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MCL coexpression mm9:1080: Difference between revisions

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{{MCL_coexpression_mm9
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V binding;0.00872320892633674;171531!GO:0051010;microtubule plus-end binding;0.00872320892633674;171531!GO:0032400;melanosome localization;0.00872320892633674;171531!GO:0051875;pigment granule localization;0.00872320892633674;171531!GO:0017022;myosin binding;0.00872320892633674;171531!GO:0033059;cellular pigmentation;0.00872320892633674;171531!GO:0048770;pigment granule;0.00872320892633674;171531!GO:0042470;melanosome;0.00872320892633674;171531!GO:0015031;protein transport;0.00872320892633674;242505,171531!GO:0045184;establishment of protein localization;0.00872320892633674;242505,171531!GO:0051648;vesicle localization;0.00872320892633674;171531!GO:0008104;protein localization;0.00899445867963646;242505,171531!GO:0033036;macromolecule localization;0.00899445867963646;242505,171531!GO:0030318;melanocyte differentiation;0.00906120316010084;171531!GO:0050931;pigment cell differentiation;0.00906120316010084;171531!GO:0017137;Rab GTPase binding;0.00949375496459958;171531!GO:0051640;organelle localization;0.0126947457716614;171531!GO:0048066;pigmentation during development;0.0128768858571382;171531!GO:0008017;microtubule binding;0.0190989957619239;171531!GO:0017016;Ras GTPase binding;0.0190989957619239;171531!GO:0031267;small GTPase binding;0.0190989957619239;171531!GO:0051020;GTPase binding;0.0190989957619239;171531!GO:0015631;tubulin binding;0.0190989957619239;171531!GO:0019899;enzyme binding;0.0441657620092987;171531!GO:0006810;transport;0.0447072859655827;242505,171531!GO:0051234;establishment of localization;0.0453412544770146;242505,171531!GO:0016023;cytoplasmic membrane-bound vesicle;0.0497916355086711;171531!GO:0006605;protein targeting;0.0497916355086711;171531!GO:0051179;localization;0.0497916355086711;242505,171531!GO:0015629;actin cytoskeleton;0.0497916355086711;171531!GO:0031988;membrane-bound 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|gostat_on_MCL_coexpression=GO:0031489;myosin V binding;0.00872320892633674;171531!GO:0051010;microtubule plus-end binding;0.00872320892633674;171531!GO:0032400;melanosome localization;0.00872320892633674;171531!GO:0051875;pigment granule localization;0.00872320892633674;171531!GO:0017022;myosin binding;0.00872320892633674;171531!GO:0033059;cellular pigmentation;0.00872320892633674;171531!GO:0048770;pigment granule;0.00872320892633674;171531!GO:0042470;melanosome;0.00872320892633674;171531!GO:0015031;protein transport;0.00872320892633674;242505,171531!GO:0045184;establishment of protein localization;0.00872320892633674;242505,171531!GO:0051648;vesicle localization;0.00872320892633674;171531!GO:0008104;protein localization;0.00899445867963646;242505,171531!GO:0033036;macromolecule localization;0.00899445867963646;242505,171531!GO:0030318;melanocyte differentiation;0.00906120316010084;171531!GO:0050931;pigment cell differentiation;0.00906120316010084;171531!GO:0017137;Rab GTPase binding;0.00949375496459958;171531!GO:0051640;organelle localization;0.0126947457716614;171531!GO:0048066;pigmentation during development;0.0128768858571382;171531!GO:0008017;microtubule binding;0.0190989957619239;171531!GO:0017016;Ras GTPase binding;0.0190989957619239;171531!GO:0031267;small GTPase binding;0.0190989957619239;171531!GO:0051020;GTPase binding;0.0190989957619239;171531!GO:0015631;tubulin binding;0.0190989957619239;171531!GO:0019899;enzyme binding;0.0441657620092987;171531!GO:0006810;transport;0.0447072859655827;242505,171531!GO:0051234;establishment of localization;0.0453412544770146;242505,171531!GO:0016023;cytoplasmic membrane-bound vesicle;0.0497916355086711;171531!GO:0006605;protein targeting;0.0497916355086711;171531!GO:0051179;localization;0.0497916355086711;242505,171531!GO:0015629;actin cytoskeleton;0.0497916355086711;171531!GO:0031988;membrane-bound vesicle;0.0497916355086711;171531!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005409!8.12e-12!47;UBERON:0000160!1.18e-09!31;UBERON:0004119!8.97e-09!118;UBERON:0000925!8.97e-09!118;UBERON:0006595!8.97e-09!118;UBERON:0007023!2.06e-08!51;UBERON:0000464!2.59e-08!57;UBERON:0001007!4.84e-08!116;UBERON:0001555!4.84e-08!116;UBERON:0007026!4.84e-08!116;UBERON:0004921!1.63e-07!114;UBERON:0001264!5.03e-07!12
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.660133,0.411716,0.480627,0.810002,0.495263,0.587291,0.206208,0.215218,0.478312,0.542749,0.575086,0.206435,0.599731,0.847296,0,0.795315,0.291368,0.561256,0.361892,0.374752,0.27937,0.598814,0.29769,1.89054,0.62766,0.184473,0.516511,0.344372,0.876948,0.50223,2.077,0.289148,0.166577,1.53201,0.101236,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.258106,0.317766,1.19315,0.469348,0.714592,0.532496,0.82704,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,1.59144,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,1.09164,0.17012,1.49715,0.963958,0.703064,0.859987,0.98764,0.610783,0.812889,0.663039,0.580284,0.975495,0.146394,1.96285,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.823238,0.254625,0.237542,0.589174,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.990132,1.35148,1.27206,0.796976,1.59063,1.21618,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.813943,0.147909,0.0736236,1.04192,0.681896,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.763807,0.573477,0.227149
}}

