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MCL coexpression mm9:1324: Difference between revisions

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{{MCL_coexpression_mm9
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transport;0.0228469674105612;229782!GO:0005338;nucleotide-sugar transmembrane transporter activity;0.0228469674105612;229782!GO:0001784;phosphotyrosine binding;0.0228469674105612;26417!GO:0045309;protein phosphorylated amino acid binding;0.0228469674105612;26417!GO:0043330;response to exogenous dsRNA;0.0228469674105612;26417!GO:0031663;lipopolysaccharide-mediated signaling pathway;0.0228469674105612;26417!GO:0032496;response to lipopolysaccharide;0.0228469674105612;26417!GO:0051219;phosphoprotein binding;0.0228469674105612;26417!GO:0004707;MAP kinase activity;0.0228469674105612;26417!GO:0043331;response to dsRNA;0.0228469674105612;26417!GO:0002237;response to molecule of bacterial origin;0.0271547771255137;26417!GO:0019233;sensory perception of pain;0.0365896572455163;26417!GO:0005351;sugar:hydrogen ion symporter activity;0.045628859221562;229782!GO:0051119;sugar transmembrane transporter activity;0.045628859221562;229782!GO:0015144;carbohydrate transmembrane transporter activity;0.045628859221562;229782!GO:0004702;receptor signaling protein serine/threonine kinase activity;0.0495272551654839;26417!GO:0051216;cartilage 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|gostat_on_MCL_coexpression=GO:0015780;nucleotide-sugar transport;0.0228469674105612;229782!GO:0005338;nucleotide-sugar transmembrane transporter activity;0.0228469674105612;229782!GO:0001784;phosphotyrosine binding;0.0228469674105612;26417!GO:0045309;protein phosphorylated amino acid binding;0.0228469674105612;26417!GO:0043330;response to exogenous dsRNA;0.0228469674105612;26417!GO:0031663;lipopolysaccharide-mediated signaling pathway;0.0228469674105612;26417!GO:0032496;response to lipopolysaccharide;0.0228469674105612;26417!GO:0051219;phosphoprotein binding;0.0228469674105612;26417!GO:0004707;MAP kinase activity;0.0228469674105612;26417!GO:0043331;response to dsRNA;0.0228469674105612;26417!GO:0002237;response to molecule of bacterial origin;0.0271547771255137;26417!GO:0019233;sensory perception of pain;0.0365896572455163;26417!GO:0005351;sugar:hydrogen ion symporter activity;0.045628859221562;229782!GO:0051119;sugar transmembrane transporter activity;0.045628859221562;229782!GO:0015144;carbohydrate transmembrane transporter activity;0.045628859221562;229782!GO:0004702;receptor signaling protein serine/threonine kinase activity;0.0495272551654839;26417!GO:0051216;cartilage development;0.0495272551654839;26417!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005409!8.23e-22!47;UBERON:0000160!2.82e-17!31;UBERON:0000344!1.70e-09!15;UBERON:0001242!5.83e-08!13;UBERON:0000060!5.83e-08!13;UBERON:0001262!5.83e-08!13;UBERON:0004786!5.83e-08!13;UBERON:0001007!2.55e-07!116;UBERON:0001555!2.55e-07!116;UBERON:0007026!2.55e-07!116;UBERON:0004119!7.06e-07!118;UBERON:0000925!7.06e-07!118;UBERON:0006595!7.06e-07!118
|tfbs_overrepresentation_for_novel_motifs=0.491922,1.24447,0.464605,0.535892,0.916672,0.550971,0.645383,0.247459,1.31693,1.00112,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,1.22315,2.01719,0.426133,1.72037,0.657163,0.345236,0.472505,0.686615,1.1909,1.40396,0.394364,1.61954,1.37295,0.960397,1.60284,0.204204,0.364821,0.335531,0.326478,1.52228,2.26816,0.752287,0.342638,1.38433,0.0995018,0.366415,0.659176,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,2.2538,1.10437,1.12205,0.66551,0.406788,0.619643,1.80673,0.663395,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.253541,0.11437,1.156,2.50016,0.19692,0.204132,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.768392,0.0610418,0.181203,0.780154,1.77427,1.33021,2.37572,0.973447,0.35304,0.2995,0.281222,0.244935,0.976308,0.775372,0.160254,0.326561,0.960112,1.08669,0.839694,0.838613,0.563071,0.8998,0.585058,0.435642,0.428007,0.484547,1.0885,0.431734,0.605144,1.33732,0.340765,0.902522,0.53982,0.858327,0.322606,1.16147,0.805995,0.688501,1.79935,1.39185,0.926209,0.65384,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.347287,0.500709,0.564999,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,0.831964,0.564002,0.778321,2.10357,0.503174,0.348692,0.540361,0.325363,1.10596,0.783181,0.678689,1.18867,0.71546,0.983048,0.48935,0.500417,1.31911,1.03816,2.1365,0.482185,0.82857,0.671017,0.325308,0.63125,3.3831
}}

Latest revision as of 16:45, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:36719487..36719504,+p1@Agr2
Mm9::chr3:116414693..116414702,-p13@Slc35a3
Mm9::chr3:116414738..116414765,-p6@Slc35a3
Mm9::chr3:116414767..116414783,-p8@Slc35a3
Mm9::chr3:116414784..116414800,-p5@Slc35a3
Mm9::chr7:133904212..133904258,+p4@Mapk3


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:0015780nucleotide-sugar transport0.0228469674105612
GO:0005338nucleotide-sugar transmembrane transporter activity0.0228469674105612
GO:0001784phosphotyrosine binding0.0228469674105612
GO:0045309protein phosphorylated amino acid binding0.0228469674105612
GO:0043330response to exogenous dsRNA0.0228469674105612
GO:0031663lipopolysaccharide-mediated signaling pathway0.0228469674105612
GO:0032496response to lipopolysaccharide0.0228469674105612
GO:0051219phosphoprotein binding0.0228469674105612
GO:0004707MAP kinase activity0.0228469674105612
GO:0043331response to dsRNA0.0228469674105612
GO:0002237response to molecule of bacterial origin0.0271547771255137
GO:0019233sensory perception of pain0.0365896572455163
GO:0005351sugar:hydrogen ion symporter activity0.045628859221562
GO:0051119sugar transmembrane transporter activity0.045628859221562
GO:0015144carbohydrate transmembrane transporter activity0.045628859221562
GO:0004702receptor signaling protein serine/threonine kinase activity0.0495272551654839
GO:0051216cartilage development0.0495272551654839



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
gastrointestinal system8.23e-2247
intestine2.82e-1731
mucosa1.70e-0915
intestinal mucosa5.83e-0813
anatomical wall5.83e-0813
wall of intestine5.83e-0813
gastrointestinal system mucosa5.83e-0813
digestive system2.55e-07116
digestive tract2.55e-07116
primitive gut2.55e-07116
endoderm-derived structure7.06e-07118
endoderm7.06e-07118
presumptive endoderm7.06e-07118


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)
MA0003.12.22936
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.0315641
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.11.12834
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.895081
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.0960184
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.12.57164
MA0101.10.458688
MA0103.10.398766
MA0105.10.199622
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.11.2824
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.13.00715
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.11.24552
MA0146.13.00399
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.21.39094
MA0138.20.788113
MA0002.20.689262
MA0137.20.416331
MA0104.20.261255
MA0047.21.64036
MA0112.20.76177
MA0065.20.380324
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.10.159217
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.0465447
MA0163.10.372305
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.147137
MA0102.21.7182
MA0258.10.290587
MA0259.12.29705
MA0442.10
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