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|ontology_enrichment_uberon=UBERON:0000489!3.12e-16!21;UBERON:0002113!6.06e-16!14;UBERON:0003918!6.06e-16!14;UBERON:0011143!6.06e-16!14;UBERON:0005095!6.06e-16!14;UBERON:0007687!6.06e-16!14;UBERON:0001008!2.43e-15!19;UBERON:0006554!6.34e-15!18;UBERON:0003064!4.42e-08!14
|ontology_enrichment_uberon=UBERON:0000489!3.12e-16!21;UBERON:0002113!6.06e-16!14;UBERON:0003918!6.06e-16!14;UBERON:0011143!6.06e-16!14;UBERON:0005095!6.06e-16!14;UBERON:0007687!6.06e-16!14;UBERON:0001008!2.43e-15!19;UBERON:0006554!6.34e-15!18;UBERON:0003064!4.42e-08!14
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,1.32583,1.64034,0.550971,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,2.43952,1.22315,0.442204,0.426133,0.108444,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.204204,0.956447,1.82948,0.326478,0.629145,0.303703,0.27383,0.342638,0.56353,0.327433,0.959963,0.161543,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,1.59824,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.599223,0.19692,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.768392,2.30747,3.064,0.780154,1.77427,1.33021,1.04409,0.973447,2.50961,0.2995,0.281222,1.27104,0.976308,0.775372,0.160254,1.56871,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,2.10971,1.0885,0.431734,0.605144,1.33732,0.340765,0.528609,0.53982,0.858327,0.862623,1.16147,0.805995,2.7714,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,1.62768,1.35909,3.72857,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,1.67199,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.183562,0.0987301,1.10596,1.42796,1.62569,1.18867,0.71546,0.983048,3.14367,0.500417,1.31911,1.03816,3.51783,0.482185,0.82857,0.671017,2.3749,0.63125,0.0323861
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,1.32583,1.64034,0.550971,0.645383,0.247459,0.257202,0.283981,0.599767,0.632897,0.692139,0.6581,0.364314,0,0.856992,2.43952,1.22315,0.442204,0.426133,0.108444,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.204204,0.956447,1.82948,0.326478,0.629145,0.303703,0.27383,0.342638,0.56353,0.327433,0.959963,0.161543,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,1.59824,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.11437,1.156,0.599223,0.19692,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.768392,2.30747,3.064,0.780154,1.77427,1.33021,1.04409,0.973447,2.50961,0.2995,0.281222,1.27104,0.976308,0.775372,0.160254,1.56871,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,2.10971,1.0885,0.431734,0.605144,1.33732,0.340765,0.528609,0.53982,0.858327,0.862623,1.16147,0.805995,2.7714,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,1.62768,1.35909,3.72857,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,1.67199,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.920761,0.183562,0.0987301,1.10596,1.42796,1.62569,1.18867,0.71546,0.983048,3.14367,0.500417,1.31911,1.03816,3.51783,0.482185,0.82857,0.671017,2.3749,0.63125,0.0323861
|tfbs_overrepresentation_jaspar=MA0003.1;0.00973143,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.12867,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.969171,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;1.15799,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;1.02391,MA0048.1;1.50576,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;2.86541,MA0056.1;0,MA0057.1;3.53394,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;2.09737,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;3.64966,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;0.725434,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;1.92698,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;2.39942,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;0.307873,MA0145.1;0.119202,MA0146.1;0.0392287,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;1.11803,MA0035.2;0.630778,MA0039.2;0.328366,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;1.24784,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.159217,MA0155.1;0.414701,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;1.36931,MA0161.1;0,MA0162.1;0.176524,MA0163.1;0.664494,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;10.8763,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}
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Revision as of 13:21, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:9809357..9809371,-p2@Gata3
Mm9::chr2:9809374..9809396,-p4@Gata3
Mm9::chr2:9809402..9809422,-p5@Gata3
Mm9::chr2:9809579..9809627,-p7@Gata3
Mm9::chr2:9811653..9811662,-p8@Gata3
Mm9::chr6:84543910..84543916,-p3@Cyp26b1


