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MCL coexpression mm9:1701: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001007!3.72e-15!116;UBERON:0001555!3.72e-15!116;UBERON:0007026!3.72e-15!116;UBERON:0004119!3.91e-15!118;UBERON:0000925!3.91e-15!118;UBERON:0006595!3.91e-15!118;UBERON:0004921!1.36e-14!114;UBERON:0005409!3.24e-10!47;UBERON:0004923!2.99e-08!24;UBERON:0000160!1.73e-07!31;UBERON:0000490!5.76e-07!66;UBERON:0001041!5.76e-07!80;UBERON:0005911!9.01e-07!69
|ontology_enrichment_uberon=UBERON:0001007!3.72e-15!116;UBERON:0001555!3.72e-15!116;UBERON:0007026!3.72e-15!116;UBERON:0004119!3.91e-15!118;UBERON:0000925!3.91e-15!118;UBERON:0006595!3.91e-15!118;UBERON:0004921!1.36e-14!114;UBERON:0005409!3.24e-10!47;UBERON:0004923!2.99e-08!24;UBERON:0000160!1.73e-07!31;UBERON:0000490!5.76e-07!66;UBERON:0001041!5.76e-07!80;UBERON:0005911!9.01e-07!69
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.52338,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,2.41764,0.668936,0.702872,0.812978,0.728641,0.424775,0,0.930881,0.397593,0.775038,0.185796,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,0.754069,0.641282,1.15581,0.645258,0.626183,1.03545,0.395107,0.704734,1.08876,2.82585,1.00043,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.4934,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.731291,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,1.26875,0.30684,0.152094,1.23259,1.31774,0.686172,0.253065,0.835925,0.997094,0.494135,0.308173,2.1819,0.794502,0.293164,1.1148,1.99513,0.297068,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.937248,0.3366,0.297538,1.05152,1.97563,1.75016,1.00062,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,2.13274,1.35621,1.16464,0.495367,0.674448,1.41481,0.399936,0.673306,1.47653,0.932233,0.991416,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.867604,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.651755,0.826123,1.18223,0.908552,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,1.35103,0.90208,0.741834,0.997706,0.701187,1.60845
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.52338,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,2.41764,0.668936,0.702872,0.812978,0.728641,0.424775,0,0.930881,0.397593,0.775038,0.185796,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,0.754069,0.641282,1.15581,0.645258,0.626183,1.03545,0.395107,0.704734,1.08876,2.82585,1.00043,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.4934,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.731291,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,1.26875,0.30684,0.152094,1.23259,1.31774,0.686172,0.253065,0.835925,0.997094,0.494135,0.308173,2.1819,0.794502,0.293164,1.1148,1.99513,0.297068,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.937248,0.3366,0.297538,1.05152,1.97563,1.75016,1.00062,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,2.13274,1.35621,1.16464,0.495367,0.674448,1.41481,0.399936,0.673306,1.47653,0.932233,0.991416,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.867604,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.651755,0.826123,1.18223,0.908552,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,1.35103,0.90208,0.741834,0.997706,0.701187,1.60845
|tfbs_overrepresentation_jaspar=MA0003.1;0.989123,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;3.97269,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;1.10192,MA0029.1;0.995171,MA0030.1;1.00195,MA0031.1;0.965177,MA0038.1;0.757669,MA0040.1;1.07552,MA0041.1;0.522007,MA0042.1;0.507715,MA0043.1;1.1618,MA0046.1;1.09955,MA0048.1;1.12075,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;3.36884,MA0056.1;0,MA0057.1;0.192781,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.881183,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;0.197245,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;0.00450236,MA0074.1;0.708108,MA0076.1;0.470037,MA0077.1;1.04318,MA0078.1;0.801834,MA0081.1;0.53877,MA0083.1;1.16099,MA0084.1;1.74401,MA0087.1;1.11687,MA0088.1;0.453686,MA0089.1;0,MA0090.1;0.566938,MA0091.1;0.617887,MA0092.1;1.39225,MA0093.1;0.440484,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;0.523409,MA0103.1;0.460936,MA0105.1;0.248108,MA0106.1;0.809991,MA0107.1;1.15122,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;0.361633,MA0115.1;1.16466,MA0116.1;1.07655,MA0117.1;1.13165,MA0119.1;4.45294,MA0122.1;1.15196,MA0124.1;1.35963,MA0125.1;1.28445,MA0130.1;0,MA0131.1;0.869325,MA0132.1;0,MA0133.1;0,MA0135.1;1.19898,MA0136.1;0.729175,MA0139.1;0.295945,MA0140.1;0.695713,MA0141.1;0.482463,MA0142.1;0.950155,MA0143.1;0.797553,MA0144.1;0.365053,MA0145.1;1.48363,MA0146.1;1.24854,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;1.30506,MA0035.2;0.700704,MA0039.2;5.64811,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;0.315156,MA0047.2;0.75686,MA0112.2;0.157681,MA0065.2;0.158101,MA0150.1;0.587557,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.587595,MA0155.1;0.515751,MA0156.1;1.18326,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;1.87338,MA0163.1;1.29282,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;5.05279,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}
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Revision as of 13:44, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:77013945..77014020,+p1@Usp25
Mm9::chr18:70727922..70728052,+p1@Mbd2
Mm9::chr19:7416282..7416319,-p3@Mark2
Mm9::chr5:138187181..138187192,+p5@Tsc22d4
Mm9::chr7:28258801..28258838,+p1@Sertad3


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:0045180basal cortex0.0293983378253333
GO:0043283biopolymer metabolic process0.0293983378253333
GO:0008327methyl-CpG binding0.0293983378253333
GO:0035197siRNA binding0.03306950599807
GO:0042711maternal behavior0.0352702744957714
GO:0033057reproductive behavior in a multicellular organism0.0486286822378505
GO:0043170macromolecule metabolic process0.0486286822378505
GO:0045178basal part of cell0.0495716550066158



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
digestive system3.72e-15116
digestive tract3.72e-15116
primitive gut3.72e-15116
endoderm-derived structure3.91e-15118
endoderm3.91e-15118
presumptive endoderm3.91e-15118
subdivision of digestive tract1.36e-14114
gastrointestinal system3.24e-1047
organ component layer2.99e-0824
intestine1.73e-0731
unilaminar epithelium5.76e-0766
foregut5.76e-0780
endo-epithelium9.01e-0769


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)
MA0003.10.989123
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.13.97269
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.11.10192
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.11.12075
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.13.36884
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.10.881183
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.00450236
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.453686
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.11.39225
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.11.15122
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.11.07655
MA0117.11.13165
MA0119.14.45294
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.295945
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.11.48363
MA0146.11.24854
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.21.30506
MA0035.20.700704
MA0039.25.64811
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.587595
MA0155.10.515751
MA0156.11.18326
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.11.87338
MA0163.11.29282
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.25.05279
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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