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MCL coexpression mm9:1300: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000160!1.22e-24!31;UBERON:0005409!8.72e-19!47;UBERON:0000344!4.09e-16!15;UBERON:0001242!2.13e-13!13;UBERON:0000060!2.13e-13!13;UBERON:0001262!2.13e-13!13;UBERON:0004786!2.13e-13!13;UBERON:0004923!6.20e-13!24;UBERON:0004119!1.87e-11!118;UBERON:0000925!1.87e-11!118;UBERON:0006595!1.87e-11!118;UBERON:0001007!5.42e-11!116;UBERON:0001555!5.42e-11!116;UBERON:0007026!5.42e-11!116;UBERON:0004921!1.40e-09!114;UBERON:0003350!2.03e-08!9;UBERON:0004808!2.03e-08!9;UBERON:0001277!2.03e-08!9
|ontology_enrichment_uberon=UBERON:0000160!1.22e-24!31;UBERON:0005409!8.72e-19!47;UBERON:0000344!4.09e-16!15;UBERON:0001242!2.13e-13!13;UBERON:0000060!2.13e-13!13;UBERON:0001262!2.13e-13!13;UBERON:0004786!2.13e-13!13;UBERON:0004923!6.20e-13!24;UBERON:0004119!1.87e-11!118;UBERON:0000925!1.87e-11!118;UBERON:0006595!1.87e-11!118;UBERON:0001007!5.42e-11!116;UBERON:0001555!5.42e-11!116;UBERON:0007026!5.42e-11!116;UBERON:0004921!1.40e-09!114;UBERON:0003350!2.03e-08!9;UBERON:0004808!2.03e-08!9;UBERON:0001277!2.03e-08!9
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.89822,0.232269,0.143775,0.426133,0.713088,0.657163,0.345236,1.19059,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,0.892985,0.589948,0.364821,0.335531,0.871288,0.629145,0.303703,0.27383,0.342638,0.56353,0.0995018,0.959963,0.368882,0.524258,0.77511,0.589246,0.0835644,1.02809,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.742129,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,0.366795,1.156,0.599223,0.19692,0.589776,0.763395,0.922432,0.430551,0.708505,0.874787,0.722675,0.240896,1.03903,0.439832,0.220054,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.685716,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,1.09461,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.528609,0.53982,0.858327,0.322606,1.16147,0.805995,1.6461,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.667976,1.10596,0.287383,0.678689,1.18867,1.70209,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,1.60971,0.325308,0.63125,0.0323861
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.346849,0.550971,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.89822,0.232269,0.143775,0.426133,0.713088,0.657163,0.345236,1.19059,0.686615,0.223823,0.572827,0.394364,0.534301,0.558142,0.960397,0.892985,0.589948,0.364821,0.335531,0.871288,0.629145,0.303703,0.27383,0.342638,0.56353,0.0995018,0.959963,0.368882,0.524258,0.77511,0.589246,0.0835644,1.02809,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.742129,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.70565,0.366795,1.156,0.599223,0.19692,0.589776,0.763395,0.922432,0.430551,0.708505,0.874787,0.722675,0.240896,1.03903,0.439832,0.220054,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.685716,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,1.09461,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.528609,0.53982,0.858327,0.322606,1.16147,0.805995,1.6461,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.667976,1.10596,0.287383,0.678689,1.18867,1.70209,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,1.60971,0.325308,0.63125,0.0323861
|tfbs_overrepresentation_jaspar=MA0003.1;0.730824,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;1.71935,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;2.3347,MA0048.1;0.943003,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;0.275911,MA0061.1;3.16246,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;0.000157319,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;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;1.16089,MA0103.1;0.398766,MA0105.1;2.43957,MA0106.1;0.737893,MA0107.1;1.79828,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.822296,MA0115.1;1.08851,MA0116.1;0.359483,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;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;1.502,MA0145.1;0.119202,MA0146.1;0.153598,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.525037,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;1.06926,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.119197,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;0.414701,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.0465447,MA0163.1;0.0423021,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.0520572,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}
}}

