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MCL coexpression mm9:1503: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000926!1.73e-12!120;UBERON:0004120!1.73e-12!120;UBERON:0006603!1.73e-12!120;UBERON:0001041!2.44e-12!80;UBERON:0001048!6.22e-12!134;UBERON:0003081!2.23e-11!87;UBERON:0005911!1.60e-10!69;UBERON:0000077!4.51e-09!35;UBERON:0000475!8.11e-09!150;UBERON:0004177!8.15e-09!29;UBERON:0005057!8.15e-09!29;UBERON:0002193!1.03e-08!48;UBERON:0002405!1.03e-08!48;UBERON:0000490!1.92e-08!66;UBERON:0001004!1.96e-08!42;UBERON:0002390!3.25e-08!45;UBERON:0003061!3.25e-08!45;UBERON:0000065!4.46e-08!41;UBERON:0004119!2.23e-07!118;UBERON:0000925!2.23e-07!118;UBERON:0006595!2.23e-07!118;UBERON:0001007!2.41e-07!116;UBERON:0001555!2.41e-07!116;UBERON:0007026!2.41e-07!116;UBERON:0003929!2.73e-07!55;UBERON:0004921!3.01e-07!114;UBERON:0003408!3.63e-07!24;UBERON:0006562!3.77e-07!24;UBERON:0001557!3.77e-07!24;UBERON:0001042!3.77e-07!24;UBERON:0008814!3.77e-07!24;UBERON:0009145!3.77e-07!24;UBERON:0002370!8.49e-07!23;UBERON:0000974!8.49e-07!23;UBERON:0004807!8.49e-07!23;UBERON:0005058!8.49e-07!23;UBERON:0003351!8.49e-07!23;UBERON:0009113!8.49e-07!23;UBERON:0003295!8.49e-07!23;UBERON:0009722!8.49e-07!23;UBERON:0005562!8.49e-07!23;UBERON:0007690!8.49e-07!23
|ontology_enrichment_uberon=UBERON:0000926!1.73e-12!120;UBERON:0004120!1.73e-12!120;UBERON:0006603!1.73e-12!120;UBERON:0001041!2.44e-12!80;UBERON:0001048!6.22e-12!134;UBERON:0003081!2.23e-11!87;UBERON:0005911!1.60e-10!69;UBERON:0000077!4.51e-09!35;UBERON:0000475!8.11e-09!150;UBERON:0004177!8.15e-09!29;UBERON:0005057!8.15e-09!29;UBERON:0002193!1.03e-08!48;UBERON:0002405!1.03e-08!48;UBERON:0000490!1.92e-08!66;UBERON:0001004!1.96e-08!42;UBERON:0002390!3.25e-08!45;UBERON:0003061!3.25e-08!45;UBERON:0000065!4.46e-08!41;UBERON:0004119!2.23e-07!118;UBERON:0000925!2.23e-07!118;UBERON:0006595!2.23e-07!118;UBERON:0001007!2.41e-07!116;UBERON:0001555!2.41e-07!116;UBERON:0007026!2.41e-07!116;UBERON:0003929!2.73e-07!55;UBERON:0004921!3.01e-07!114;UBERON:0003408!3.63e-07!24;UBERON:0006562!3.77e-07!24;UBERON:0001557!3.77e-07!24;UBERON:0001042!3.77e-07!24;UBERON:0008814!3.77e-07!24;UBERON:0009145!3.77e-07!24;UBERON:0002370!8.49e-07!23;UBERON:0000974!8.49e-07!23;UBERON:0004807!8.49e-07!23;UBERON:0005058!8.49e-07!23;UBERON:0003351!8.49e-07!23;UBERON:0009113!8.49e-07!23;UBERON:0003295!8.49e-07!23;UBERON:0009722!8.49e-07!23;UBERON:0005562!8.49e-07!23;UBERON:0007690!8.49e-07!23
|tfbs_overrepresentation_for_novel_motifs=1.37236,0.293744,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.836099,0.746305,0.668936,0.702872,0.812978,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.545768,0.489529,0.145201,0.727684,0.404661,1.32977,1.78963,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,1.3018,0.425309,0.0566307,1.7724,0.699032,0.947152,0.876199,0.401916,0.631725,0.419293,0.426986,0.227872,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,1.74508,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,1.26875,0.30684,0.46305,1.23259,2.03319,0.686172,0.70455,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,2.60379,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,1.03353,0.673306,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,1.85301,0.651755,1.93643,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,2.37965,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.997706,0.701187,0.745913
|tfbs_overrepresentation_for_novel_motifs=1.37236,0.293744,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.836099,0.746305,0.668936,0.702872,0.812978,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.545768,0.489529,0.145201,0.727684,0.404661,1.32977,1.78963,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,1.3018,0.425309,0.0566307,1.7724,0.699032,0.947152,0.876199,0.401916,0.631725,0.419293,0.426986,0.227872,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,1.74508,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,1.26875,0.30684,0.46305,1.23259,2.03319,0.686172,0.70455,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,2.60379,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,1.03353,0.673306,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,1.85301,0.651755,1.93643,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,2.37965,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.997706,0.701187,0.745913
|tfbs_overrepresentation_jaspar=MA0003.1;3.33169,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;1.01283,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;3.12241,MA0068.1;0.197245,MA0069.1;1.08414,MA0070.1;1.07418,MA0071.1;0.644448,MA0072.1;1.06547,MA0073.1;0.0481612,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;0.248108,MA0106.1;0.809991,MA0107.1;0.454197,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;0.524046,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;0.21827,MA0147.1;0.378658,MA0148.1;0.621195,MA0149.1;0.529387,MA0062.2;0.706751,MA0035.2;0.700704,MA0039.2;3.82077,MA0138.2;0.861035,MA0002.2;0.299191,MA0137.2;0.479301,MA0104.2;0.845917,MA0047.2;0.75686,MA0112.2;0.157681,MA0065.2;0.477991,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;1.01146,MA0160.1;0.624415,MA0161.1;0,MA0162.1;3.09272,MA0163.1;0.855539,MA0164.1;0.729558,MA0080.2;1.15331,MA0018.2;2.93398,MA0099.2;0.854449,MA0079.2;1.4428,MA0102.2;1.79669,MA0258.1;0.346619,MA0259.1;0.366802,MA0442.1;0
}}
}}

