortex1.49e-0710
embryo5.63e-07320


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)
MA0003.14.94208
MA0004.10.536396
MA0006.12.54161
MA0007.10.52077
MA0009.10.987341
MA0014.12.76368
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
MA0055.10.807132
MA0056.10
MA0057.10.149949
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
MA0073.10.0960184
MA0074.10.638014
MA0076.11.04996
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.11.19273
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
MA0105.11.72386
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
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
MA0139.10.682297
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.379391
MA0146.12.42438
MA0147.11.54778
MA0148.10.553294
MA0149.10.464445
MA0062.21.11803
MA0035.20.630778
MA0039.20.181031
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.22.05302
MA0047.20.685741
MA0112.21.24549
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.11.33283
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.15.28077
MA0163.14.40286
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.25.38967
MA0102.21.7182
MA0258.10.290587
MA0259.12.29705
MA0442.10
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