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MCL coexpression mm9:1812: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0005172!5.00e-12!49;UBERON:0005173!5.00e-12!49;UBERON:0002417!5.00e-12!49;UBERON:0000916!5.00e-12!49;UBERON:0000466!1.69e-11!79;UBERON:0002365!2.44e-10!25;UBERON:0002330!2.44e-10!25;UBERON:0005177!2.90e-10!79;UBERON:0002107!6.83e-10!22;UBERON:0007499!6.83e-10!22;UBERON:0006925!6.83e-10!22;UBERON:0009497!6.83e-10!22;UBERON:0000015!6.83e-10!22;UBERON:0002423!6.83e-10!22;UBERON:0006235!6.83e-10!22;UBERON:0008835!6.83e-10!22;UBERON:0003894!6.83e-10!22;UBERON:0004161!6.83e-10!22;UBERON:0008836!6.83e-10!22;UBERON:0005256!7.24e-10!45;UBERON:0000949!1.89e-09!72;UBERON:0009854!2.25e-09!23;UBERON:0009856!2.25e-09!23;UBERON:0002100!2.72e-08!90;UBERON:0009569!5.06e-08!66;UBERON:0003886!7.47e-08!38;UBERON:0002553!1.39e-07!39;UBERON:0002530!1.40e-07!65;UBERON:0002323!1.42e-07!37;UBERON:0004458!1.42e-07!37;UBERON:0003104!2.17e-07!61;UBERON:0009142!2.17e-07!61;UBERON:0002368!2.26e-07!60;UBERON:0000475!4.14e-07!150
|ontology_enrichment_uberon=UBERON:0005172!5.00e-12!49;UBERON:0005173!5.00e-12!49;UBERON:0002417!5.00e-12!49;UBERON:0000916!5.00e-12!49;UBERON:0000466!1.69e-11!79;UBERON:0002365!2.44e-10!25;UBERON:0002330!2.44e-10!25;UBERON:0005177!2.90e-10!79;UBERON:0002107!6.83e-10!22;UBERON:0007499!6.83e-10!22;UBERON:0006925!6.83e-10!22;UBERON:0009497!6.83e-10!22;UBERON:0000015!6.83e-10!22;UBERON:0002423!6.83e-10!22;UBERON:0006235!6.83e-10!22;UBERON:0008835!6.83e-10!22;UBERON:0003894!6.83e-10!22;UBERON:0004161!6.83e-10!22;UBERON:0008836!6.83e-10!22;UBERON:0005256!7.24e-10!45;UBERON:0000949!1.89e-09!72;UBERON:0009854!2.25e-09!23;UBERON:0009856!2.25e-09!23;UBERON:0002100!2.72e-08!90;UBERON:0009569!5.06e-08!66;UBERON:0003886!7.47e-08!38;UBERON:0002553!1.39e-07!39;UBERON:0002530!1.40e-07!65;UBERON:0002323!1.42e-07!37;UBERON:0004458!1.42e-07!37;UBERON:0003104!2.17e-07!61;UBERON:0009142!2.17e-07!61;UBERON:0002368!2.26e-07!60;UBERON:0000475!4.14e-07!150
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,0.529553,1.46803,1.04755,0.618805,0.715644,0.812379,0.836099,0.746305,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.545768,0.489529,0.874994,0.727684,0.404661,0.537749,0.757752,0.754069,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.704734,0.425309,0.0566307,0.384813,0.699032,0.360612,0.328675,1.03785,0.631725,1.94388,0.426986,0.227872,0.591277,0.847828,0.658142,1.78464,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,1.5593,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,0.152094,1.23259,0.257421,0.686172,0.70455,0.835925,0.997094,1.23692,0.308173,0.948899,0.794502,0.293164,1.1148,0.0793594,0.0882907,0.227755,1.9856,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.89388,0.297538,1.05152,0.848095,0.20438,1.00062,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.328405,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.745913
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.612204,0.529553,1.46803,1.04755,0.618805,0.715644,0.812379,0.836099,0.746305,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.545768,0.489529,0.874994,0.727684,0.404661,0.537749,0.757752,0.754069,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.704734,0.425309,0.0566307,0.384813,0.699032,0.360612,0.328675,1.03785,0.631725,1.94388,0.426986,0.227872,0.591277,0.847828,0.658142,1.78464,0.459555,0.912738,0.786094,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,1.5593,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.827208,0.152094,1.23259,0.257421,0.686172,0.70455,0.835925,0.997094,1.23692,0.308173,0.948899,0.794502,0.293164,1.1148,0.0793594,0.0882907,0.227755,1.9856,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.89388,0.297538,1.05152,0.848095,0.20438,1.00062,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.328405,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.745913
|tfbs_overrepresentation_jaspar=MA0003.1;0.0185483,MA0004.1;0.603793,MA0006.1;0.419915,MA0007.1;0.587678,MA0009.1;1.06266,MA0014.1;0.0502051,MA0017.1;1.14026,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;0.28842,MA0056.1;0,MA0057.1;0.562607,MA0058.1;0.50032,MA0059.1;0.513699,MA0060.1;0.330907,MA0061.1;0.364227,MA0063.1;0,MA0066.1;0.746072,MA0067.1;1.41352,MA0068.1;2.42244,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;10.5963,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;0.888325,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;0.523409,MA0103.1;0.460936,MA0105.1;0.693075,MA0106.1;1.89733,MA0107.1;0.454197,MA0108.2;0.897859,MA0109.1;0,MA0111.1;0.582193,MA0113.1;0.780358,MA0114.1;0.949408,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;0.0604336,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.706751,MA0035.2;0.700704,MA0039.2;0.0511423,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;0.315156,MA0047.2;0.75686,MA0112.2;0.47695,MA0065.2;0.158101,MA0150.1;1.43499,MA0151.1;0,MA0152.1;0.756973,MA0153.1;1.21594,MA0154.1;0.203217,MA0155.1;0.173445,MA0156.1;1.18326,MA0157.1;0.91689,MA0158.1;0,MA0159.1;0.389847,MA0160.1;0.624415,MA0161.1;0,MA0162.1;0.526186,MA0163.1;0.230013,MA0164.1;0.729558,MA0080.2;1.15331,MA0018.2;0.739807,MA0099.2;0.854449,MA0079.2;0.435944,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}
}}

