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MCL coexpression mm9:1358: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000025!4.86e-15!114;UBERON:0004111!1.97e-14!122;UBERON:0001017!9.91e-09!73;UBERON:0001016!1.49e-08!75;UBERON:0010314!3.36e-08!92;UBERON:0004535!3.32e-07!23;UBERON:0001009!3.32e-07!23;UBERON:0003914!3.93e-07!47
|ontology_enrichment_uberon=UBERON:0000025!4.86e-15!114;UBERON:0004111!1.97e-14!122;UBERON:0001017!9.91e-09!73;UBERON:0001016!1.49e-08!75;UBERON:0010314!3.36e-08!92;UBERON:0004535!3.32e-07!23;UBERON:0001009!3.32e-07!23;UBERON:0003914!3.93e-07!47
|tfbs_overrepresentation_for_novel_motifs=1.23219,0.819928,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.7141,0.283981,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.442204,0.426133,0.713088,0.657163,0.91309,0.472505,1.64218,0.63639,1.40396,0.394364,0.534301,0.558142,0.960397,0.892985,0.589948,0.956447,0.144368,0.326478,0.629145,1.48701,0.752287,0.342638,0.56353,0.327433,0.366415,1.45501,0.524258,0.77511,0.589246,0.284064,1.02809,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,1.72013,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.70565,1.21401,1.156,0.599223,0.57254,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.676326,1.03903,2.18121,0.220054,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.483322,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.902522,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,1.30967,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,1.10885,1.10596,0.287383,1.62569,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,0.5667
|tfbs_overrepresentation_for_novel_motifs=1.23219,0.819928,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.7141,0.283981,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.442204,0.426133,0.713088,0.657163,0.91309,0.472505,1.64218,0.63639,1.40396,0.394364,0.534301,0.558142,0.960397,0.892985,0.589948,0.956447,0.144368,0.326478,0.629145,1.48701,0.752287,0.342638,0.56353,0.327433,0.366415,1.45501,0.524258,0.77511,0.589246,0.284064,1.02809,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,1.72013,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.70565,1.21401,1.156,0.599223,0.57254,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.676326,1.03903,2.18121,0.220054,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.483322,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.902522,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,1.30967,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,1.10885,1.10596,0.287383,1.62569,1.18867,0.71546,0.376898,0.48935,1.25034,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,0.5667
|tfbs_overrepresentation_jaspar=MA0003.1;3.21844,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;1.29371,MA0009.1;0.987341,MA0014.1;0.304529,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;0.457693,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;1.38604,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.467569,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.0198269,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;0.729877,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;2.36749,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;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.944657,MA0117.1;1.05576,MA0119.1;0.459301,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;1.07584,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.829535,MA0145.1;0.119202,MA0146.1;2.42438,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;2.61252,MA0138.2;0.788113,MA0002.2;0.689262,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.76177,MA0065.2;0.763394,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.480757,MA0155.1;1.33283,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;1.58527,MA0160.1;1.36931,MA0161.1;0,MA0162.1;2.04167,MA0163.1;1.4645,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.911432,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
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Revision as of 13:13, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:26588519..26588569,-p1@Zcchc24
Mm9::chr15:78004386..78004418,-p2@Ift27
Mm9::chr5:116102983..116103001,-p1@Ccdc64
Mm9::chr5:137463227..137463253,+p3@Plod3
Mm9::chr5:34000486..34000536,-p2@Tmem129
Mm9::chr7:150238681..150238702,+p1@Cd81


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:0008475procollagen-lysine 5-dioxygenase activity0.0207066553792883
GO:0030307positive regulation of cell growth0.0207066553792883
GO:0045793positive regulation of cell size0.0230048737377879
GO:0030890positive regulation of B cell proliferation0.037222988647217
GO:0031418L-ascorbic acid binding0.037222988647217
GO:0030888regulation of B cell proliferation0.037222988647217
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0.037222988647217
GO:0050871positive regulation of B cell activation0.037222988647217
GO:0045927positive regulation of growth0.037222988647217
GO:0042100B cell proliferation0.037222988647217
GO:0032946positive regulation of mononuclear cell proliferation0.0392164037242194
GO:0050671positive regulation of lymphocyte proliferation0.0392164037242194
GO:0050864regulation of B cell activation0.0392164037242194
GO:0032944regulation of mononuclear cell proliferation0.0441788138872621
GO:0050670regulation of lymphocyte proliferation0.0441788138872621
GO:0051213dioxygenase activity0.0441788138872621
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0441788138872621
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0441788138872621
GO:0051251positive regulation of lymphocyte activation0.0441788138872621
GO:0032943mononuclear cell proliferation0.0472716327546309
GO:0046651lymphocyte proliferation0.0472716327546309
GO:0001558regulation of cell growth0.0472716327546309
GO:0051249regulation of lymphocyte activation0.0472716327546309
GO:0042113B cell activation0.0472716327546309
GO:0050865regulation of cell activation0.0472716327546309
GO:0016049cell growth0.0496599180348516



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 cell3.25e-0749
oligodendrocyte precursor cell6.68e-078

Uber Anatomy
Ontology termp-valuen
tube4.86e-15114
anatomical conduit1.97e-14122
central nervous system9.91e-0973
nervous system1.49e-0875
structure with developmental contribution from neural crest3.36e-0892
cardiovascular system3.32e-0723
circulatory system3.32e-0723
epithelial tube3.93e-0747


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)
MA0003.13.21844
MA0004.10.536396
MA0006.10.359699
MA0007.11.29371
MA0009.10.987341
MA0014.10.304529
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
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.11.38604
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
MA0073.10.0198269
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.12.36749
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
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.944657
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
MA0141.11.07584
MA0142.10.876028
MA0143.10.725672
MA0144.10.829535
MA0145.10.119202
MA0146.12.42438
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.22.61252
MA0138.20.788113
MA0002.20.689262
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
MA0154.10.480757
MA0155.11.33283
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.11.58527
MA0160.11.36931
MA0161.10
MA0162.12.04167
MA0163.11.4645
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.911432
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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