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MCL coexpression mm9:1304: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003102!2.64e-12!22;UBERON:0000014!1.49e-09!5;UBERON:0001003!1.49e-09!5;UBERON:0002097!1.49e-09!5;UBERON:0002199!1.49e-09!5;UBERON:0007029!1.49e-09!5;UBERON:0007376!1.49e-09!5;UBERON:0002416!1.49e-09!5;UBERON:0007383!1.49e-09!5
|ontology_enrichment_uberon=UBERON:0003102!2.64e-12!22;UBERON:0000014!1.49e-09!5;UBERON:0001003!1.49e-09!5;UBERON:0002097!1.49e-09!5;UBERON:0002199!1.49e-09!5;UBERON:0007029!1.49e-09!5;UBERON:0007376!1.49e-09!5;UBERON:0002416!1.49e-09!5;UBERON:0007383!1.49e-09!5
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.916672,0.550971,0.645383,0.247459,0.257202,0.0835344,0.599767,1.53013,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.86893,1.91365,0.108444,0.657163,1.63467,0.472505,0.686615,0.223823,1.40396,0.394364,0.181062,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.326478,0.629145,0.820134,0.27383,0.342638,0.56353,1.11416,0.366415,0.0417367,0.524258,0.77511,0.589246,0.594982,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.366795,1.156,0.599223,1.08629,1.11463,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,1.9468,1.03903,0.198949,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.685716,0.976308,0.775372,0.160254,0.871473,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,1.10269,0.605144,1.33732,0.340765,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.937314,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.0987301,1.10596,0.287383,0.678689,1.18867,0.71546,1.74506,1.22669,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,0.131395
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.916672,0.550971,0.645383,0.247459,0.257202,0.0835344,0.599767,1.53013,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.86893,1.91365,0.108444,0.657163,1.63467,0.472505,0.686615,0.223823,1.40396,0.394364,0.181062,0.558142,0.960397,0.336199,0.589948,0.364821,0.144368,0.326478,0.629145,0.820134,0.27383,0.342638,0.56353,1.11416,0.366415,0.0417367,0.524258,0.77511,0.589246,0.594982,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.614918,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.366795,1.156,0.599223,1.08629,1.11463,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,1.9468,1.03903,0.198949,0.0610418,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.2995,0.281222,0.685716,0.976308,0.775372,0.160254,0.871473,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,1.10269,0.605144,1.33732,0.340765,0.0704207,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.937314,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.0987301,1.10596,0.287383,0.678689,1.18867,0.71546,1.74506,1.22669,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.86867,0.63125,0.131395
|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;2.01886,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;0.212634,MA0056.1;0,MA0057.1;0.149949,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;7.1726,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;6.52667,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;0.358337,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;1.03097,MA0105.1;0.57901,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;0.824407,MA0109.1;0,MA0111.1;0.515457,MA0113.1;1.68825,MA0114.1;0.304661,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;1.2655,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.379391,MA0146.1;0.0392287,MA0147.1;0.858298,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.591842,MA0035.2;0.630778,MA0039.2;0.0823004,MA0138.2;0.788113,MA0002.2;0.246463,MA0137.2;0.416331,MA0104.2;1.33199,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;1.13945,MA0154.1;0.933846,MA0155.1;0.414701,MA0156.1;0.406559,MA0157.1;1.96555,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.176524,MA0163.1;3.72829,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;1.83891,MA0079.2;9.24173,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.833237,MA0442.1;0
}}
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Revision as of 13:07, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:73012488..73012510,-p2@Ctns
Mm9::chr13:106084899..106084909,-p10@Rnf180
Mm9::chr14:56983841..56983853,+p1@Atp12a
Mm9::chr2:113245260..113245269,+p17@Fmn1
Mm9::chr2:113245271..113245284,+p11@Fmn1
Mm9::chr2:113245288..113245314,+p6@Fmn1


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:0015184L-cystine transmembrane transporter activity0.00467503058857905
GO:0000101sulfur amino acid transport0.00467503058857905
GO:0051125regulation of actin nucleation0.00467503058857905
GO:0000099sulfur amino acid transmembrane transporter activity0.00467503058857905
GO:0015811L-cystine transport0.00467503058857905
GO:0051127positive regulation of actin nucleation0.00467503058857905
GO:0008900hydrogen:potassium-exchanging ATPase activity0.00801367951130475
GO:0030838positive regulation of actin filament polymerization0.00934852440535652
GO:0045010actin nucleation0.00934852440535652
GO:0051130positive regulation of cellular component organization and biogenesis0.016823195403582
GO:0015807L-amino acid transport0.023357868680412
GO:0030833regulation of actin filament polymerization0.023357868680412
GO:0030041actin filament polymerization0.0366328029020975
GO:0015179L-amino acid transmembrane transporter activity0.0459991902383788
GO:0008064regulation of actin polymerization and/or depolymerization0.0460173561850889
GO:0032535regulation of cellular component size0.0460173561850889
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0460173561850889
GO:0030832regulation of actin filament length0.0460173561850889
GO:0051493regulation of cytoskeleton organization and biogenesis0.0460173561850889
GO:0033043regulation of organelle organization and biogenesis0.0460173561850889
GO:0015171amino acid transmembrane transporter activity0.0460173561850889
GO:0051258protein polymerization0.0460173561850889
GO:0022891substrate-specific transmembrane transporter activity0.0460173561850889
GO:0008154actin polymerization and/or depolymerization0.0460173561850889
GO:0006865amino acid transport0.0460173561850889
GO:0015837amine transport0.0460173561850889
GO:0015992proton transport0.0460173561850889
GO:0022857transmembrane transporter activity0.0460173561850889
GO:0051128regulation of cellular component organization and biogenesis0.0460173561850889
GO:0046943carboxylic acid transmembrane transporter activity0.0460173561850889
GO:0006818hydrogen transport0.0460173561850889
GO:0005342organic acid transmembrane transporter activity0.0460173561850889
GO:0044425membrane part0.0460173561850889
GO:0015662ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism0.0460173561850889
GO:0046942carboxylic acid transport0.0460173561850889
GO:0015849organic acid transport0.0460173561850889
GO:0005912adherens junction0.0460173561850889
GO:0022892substrate-specific transporter activity0.0465164382921448



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
surface structure2.64e-1222
zone of skin1.49e-095
skin epidermis1.49e-095
skin of body1.49e-095
integument1.49e-095
surface1.49e-095
outer epithelium1.49e-095
integumental system1.49e-095
enveloping layer of ectoderm1.49e-095


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
MA0041.12.01886
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.212634
MA0056.10
MA0057.10.149949
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.17.1726
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.16.52667
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.11.03097
MA0105.10.57901
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.11.68825
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
MA0139.11.2655
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.379391
MA0146.10.0392287
MA0147.10.858298
MA0148.10.553294
MA0149.10.464445
MA0062.20.591842
MA0035.20.630778
MA0039.20.0823004
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.21.33199
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.933846
MA0155.10.414701
MA0156.10.406559
MA0157.11.96555
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.176524
MA0163.13.72829
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.21.83891
MA0079.29.24173
MA0102.21.7182
MA0258.10.290587
MA0259.10.833237
MA0442.10
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