Revision as of 13:26, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:17667803..17667904,-p1@Heca
Mm9::chr11:77161761..77161771,+p3@Ssh2
Mm9::chr11:77161774..77161794,+p2@Ssh2
Mm9::chr12:85559785..85559840,-p1@C130039O16Rik
Mm9::chr4:100937819..100937836,-p1@Jak1


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:0004718Janus kinase activity0.0399802800961384
GO:0004716receptor signaling protein tyrosine kinase activity0.0399802800961384



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
mesoderm1.73e-12120
mesoderm-derived structure1.73e-12120
presumptive mesoderm1.73e-12120
foregut2.44e-1280
primordium6.22e-12134
lateral plate mesoderm2.23e-1187
endo-epithelium1.60e-1069
mixed endoderm/mesoderm-derived structure4.51e-0935
organism subdivision8.11e-09150
hemopoietic organ8.15e-0929
immune organ8.15e-0929
hemolymphoid system1.03e-0848
immune system1.03e-0848
unilaminar epithelium1.92e-0866
respiratory system1.96e-0842
hematopoietic system3.25e-0845
blood island3.25e-0845
respiratory tract4.46e-0841
endoderm-derived structure2.23e-07118
endoderm2.23e-07118
presumptive endoderm2.23e-07118
digestive system2.41e-07116
digestive tract2.41e-07116
primitive gut2.41e-07116
gut epithelium2.73e-0755
subdivision of digestive tract3.01e-07114
gland of gut3.63e-0724
pharynx3.77e-0724
upper respiratory tract3.77e-0724
chordate pharynx3.77e-0724
pharyngeal arch system3.77e-0724
pharyngeal region of foregut3.77e-0724
thymus8.49e-0723
neck8.49e-0723
respiratory system epithelium8.49e-0723
hemolymphoid system gland8.49e-0723
pharyngeal epithelium8.49e-0723
thymic region8.49e-0723
pharyngeal gland8.49e-0723
entire pharyngeal arch endoderm8.49e-0723
thymus primordium8.49e-0723
early pharyngeal endoderm8.49e-0723


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)
MA0003.13.33169
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
MA0055.11.01283
MA0056.10
MA0057.10.562607
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.13.12241
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.0481612
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
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.10.419688
MA0117.11.13165
MA0119.10.524046
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
MA0146.10.21827
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.706751
MA0035.20.700704
MA0039.23.82077
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.845917
MA0047.20.75686
MA0112.20.157681
MA0065.20.477991
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
MA0159.11.01146
MA0160.10.624415
MA0161.10
MA0162.13.09272
MA0163.10.855539
MA0164.10.729558
MA0080.21.15331
MA0018.22.93398
MA0099.20.854449
MA0079.21.4428
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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