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MCL coexpression mm9:1731: Difference between revisions

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{{MCL_coexpression_mm9
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acid metabolic process;0.00284884676491536;14275!GO:0006620;posttranslational protein targeting to membrane;0.00379846235322048;14275!GO:0008517;folic acid transporter activity;0.00379846235322048;14275!GO:0051183;vitamin transporter activity;0.00447675920200985;14275!GO:0051184;cofactor transporter activity;0.00447675920200985;14275!GO:0005542;folic acid binding;0.00447675920200985;14275!GO:0006760;folic acid and derivative metabolic process;0.00447675920200985;14275!GO:0042558;pteridine and derivative metabolic process;0.00462937599298745;14275!GO:0045047;protein targeting to ER;0.00601423205926575;14275!GO:0006612;protein targeting to membrane;0.00769188626527147;14275!GO:0006767;water-soluble vitamin metabolic process;0.0101004567119726;14275!GO:0006752;group transfer coenzyme metabolic process;0.0128198104421191;14275!GO:0006766;vitamin metabolic process;0.0134302776060295;14275!GO:0046483;heterocycle metabolic process;0.0134302776060295;14275!GO:0019842;vitamin binding;0.0197743481329419;14275!GO:0006725;aromatic compound metabolic process;0.0197743481329419;14275!GO:0048503;GPI anchor binding;0.0197743481329419;14275!GO:0006732;coenzyme metabolic process;0.0242721744370788;14275!GO:0035091;phosphoinositide binding;0.0242721744370788;14275!GO:0045045;secretory pathway;0.0242721744370788;14275!GO:0051186;cofactor metabolic process;0.0242721744370788;14275!GO:0006605;protein targeting;0.0242721744370788;14275!GO:0005543;phospholipid binding;0.0242721744370788;14275!GO:0032940;secretion by cell;0.0242721744370788;14275!GO:0032787;monocarboxylic acid metabolic process;0.0242721744370788;14275!GO:0046903;secretion;0.0283788966197337;14275!GO:0008289;lipid binding;0.0375625721596247;14275!GO:0006886;intracellular protein transport;0.0391716430175862;14275!GO:0005624;membrane fraction;0.0411704306671639;14275!GO:0019752;carboxylic acid metabolic process;0.0411704306671639;14275!GO:0006082;organic acid metabolic 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|gostat_on_MCL_coexpression=GO:0046655;folic acid metabolic process;0.00284884676491536;14275!GO:0006620;posttranslational protein targeting to membrane;0.00379846235322048;14275!GO:0008517;folic acid transporter activity;0.00379846235322048;14275!GO:0051183;vitamin transporter activity;0.00447675920200985;14275!GO:0051184;cofactor transporter activity;0.00447675920200985;14275!GO:0005542;folic acid binding;0.00447675920200985;14275!GO:0006760;folic acid and derivative metabolic process;0.00447675920200985;14275!GO:0042558;pteridine and derivative metabolic process;0.00462937599298745;14275!GO:0045047;protein targeting to ER;0.00601423205926575;14275!GO:0006612;protein targeting to membrane;0.00769188626527147;14275!GO:0006767;water-soluble vitamin metabolic process;0.0101004567119726;14275!GO:0006752;group transfer coenzyme metabolic process;0.0128198104421191;14275!GO:0006766;vitamin metabolic process;0.0134302776060295;14275!GO:0046483;heterocycle metabolic process;0.0134302776060295;14275!GO:0019842;vitamin binding;0.0197743481329419;14275!GO:0006725;aromatic compound metabolic process;0.0197743481329419;14275!GO:0048503;GPI anchor binding;0.0197743481329419;14275!GO:0006732;coenzyme metabolic process;0.0242721744370788;14275!GO:0035091;phosphoinositide binding;0.0242721744370788;14275!GO:0045045;secretory pathway;0.0242721744370788;14275!GO:0051186;cofactor metabolic process;0.0242721744370788;14275!GO:0006605;protein targeting;0.0242721744370788;14275!GO:0005543;phospholipid binding;0.0242721744370788;14275!GO:0032940;secretion by cell;0.0242721744370788;14275!GO:0032787;monocarboxylic acid metabolic process;0.0242721744370788;14275!GO:0046903;secretion;0.0283788966197337;14275!GO:0008289;lipid binding;0.0375625721596247;14275!GO:0006886;intracellular protein transport;0.0391716430175862;14275!GO:0005624;membrane fraction;0.0411704306671639;14275!GO:0019752;carboxylic acid metabolic process;0.0411704306671639;14275!GO:0006082;organic acid metabolic process;0.0411704306671639;14275!GO:0000267;cell fraction;0.044157124856188;14275!GO:0046907;intracellular transport;0.0490346958324825;14275!
|ontology_enrichment_celltype=CL:0002453!3.37e-08!8
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005156!1.69e-09!26;UBERON:0000990!1.69e-09!26;UBERON:0003133!2.16e-09!24;UBERON:0006554!1.39e-08!18;UBERON:0000991!3.40e-08!18;UBERON:0005564!3.40e-08!18;UBERON:0001008!5.84e-08!19;UBERON:0002113!9.06e-08!14;UBERON:0003918!9.06e-08!14;UBERON:0011143!9.06e-08!14;UBERON:0005095!9.06e-08!14;UBERON:0007687!9.06e-08!14;UBERON:0003103!1.38e-07!43;UBERON:0004176!1.77e-07!17;UBERON:0009196!1.77e-07!17;UBERON:0009117!1.77e-07!17;UBERON:0000473!8.64e-07!14
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.087078,0.529553,0.603273,0.406364,0.618805,0.715644,0.812379,0.310789,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.283802,0.545768,0.489529,0.874994,0.727684,0.404661,0.537749,0.757752,0.274609,0.641282,0.456327,0.227599,0.626183,1.03545,0.395107,0.253145,0.425309,0.0566307,0.384813,0.699032,0.947152,0.328675,0.401916,0.631725,0.419293,0.426986,0.0637209,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.714607,0.245132,1.30151,0.835925,0.997094,1.23692,0.830212,0.948899,0.794502,0.293164,1.1148,0.272382,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,1.06179,0.356133,0.3366,0.297538,2.39081,1.97563,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.673306,0.607321,0.932233,0.991416,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,1.05179,0.230371,0.133815,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.425122
}}

