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MCL coexpression mm9:1248: Difference between revisions

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{{MCL_coexpression_mm9
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of skeletal muscle regeneration;0.00575216387474856;74318!GO:0043415;positive regulation of skeletal muscle regeneration;0.00575216387474856;74318!GO:0051149;positive regulation of muscle cell differentiation;0.00575216387474856;74318!GO:0051155;positive regulation of striated muscle cell differentiation;0.00575216387474856;74318!GO:0051153;regulation of striated muscle cell differentiation;0.00575216387474856;74318!GO:0043403;skeletal muscle regeneration;0.00575216387474856;74318!GO:0051147;regulation of muscle cell differentiation;0.00657372147411718;74318!GO:0031099;regeneration;0.0140577633669742;74318!GO:0042246;tissue regeneration;0.0140577633669742;74318!GO:0051146;striated muscle cell differentiation;0.0333387866712209;74318!GO:0045597;positive regulation of cell differentiation;0.0459605804354191;74318!GO:0048589;developmental 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|gostat_on_MCL_coexpression=GO:0043416;regulation of skeletal muscle regeneration;0.00575216387474856;74318!GO:0043415;positive regulation of skeletal muscle regeneration;0.00575216387474856;74318!GO:0051149;positive regulation of muscle cell differentiation;0.00575216387474856;74318!GO:0051155;positive regulation of striated muscle cell differentiation;0.00575216387474856;74318!GO:0051153;regulation of striated muscle cell differentiation;0.00575216387474856;74318!GO:0043403;skeletal muscle regeneration;0.00575216387474856;74318!GO:0051147;regulation of muscle cell differentiation;0.00657372147411718;74318!GO:0031099;regeneration;0.0140577633669742;74318!GO:0042246;tissue regeneration;0.0140577633669742;74318!GO:0051146;striated muscle cell differentiation;0.0333387866712209;74318!GO:0045597;positive regulation of cell differentiation;0.0459605804354191;74318!GO:0048589;developmental growth;0.0459605804354191;74318!
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|ontology_enrichment_uberon=UBERON:0007100!7.65e-11!18;UBERON:0000948!7.65e-11!18;UBERON:0005498!7.65e-11!18;UBERON:0004140!7.65e-11!18;UBERON:0009881!7.65e-11!18;UBERON:0004141!7.65e-11!18;UBERON:0003084!7.65e-11!18;UBERON:0007005!7.65e-11!18;UBERON:0004139!7.65e-11!18;UBERON:0004291!7.65e-11!18;UBERON:0002048!1.11e-10!14;UBERON:0000117!1.11e-10!14;UBERON:0000171!1.11e-10!14;UBERON:0000170!1.11e-10!14;UBERON:0005597!1.11e-10!14;UBERON:0000118!1.11e-10!14;UBERON:0005153!1.23e-07!17;UBERON:0005178!1.23e-07!17;UBERON:0005181!1.23e-07!17;UBERON:0002224!1.23e-07!17;UBERON:0000915!1.23e-07!17;UBERON:0008947!1.23e-07!17;UBERON:0003258!1.23e-07!17;UBERON:0004535!1.43e-07!23;UBERON:0001009!1.43e-07!23;UBERON:0003103!3.32e-07!43
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.0600685,0.464605,0.535892,0.346849,0.550971,0.645383,0.691572,0.7141,0.0835344,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.232269,0.143775,1.09054,0.35122,0.657163,0.345236,0.472505,0.686615,0.223823,0.572827,0.394364,0.181062,0.558142,0.960397,0.336199,0.204204,0.364821,0.335531,0.326478,0.629145,0.303703,0.27383,0.342638,0.56353,0.327433,0.366415,0.161543,0.524258,0.77511,0.589246,0.284064,0.397446,0.839084,0.714419,0.174327,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,2.0186,1.2599,1.61148,0.935192,1.46355,0.444872,0.253541,0.366795,1.156,0.208101,0.19692,0.589776,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.198949,0.220054,0.181203,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.810643,0.769162,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.247162,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.325363,1.10596,0.287383,0.678689,1.18867,0.71546,0.376898,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,0.671017,0.325308,0.63125,0.0323861
|tfbs_overrepresentation_jaspar=MA0003.1;0.135108,MA0004.1;0.536396,MA0006.1;0.359699,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;0.212634,MA0056.1;0,MA0057.1;0.457693,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;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;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;0.359483,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;0.307873,MA0145.1;0.119202,MA0146.1;0.0392287,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;1.17328,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.00481054,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;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;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;0.000341844,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}

Latest revision as of 16:37, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:6893990..6894006,-p@chr10:6893990..6894006
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Mm9::chr10:6955274..6955276,-p@chr10:6955274..6955276
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Mm9::chr14:102293240..102293254,+p@chr14:102293240..102293254
+
Mm9::chr16:38622460..38622476,-p@chr16:38622460..38622476
-
Mm9::chr5:77544170..77544181,-p6@Hopx
Mm9::chr9:30750126..30750131,+p1@Adamts8


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:0043416regulation of skeletal muscle regeneration0.00575216387474856
GO:0043415positive regulation of skeletal muscle regeneration0.00575216387474856
GO:0051149positive regulation of muscle cell differentiation0.00575216387474856
GO:0051155positive regulation of striated muscle cell differentiation0.00575216387474856
GO:0051153regulation of striated muscle cell differentiation0.00575216387474856
GO:0043403skeletal muscle regeneration0.00575216387474856
GO:0051147regulation of muscle cell differentiation0.00657372147411718
GO:0031099regeneration0.0140577633669742
GO:0042246tissue regeneration0.0140577633669742
GO:0051146striated muscle cell differentiation0.0333387866712209
GO:0045597positive regulation of cell differentiation0.0459605804354191
GO:0048589developmental growth0.0459605804354191



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
primary circulatory organ7.65e-1118
heart7.65e-1118
primitive heart tube7.65e-1118
primary heart field7.65e-1118
anterior lateral plate mesoderm7.65e-1118
heart tube7.65e-1118
heart primordium7.65e-1118
cardiac mesoderm7.65e-1118
cardiogenic plate7.65e-1118
heart rudiment7.65e-1118
lung1.11e-1014
respiratory tube1.11e-1014
respiration organ1.11e-1014
pair of lungs1.11e-1014
lung primordium1.11e-1014
lung bud1.11e-1014
epithelial bud1.23e-0717
thoracic cavity element1.23e-0717
thoracic segment organ1.23e-0717
thoracic cavity1.23e-0717
thoracic segment of trunk1.23e-0717
respiratory primordium1.23e-0717
endoderm of foregut1.23e-0717
cardiovascular system1.43e-0723
circulatory system1.43e-0723
compound organ3.32e-0743


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)
MA0003.10.135108
MA0004.10.536396
MA0006.10.359699
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
MA0055.10.212634
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
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
MA0073.10.000157319
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
MA0101.10.458688
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
MA0116.10.359483
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
MA0144.10.307873
MA0145.10.119202
MA0146.10.0392287
MA0147.10.320675
MA0148.10.553294
MA0149.11.17328
MA0062.20.204999
MA0035.20.630778
MA0039.20.00481054
MA0138.20.788113
MA0002.20.246463
MA0137.20.416331
MA0104.20.261255
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
MA0157.10.843181
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
MA0079.20.000341844
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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