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MCL coexpression mm9:1441: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_uberon=UBERON:0002384!7.23e-28!46;UBERON:0002390!3.43e-09!45;UBERON:0003061!3.43e-09!45;UBERON:0002193!1.75e-08!48;UBERON:0002405!1.75e-08!48;UBERON:0002370!6.43e-07!23;UBERON:0000974!6.43e-07!23;UBERON:0004807!6.43e-07!23;UBERON:0005058!6.43e-07!23;UBERON:0003351!6.43e-07!23;UBERON:0009113!6.43e-07!23;UBERON:0003295!6.43e-07!23;UBERON:0009722!6.43e-07!23;UBERON:0005562!6.43e-07!23;UBERON:0007690!6.43e-07!23
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.819928,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,1.00112,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.89822,0.232269,0.143775,0.426133,0.108444,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,0.181062,0.558142,0.960397,0.892985,0.204204,0.364821,0.335531,0.326478,0.629145,0.303703,0.27383,0.342638,0.56353,0.671603,0.366415,0.0417367,0.524258,0.77511,0.589246,0.594982,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,2.01303,0.11437,1.156,0.208101,0.19692,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.676326,1.03903,0.0539203,3.57522,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,2.1552,0.244935,0.976308,0.775372,0.483322,1.56871,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.247162,1.33416,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,3.869,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.540361,0.0987301,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.0323861
|tfbs_overrepresentation_jaspar=MA0003.1;0.04894,MA0004.1;0.536396,MA0006.1;0.945134,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.0315641,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;0.161427,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.0585191,MA0056.1;0,MA0057.1;0.149949,MA0058.1;1.11298,MA0059.1;1.14076,MA0060.1;0.275911,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.153907,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.169297,MA0074.1;1.54084,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;1.19271,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.111145,MA0089.1;0,MA0090.1;0.500693,MA0091.1;0.55008,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;0.199622,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;1.2824,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;3.00715,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.119202,MA0146.1;0.0392287,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.0823004,MA0138.2;0.788113,MA0002.2;1.97607,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.763394,MA0150.1;2.22913,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;0.132921,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.70356,MA0163.1;0.163321,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.000341844,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}

Latest revision as of 16:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:34813838..34813855,+p@chr2:34813838..34813855
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Mm9::chr2:34813870..34813875,+p@chr2:34813870..34813875
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Mm9::chr2:34819214..34819229,+p@chr2:34819214..34819229
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Mm9::chr6:108499886..108499901,+p@chr6:108499886..108499901
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Mm9::chr8:129391962..129391969,+p@chr8:129391962..129391969
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Mm9::chr9:107215852..107215865,+p@chr9:107215852..107215865
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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

no results for this coexpression

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
lymphoid lineage restricted progenitor cell8.38e-4212
hematopoietic cell1.32e-4132
hematopoietic oligopotent progenitor cell1.32e-4132
hematopoietic stem cell1.32e-4132
angioblastic mesenchymal cell1.32e-4132
hematopoietic multipotent progenitor cell1.32e-4132
lymphocyte2.00e-3813
common lymphoid progenitor2.00e-3813
T cell2.11e-3811
pro-T cell2.11e-3811
mature alpha-beta T cell2.07e-329
alpha-beta T cell2.07e-329
immature T cell2.07e-329
mature T cell2.07e-329
immature alpha-beta T cell2.07e-329
nucleate cell8.09e-3116
hematopoietic lineage restricted progenitor cell1.16e-2925
CD4-positive, alpha-beta T cell5.08e-298
leukocyte7.05e-2917
nongranular leukocyte7.05e-2917
connective tissue cell7.23e-2846
mesenchymal cell7.23e-2846
motile cell1.01e-2554
thymocyte8.22e-226
double negative thymocyte8.22e-226
naive T cell8.22e-226
double-positive, alpha-beta thymocyte8.22e-226
CD4-positive, alpha-beta thymocyte8.22e-226
naive thymus-derived CD4-positive, alpha-beta T cell8.22e-226
DN4 thymocyte8.22e-226
DN1 thymic pro-T cell8.22e-226
DN2 thymocyte8.22e-226
DN3 thymocyte8.22e-226
immature single positive thymocyte8.22e-226
early T lineage precursor8.22e-226
mature CD4 single-positive thymocyte8.22e-226
resting double-positive thymocyte8.22e-226
double-positive blast8.22e-226
CD69-positive double-positive thymocyte8.22e-226
CD69-positive, CD4-positive single-positive thymocyte8.22e-226
CD4-positive, CD8-intermediate double-positive thymocyte8.22e-226
CD24-positive, CD4 single-positive thymocyte8.22e-226
stem cell4.18e-1697
somatic stem cell2.81e-1291
multi fate stem cell2.81e-1291
common myeloid progenitor8.11e-1119
animal cell4.61e-10115
eukaryotic cell4.61e-10115
somatic cell1.04e-09118

Uber Anatomy
Ontology termp-valuen
connective tissue7.23e-2846
hematopoietic system3.43e-0945
blood island3.43e-0945
hemolymphoid system1.75e-0848
immune system1.75e-0848
thymus6.43e-0723
neck6.43e-0723
respiratory system epithelium6.43e-0723
hemolymphoid system gland6.43e-0723
pharyngeal epithelium6.43e-0723
thymic region6.43e-0723
pharyngeal gland6.43e-0723
entire pharyngeal arch endoderm6.43e-0723
thymus primordium6.43e-0723
early pharyngeal endoderm6.43e-0723


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)
MA0003.10.04894
MA0004.10.536396
MA0006.10.945134
MA0007.10.52077
MA0009.10.987341
MA0014.10.0315641
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
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.149949
MA0058.11.11298
MA0059.11.14076
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
MA0073.10.169297
MA0074.11.54084
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.11.19271
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
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.11.2824
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.13.00715
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
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.0823004
MA0138.20.788113
MA0002.21.97607
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.763394
MA0150.12.22913
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.70356
MA0163.10.163321
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.000341844
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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