Latest revision as of 17:24, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:53526008..53526024,-p2@5830416P10Rik
Mm9::chr7:109016961..109017012,-p4@Folr1
Mm9::chr7:109017023..109017036,-p15@Folr1
Mm9::chr7:109017526..109017537,-p18@Folr1
Mm9::chr7:109017548..109017587,-p11@Folr1


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:0046655folic acid metabolic process0.00284884676491536
GO:0006620posttranslational protein targeting to membrane0.00379846235322048
GO:0008517folic acid transporter activity0.00379846235322048
GO:0051183vitamin transporter activity0.00447675920200985
GO:0051184cofactor transporter activity0.00447675920200985
GO:0005542folic acid binding0.00447675920200985
GO:0006760folic acid and derivative metabolic process0.00447675920200985
GO:0042558pteridine and derivative metabolic process0.00462937599298745
GO:0045047protein targeting to ER0.00601423205926575
GO:0006612protein targeting to membrane0.00769188626527147
GO:0006767water-soluble vitamin metabolic process0.0101004567119726
GO:0006752group transfer coenzyme metabolic process0.0128198104421191
GO:0006766vitamin metabolic process0.0134302776060295
GO:0046483heterocycle metabolic process0.0134302776060295
GO:0019842vitamin binding0.0197743481329419
GO:0006725aromatic compound metabolic process0.0197743481329419
GO:0048503GPI anchor binding0.0197743481329419
GO:0006732coenzyme metabolic process0.0242721744370788
GO:0035091phosphoinositide binding0.0242721744370788
GO:0045045secretory pathway0.0242721744370788
GO:0051186cofactor metabolic process0.0242721744370788
GO:0006605protein targeting0.0242721744370788
GO:0005543phospholipid binding0.0242721744370788
GO:0032940secretion by cell0.0242721744370788
GO:0032787monocarboxylic acid metabolic process0.0242721744370788
GO:0046903secretion0.0283788966197337
GO:0008289lipid binding0.0375625721596247
GO:0006886intracellular protein transport0.0391716430175862
GO:0005624membrane fraction0.0411704306671639
GO:0019752carboxylic acid metabolic process0.0411704306671639
GO:0006082organic acid metabolic process0.0411704306671639
GO:0000267cell fraction0.044157124856188
GO:0046907intracellular transport0.0490346958324825



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
oligodendrocyte precursor cell3.37e-088

Uber Anatomy
Ontology termp-valuen
reproductive structure1.69e-0926
reproductive system1.69e-0926
reproductive organ2.16e-0924
urinary system structure1.39e-0818
gonad3.40e-0818
gonad primordium3.40e-0818
renal system5.84e-0819
kidney9.06e-0814
kidney mesenchyme9.06e-0814
upper urinary tract9.06e-0814
kidney rudiment9.06e-0814
kidney field9.06e-0814
compound organ1.38e-0743
external genitalia1.77e-0717
indifferent external genitalia1.77e-0717
indifferent gonad1.77e-0717
testis8.64e-0714


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)
MA0003.10.0833043
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.0502051
MA0017.12.9605
MA0019.10.874061
MA0024.12.32185
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
MA0055.10.0851423
MA0056.10
MA0057.11.06992
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.955135
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.11.08757
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
MA0090.11.39153
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
MA0114.11.69206
MA0115.11.16466
MA0116.11.07655
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
MA0141.11.21195
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.10.927481
MA0146.10.822925
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.20.254018
MA0035.20.700704
MA0039.20.140205
MA0138.20.861035
MA0002.20.299191
MA0137.20.479301
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.929207
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.515751
MA0156.11.18326
MA0157.10.91689
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.0699535
MA0163.10.0644585
MA0164.11.7313
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.0381166
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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