Revision as of 13:54, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr5:125758107..125758123,-p@chr5:125758107..125758123
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Mm9::chr5:125758205..125758235,-p@chr5:125758205..125758235
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Mm9::chr5:125770095..125770131,-p@chr5:125770095..125770131
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Mm9::chr7:151027144..151027159,+p4@Dhcr7
Mm9::chr7:151033782..151033809,+p@chr7:151033782..151033809
+


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:0008203cholesterol metabolic process0.000634016565012102
GO:0016125sterol metabolic process0.000634016565012102
GO:0008202steroid metabolic process0.001654991596933
GO:00475987-dehydrocholesterol reductase activity0.00232838437517121
GO:0006066alcohol metabolic process0.00327912857149358
GO:0043534blood vessel endothelial cell migration0.00465638604416634
GO:0006707cholesterol catabolic process0.00465638604416634
GO:0016127sterol catabolic process0.00465638604416634
GO:0008283cell proliferation0.00532100087915992
GO:0006706steroid catabolic process0.00532100087915992
GO:0043542endothelial cell migration0.00532100087915992
GO:0044255cellular lipid metabolic process0.00532100087915992
GO:0001935endothelial cell proliferation0.00532100087915992
GO:0016599caveolar membrane0.00532100087915992
GO:0005901caveola0.00539204299110468
GO:0006629lipid metabolic process0.00539204299110468
GO:0000299integral to membrane of membrane fraction0.00657228069792494
GO:0030301cholesterol transport0.00698247418228115
GO:0015918sterol transport0.00698247418228115
GO:0016628oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor0.00698247418228115
GO:0006695cholesterol biosynthetic process0.00975142626251612
GO:0044242cellular lipid catabolic process0.011734148517821
GO:0016126sterol biosynthetic process0.011734148517821
GO:0009791post-embryonic development0.0120200993621696
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.0156291691335456
GO:0035264multicellular organism growth0.0215828059196272
GO:0030324lung development0.0215828059196272
GO:0030323respiratory tube development0.0215828059196272
GO:0006694steroid biosynthetic process0.0221185166423629
GO:0006869lipid transport0.0229274507513982
GO:0016042lipid catabolic process0.0278701945656588



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
abdomen element5.00e-1249
abdominal segment element5.00e-1249
abdominal segment of trunk5.00e-1249
abdomen5.00e-1249
immaterial anatomical entity1.69e-1179
exocrine gland2.44e-1025
exocrine system2.44e-1025
trunk region element2.90e-1079
liver6.83e-1022
epithelial sac6.83e-1022
digestive gland6.83e-1022
epithelium of foregut-midgut junction6.83e-1022
anatomical boundary6.83e-1022
hepatobiliary system6.83e-1022
foregut-midgut junction6.83e-1022
hepatic diverticulum6.83e-1022
liver primordium6.83e-1022
septum transversum6.83e-1022
liver bud6.83e-1022
trunk mesenchyme7.24e-1045
endocrine system1.89e-0972
digestive tract diverticulum2.25e-0923
sac2.25e-0923
trunk2.72e-0890
subdivision of trunk5.06e-0866
body cavity precursor7.47e-0838
anatomical cavity1.39e-0739
gland1.40e-0765
body cavity1.42e-0737
body cavity or lining1.42e-0737
mesenchyme2.17e-0761
entire embryonic mesenchyme2.17e-0761
endocrine gland2.26e-0760
organism subdivision4.14e-07150


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)
MA0003.10.0185483
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.0502051
MA0017.11.14026
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
MA0055.10.28842
MA0056.10
MA0057.10.562607
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.12.42244
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.110.5963
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.10.801834
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.888325
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.693075
MA0106.11.89733
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.949408
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
MA0146.10.0604336
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.706751
MA0035.20.700704
MA0039.20.0511423
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.47695
MA0065.20.158101
MA0150.11.43499
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.11.18326
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.526186
MA0163.10.230013
MA0164.10.729558
MA0080.21.15331
MA0018.20.739807
MA0099.20.854449
MA0079.20.435944
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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