Revision as of 13:07, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:70272480..70272491,+p9@Zmynd15
Mm9::chr15:44258946..44258959,+p@chr15:44258946..44258959
+
Mm9::chr16:45455027..45455039,-p4@Gm17783
p4@Gm609
Mm9::chr18:20714918..20714920,+p@chr18:20714918..20714920
+
Mm9::chr2:133377954..133377973,+p1@Bmp2
Mm9::chr4:115500720..115500735,+p2@Mob3c


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:0048711positive regulation of astrocyte differentiation0.00878367895802332
GO:0048710regulation of astrocyte differentiation0.00878367895802332
GO:0014015positive regulation of gliogenesis0.00878367895802332
GO:0045687positive regulation of glial cell differentiation0.00878367895802332
GO:0045778positive regulation of ossification0.00878367895802332
GO:0048708astrocyte differentiation0.00878367895802332
GO:0046852positive regulation of bone remodeling0.00878367895802332
GO:0045669positive regulation of osteoblast differentiation0.00878367895802332
GO:0001837epithelial to mesenchymal transition0.00878367895802332
GO:0045685regulation of glial cell differentiation0.00878367895802332
GO:0014013regulation of gliogenesis0.00878367895802332
GO:0045667regulation of osteoblast differentiation0.0107347251399441
GO:0035051cardiac cell differentiation0.0123852030744534
GO:0001658ureteric bud branching0.0137995202431396
GO:0030278regulation of ossification0.0160967928574096
GO:0030282bone mineralization0.0160967928574096
GO:0001649osteoblast differentiation0.0163769478384945
GO:0030509BMP signaling pathway0.0163769478384945
GO:0046850regulation of bone remodeling0.0163769478384945
GO:0001657ureteric bud development0.0167337812634476
GO:0042475odontogenesis of dentine-containing teeth0.0167337812634476
GO:0042476odontogenesis0.0167337812634476
GO:0010001glial cell differentiation0.0167337812634476
GO:0048762mesenchymal cell differentiation0.0167337812634476
GO:0014031mesenchymal cell development0.0167337812634476
GO:0042063gliogenesis0.0169143837043772
GO:0001656metanephros development0.0170116307788382
GO:0045597positive regulation of cell differentiation0.0170116307788382
GO:0007179transforming growth factor beta receptor signaling pathway0.0170116307788382
GO:0051216cartilage development0.0171586166958898
GO:0048754branching morphogenesis of a tube0.0200590078487712
GO:0001763morphogenesis of a branching structure0.0211044547701272
GO:0051094positive regulation of developmental process0.0224102760419235
GO:0001822kidney development0.0230095602216914
GO:0001655urogenital system development0.0235135084794501
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0235135084794501
GO:0001503ossification0.02649465235916
GO:0031214biomineral formation0.02649465235916
GO:0045165cell fate commitment0.0274585620368124
GO:0046849bone remodeling0.0275729885512682
GO:0051240positive regulation of multicellular organismal process0.0300718626747224
GO:0008285negative regulation of cell proliferation0.0300718626747224
GO:0048771tissue remodeling0.0301167926939151
GO:0035239tube morphogenesis0.0354104308655744
GO:0008083growth factor activity0.0354104308655744
GO:0045595regulation of cell differentiation0.0355666753409223
GO:0007507heart development0.0386596207918497
GO:0001501skeletal development0.0400698994370635
GO:0035295tube development0.0438062238145681
GO:0006954inflammatory response0.0444166115299627
GO:0005125cytokine activity0.0447944175979461
GO:0007417central nervous system development0.0474007754684157



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>


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)
MA0003.10.730824
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.11.71935
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
MA0046.12.3347
MA0048.10.943003
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.13.16246
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.153907
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.000157319
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.111145
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.11.16089
MA0103.10.398766
MA0105.12.43957
MA0106.10.737893
MA0107.11.79828
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.822296
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
MA0146.10.153598
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.525037
MA0138.20.788113
MA0002.20.246463
MA0137.21.06926
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.763394
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.480757
MA0155.10.414701
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.0465447
MA0163.10.0423021
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.0520572
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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