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MCL coexpression mm9:1364: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000055!3.21e-22!49;CL:0000221!8.59e-20!44;CL:0000133!8.59e-20!44;CL:0002321!1.04e-19!70;CL:0002319!2.91e-19!43;CL:0002371!1.20e-17!118;CL:0000548!4.94e-16!115;CL:0000255!4.94e-16!115;CL:0000393!6.77e-16!39;CL:0000211!6.77e-16!39;CL:0000723!1.30e-14!91;CL:0000048!1.30e-14!91;CL:0000540!3.93e-13!33;CL:0000047!3.93e-13!33;CL:0000031!3.93e-13!33;CL:0000404!3.93e-13!33;CL:0000034!7.93e-12!97;CL:0000117!1.80e-11!23;CL:0000337!1.80e-11!23;CL:0000333!2.71e-07!10;CL:0000095!2.71e-07!10;CL:0000243!2.71e-07!10;CL:0000123!2.71e-07!10;CL:0000125!2.71e-07!10;CL:0000030!2.71e-07!10;CL:0000339!2.71e-07!10
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001016!4.95e-17!75;UBERON:0001017!3.48e-16!73;UBERON:0010314!9.92e-12!92;UBERON:0000073!1.05e-10!54;UBERON:0004121!4.48e-10!95;UBERON:0000924!4.48e-10!95;UBERON:0006601!4.48e-10!95;UBERON:0001049!1.11e-09!52;UBERON:0005068!1.11e-09!52;UBERON:0006241!1.11e-09!52;UBERON:0007135!1.11e-09!52;UBERON:0002020!1.74e-09!34;UBERON:0002346!1.16e-08!64;UBERON:0003075!1.16e-08!64;UBERON:0007284!1.16e-08!64;UBERON:0002616!7.27e-08!46;UBERON:0003528!1.81e-07!29;UBERON:0002791!1.81e-07!29;UBERON:0001893!1.81e-07!29;UBERON:0002780!1.84e-07!39;UBERON:0001890!1.84e-07!39;UBERON:0006240!1.84e-07!39;UBERON:0000955!1.93e-07!47;UBERON:0006238!1.93e-07!47;UBERON:0003080!2.54e-07!40
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.473747,1.17362,0.535892,0.346849,0.550971,1.55624,0.247459,0.257202,1.00112,0.599767,0.632897,1.28144,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.442204,0.426133,0.35122,0.657163,0.91309,1.19059,0.686615,1.85593,0.572827,0.394364,0.534301,0.558142,0.960397,0.892985,0.204204,0.364821,0.335531,0.326478,0.629145,0.303703,0.27383,0.342638,1.38433,0.0995018,0.959963,0.368882,0.524258,0.77511,0.589246,0.284064,0.397446,1.95713,0.714419,0.174327,1.10437,1.12205,1.59824,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.742129,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.208101,1.08629,0.204132,0.763395,0.922432,0.430551,1.30789,0.874787,0.722675,0.240896,1.03903,1.6478,0.0610418,0.534643,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.810643,1.40549,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,1.11115,1.09461,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.247162,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,1.79935,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,1.25097,1.38743,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.325363,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.895201
}}

Latest revision as of 16:49, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:56290695..56290706,-p3@Nedd8
Mm9::chr14:56290710..56290755,-p1@Nedd8
Mm9::chr17:23966062..23966110,-p1@Tceb2
Mm9::chr1:94538519..94538553,-p1@Myeov2
Mm9::chr6:124691002..124691111,-p1@Grcc10
Mm9::chr7:20158728..20158752,-p1@Gemin7


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:0045116protein neddylation0.0120528132361804



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
non-terminally differentiated cell3.21e-2249
ectodermal cell8.59e-2044
neurectodermal cell8.59e-2044
embryonic cell1.04e-1970
neural cell2.91e-1943
somatic cell1.20e-17118
animal cell4.94e-16115
eukaryotic cell4.94e-16115
electrically responsive cell6.77e-1639
electrically active cell6.77e-1639
somatic stem cell1.30e-1491
multi fate stem cell1.30e-1491
neuron3.93e-1333
neuronal stem cell3.93e-1333
neuroblast3.93e-1333
electrically signaling cell3.93e-1333
stem cell7.93e-1297
CNS neuron (sensu Vertebrata)1.80e-1123
neuroblast (sensu Vertebrata)1.80e-1123
migratory neural crest cell2.71e-0710
neuron associated cell2.71e-0710
glial cell (sensu Vertebrata)2.71e-0710
neuron associated cell (sensu Vertebrata)2.71e-0710
glial cell2.71e-0710
glioblast2.71e-0710
glioblast (sensu Vertebrata)2.71e-0710


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)
MA0003.11.03722
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.11.71935
MA0017.11.00628
MA0019.11.87871
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.12.59368
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
MA0066.11.61836
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.169297
MA0074.10.638014
MA0076.12.76767
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.13.05316
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.11.25163
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.11.16089
MA0103.10.398766
MA0105.10.199622
MA0106.11.74856
MA0107.11.0169
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
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.11.502
MA0145.10.119202
MA0146.10.353523
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.24.14052
MA0035.20.630778
MA0039.21.05907
MA0138.20.788113
MA0002.20.689262
MA0137.22.80903
MA0104.21.33199
MA0047.20.685741
MA0112.20.37938
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.414701
MA0156.11.04798
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.11.08528
MA0163.11.03138
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.21.11318
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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