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:0001709cell fate determination0.000230308074329499
GO:0042445hormone metabolic process0.0013518082623688
GO:0045165cell fate commitment0.00137684174870896
GO:0032753positive regulation of interleukin-4 production0.00380759327233879
GO:0032673regulation of interleukin-4 production0.00609198234583313
GO:0048485sympathetic nervous system development0.00652694513134735
GO:0042421norepinephrine biosynthetic process0.00652694513134735
GO:0042415norepinephrine metabolic process0.00761435209513292
GO:0048384retinoic acid receptor signaling pathway0.00761435209513292
GO:0032633interleukin-4 production0.00761435209513292
GO:0048483autonomic nervous system development0.00969046256227709
GO:0042573retinoic acid metabolic process0.0101510787109361
GO:0007140male meiosis0.0101510787109361
GO:0009954proximal/distal pattern formation0.0101510787109361
GO:0042423catecholamine biosynthetic process0.0101510787109361
GO:0042136neurotransmitter biosynthetic process0.0123706101935708
GO:0006776vitamin A metabolic process0.0143285785579013
GO:0030522intracellular receptor-mediated signaling pathway0.0152232802682254
GO:0001819positive regulation of cytokine production0.0160236271775587
GO:0006775fat-soluble vitamin metabolic process0.0167437725060497
GO:0042401biogenic amine biosynthetic process0.0173951736223902
GO:0042398amino acid derivative biosynthetic process0.0182619282851489
GO:0018958phenol metabolic process0.0182619282851489
GO:0006584catecholamine metabolic process0.0182619282851489
GO:0001817regulation of cytokine production0.0182619282851489
GO:0042446hormone biosynthetic process0.02085066892257
GO:0042133neurotransmitter metabolic process0.02085066892257
GO:0042035regulation of cytokine biosynthetic process0.026680634111376
GO:0009309amine biosynthetic process0.026680634111376
GO:0042089cytokine biosynthetic process0.026680634111376
GO:0042107cytokine metabolic process0.026680634111376
GO:0006766vitamin metabolic process0.026680634111376
GO:0030326embryonic limb morphogenesis0.026680634111376
GO:0035113embryonic appendage morphogenesis0.026680634111376
GO:0006576biogenic amine metabolic process0.026680634111376
GO:0051327M phase of meiotic cell cycle0.026680634111376
GO:0007126meiosis0.026680634111376
GO:0051321meiotic cell cycle0.026680634111376
GO:0035107appendage morphogenesis0.026680634111376
GO:0035108limb morphogenesis0.026680634111376
GO:0044271nitrogen compound biosynthetic process0.026680634111376
GO:0048869cellular developmental process0.026680634111376
GO:0030154cell differentiation0.026680634111376
GO:0060173limb development0.026680634111376
GO:0048736appendage development0.026680634111376
GO:0006575amino acid derivative metabolic process0.0284484799788564
GO:0001505regulation of neurotransmitter levels0.0284484799788564
GO:0001816cytokine production0.0308517453939281
GO:0048856anatomical structure development0.0308517453939281
GO:0006725aromatic compound metabolic process0.034315035247569
GO:0007275multicellular organismal development0.0371332501642451
GO:0006417regulation of translation0.0382321834006277
GO:0031326regulation of cellular biosynthetic process0.0397928047893852
GO:0046914transition metal ion binding0.0400064471977561
GO:0003002regionalization0.0405438248376606
GO:0009889regulation of biosynthetic process0.0419776548845426
GO:0016563transcription activator activity0.0473309004601403
GO:0007268synaptic transmission0.0492356523214464
GO:0007283spermatogenesis0.0492356523214464
GO:0048232male gamete generation0.0492356523214464
GO:0048598embryonic morphogenesis0.0499103697559423



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
CNS neuron (sensu Vertebrata)3.86e-0923
neuroblast (sensu Vertebrata)3.86e-0923

Uber Anatomy
Ontology termp-valuen
cavitated compound organ3.12e-1621
kidney6.06e-1614
kidney mesenchyme6.06e-1614
upper urinary tract6.06e-1614
kidney rudiment6.06e-1614
kidney field6.06e-1614
renal system2.43e-1519
urinary system structure6.34e-1518
intermediate mesoderm4.42e-0814


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)
MA0003.10.00973143
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.12867
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
MA0041.11.15799
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.11.50576
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.12.86541
MA0056.10
MA0057.13.53394
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.12.09737
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.13.64966
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.725434
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
MA0108.21.92698
MA0109.10
MA0111.11.2824
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.12.39942
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
MA0144.10.307873
MA0145.10.119202
MA0146.10.0392287
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.21.11803
MA0035.20.630778
MA0039.20.328366
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.21.24784
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.414701
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.11.36931
MA0161.10
MA0162.10.176524
MA0163.10.664494
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.210.8763
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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