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MCL coexpression mm9:1570: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004535!2.38e-11!23;UBERON:0001009!2.38e-11!23;UBERON:0004872!2.83e-10!33;UBERON:0007100!1.26e-09!18;UBERON:0000948!1.26e-09!18;UBERON:0005498!1.26e-09!18;UBERON:0004140!1.26e-09!18;UBERON:0009881!1.26e-09!18;UBERON:0004141!1.26e-09!18;UBERON:0003084!1.26e-09!18;UBERON:0007005!1.26e-09!18;UBERON:0004139!1.26e-09!18;UBERON:0004291!1.26e-09!18
|ontology_enrichment_uberon=UBERON:0004535!2.38e-11!23;UBERON:0001009!2.38e-11!23;UBERON:0004872!2.83e-10!33;UBERON:0007100!1.26e-09!18;UBERON:0000948!1.26e-09!18;UBERON:0005498!1.26e-09!18;UBERON:0004140!1.26e-09!18;UBERON:0009881!1.26e-09!18;UBERON:0004141!1.26e-09!18;UBERON:0003084!1.26e-09!18;UBERON:0007005!1.26e-09!18;UBERON:0004139!1.26e-09!18;UBERON:0004291!1.26e-09!18
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.52338,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.836099,0.370407,0.668936,1.67597,0.300533,0.728641,0.424775,0,0.930881,0.397593,1.41491,1.64643,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,0.754069,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,1.3018,1.08876,0.0566307,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.227872,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.46305,1.23259,0.257421,0.245132,1.30151,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.272382,3.42313,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,1.46478,1.05152,0.848095,0.20438,1.00062,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,1.35621,1.16464,0.495367,0.674448,1.41481,0.399936,0.673306,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.416978,1.18223,1.62749,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,1.14345
|tfbs_overrepresentation_for_novel_motifs=0.557864,1.52338,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.836099,0.370407,0.668936,1.67597,0.300533,0.728641,0.424775,0,0.930881,0.397593,1.41491,1.64643,0.489529,0.44579,0.727684,0.404661,0.537749,0.757752,0.754069,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,1.3018,1.08876,0.0566307,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,0.426986,0.227872,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.46305,1.23259,0.257421,0.245132,1.30151,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.272382,3.42313,0.645625,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,1.46478,1.05152,0.848095,0.20438,1.00062,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,1.35621,1.16464,0.495367,0.674448,1.41481,0.399936,0.673306,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.416978,1.18223,1.62749,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,1.14345
|tfbs_overrepresentation_jaspar=MA0003.1;0.406907,MA0004.1;0.603793,MA0006.1;1.07705,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.418772,MA0017.1;0.449113,MA0019.1;0.874061,MA0024.1;1.01759,MA0025.1;1.30092,MA0027.1;2.72141,MA0028.1;0.43138,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;0.205696,MA0050.1;0.645342,MA0051.1;0.767098,MA0052.1;1.08379,MA0055.1;1.50466,MA0056.1;0,MA0057.1;1.06992,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.330907,MA0061.1;2.56329,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;0.573319,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;12.6621,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;0.567278,MA0093.1;0.440484,MA0095.1;0,MA0098.1;0,MA0100.1;0.695835,MA0101.1;2.2382,MA0103.1;0.460936,MA0105.1;0.693075,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;0.419688,MA0117.1;1.13165,MA0119.1;1.30068,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;0.476962,MA0146.1;1.74263,MA0147.1;0.986917,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.254018,MA0035.2;0.700704,MA0039.2;2.26967,MA0138.2;0.861035,MA0002.2;0.809945,MA0137.2;0.479301,MA0104.2;0.845917,MA0047.2;0.75686,MA0112.2;0.927461,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;0.99229,MA0156.1;0.469089,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.526186,MA0163.1;1.79895,MA0164.1;0.729558,MA0080.2;0.455167,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.765158,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.960816,MA0442.1;0
}}
}}

Revision as of 13:32, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:53914471..53914527,+p1@P4ha2
Mm9::chr1:184447871..184447905,-p4@Capn2
Mm9::chr7:3290554..3290587,+p1@Myadm
Mm9::chr7:3290589..3290615,+p2@Myadm
Mm9::chr7:3298094..3298120,+p@chr7:3298094..3298120
+


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:0019511peptidyl-proline hydroxylation0.0093672964811066
GO:0031545peptidyl-proline 4-dioxygenase activity0.0093672964811066
GO:0018401peptidyl-proline hydroxylation to 4-hydroxy-L-proline0.0093672964811066
GO:00194714-hydroxyproline metabolic process0.0093672964811066
GO:0004656procollagen-proline 4-dioxygenase activity0.0093672964811066
GO:0018208peptidyl-proline modification0.00993283416100164
GO:0019798procollagen-proline dioxygenase activity0.00993283416100164
GO:0031543peptidyl-proline dioxygenase activity0.00993283416100164
GO:0014902myotube differentiation0.00993283416100164
GO:0000768syncytium formation by plasma membrane fusion0.00993283416100164
GO:0007520myoblast fusion0.00993283416100164
GO:0006949syncytium formation0.0104052560816558
GO:0045026plasma membrane fusion0.0156027531384348
GO:0004198calcium-dependent cysteine-type endopeptidase activity0.0156027531384348
GO:0031418L-ascorbic acid binding0.0190616721487593
GO:0048628myoblast maturation0.0190616721487593
GO:0006944membrane fusion0.0190616721487593
GO:0048627myoblast development0.0190616721487593
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0.0205175648105699
GO:0001824blastocyst development0.0241617432618843
GO:0045445myoblast differentiation0.0267153414079534
GO:0051213dioxygenase activity0.0366732105111305
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.0366732105111305
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0366732105111305
GO:0042692muscle cell differentiation0.0366732105111305
GO:0048741skeletal muscle fiber development0.0366732105111305
GO:0048747muscle fiber development0.0366732105111305
GO:0046483heterocycle metabolic process0.0366732105111305
GO:0048469cell maturation0.0396831511208595
GO:0004197cysteine-type endopeptidase activity0.0430045899037992
GO:0006575amino acid derivative metabolic process0.0434026917891086
GO:0021700developmental maturation0.0434026917891086
GO:0018193peptidyl-amino acid modification0.0434026917891086
GO:0007519skeletal muscle development0.0434026917891086
GO:0019842vitamin binding0.0465752133802208



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>


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)
MA0003.10.406907
MA0004.10.603793
MA0006.11.07705
MA0007.10.587678
MA0009.11.06266
MA0014.10.418772
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
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
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.11.50466
MA0056.10
MA0057.11.06992
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.12.56329
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.573319
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.112.6621
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
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.12.2382
MA0103.10.460936
MA0105.10.693075
MA0106.10.809991
MA0107.11.15122
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.11.30068
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
MA0145.10.476962
MA0146.11.74263
MA0147.10.986917
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.22.26967
MA0138.20.861035
MA0002.20.809945
MA0137.20.479301
MA0104.20.845917
MA0047.20.75686
MA0112.20.927461
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.587595
MA0155.10.99229
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.526186
MA0163.11.79895
MA0164.10.729558
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.765158
MA0102.21.79669
MA0258.10.346619
MA0259.10.960816
MA0442.10
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