Latest revision as of 16:21, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:57786904..57786931,+p@chr11:57786904..57786931
+
Mm9::chr1:92811641..92811691,+p1@Mlph
Mm9::chr1:92811692..92811712,+p2@Mlph
Mm9::chr3:100293431..100293483,+p1@ENSMUST00000122898
Mm9::chr4:57833953..57833973,+p@chr4:57833953..57833973
+
Mm9::chr4:73364442..73364446,-p@chr4:73364442..73364446
-
Mm9::chr4:73436897..73436957,-p1@Rasef


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:0031489myosin V binding0.00872320892633674
GO:0051010microtubule plus-end binding0.00872320892633674
GO:0032400melanosome localization0.00872320892633674
GO:0051875pigment granule localization0.00872320892633674
GO:0017022myosin binding0.00872320892633674
GO:0033059cellular pigmentation0.00872320892633674
GO:0048770pigment granule0.00872320892633674
GO:0042470melanosome0.00872320892633674
GO:0015031protein transport0.00872320892633674
GO:0045184establishment of protein localization0.00872320892633674
GO:0051648vesicle localization0.00872320892633674
GO:0008104protein localization0.00899445867963646
GO:0033036macromolecule localization0.00899445867963646
GO:0030318melanocyte differentiation0.00906120316010084
GO:0050931pigment cell differentiation0.00906120316010084
GO:0017137Rab GTPase binding0.00949375496459958
GO:0051640organelle localization0.0126947457716614
GO:0048066pigmentation during development0.0128768858571382
GO:0008017microtubule binding0.0190989957619239
GO:0017016Ras GTPase binding0.0190989957619239
GO:0031267small GTPase binding0.0190989957619239
GO:0051020GTPase binding0.0190989957619239
GO:0015631tubulin binding0.0190989957619239
GO:0019899enzyme binding0.0441657620092987
GO:0006810transport0.0447072859655827
GO:0051234establishment of localization0.0453412544770146
GO:0016023cytoplasmic membrane-bound vesicle0.0497916355086711
GO:0006605protein targeting0.0497916355086711
GO:0051179localization0.0497916355086711
GO:0015629actin cytoskeleton0.0497916355086711
GO:0031988membrane-bound vesicle0.0497916355086711



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 system8.12e-1247
intestine1.18e-0931
endoderm-derived structure8.97e-09118
endoderm8.97e-09118
presumptive endoderm8.97e-09118
adult organism2.06e-0851
anatomical space2.59e-0857
digestive system4.84e-08116
digestive tract4.84e-08116
primitive gut4.84e-08116
subdivision of digestive tract1.63e-07114
pancreas5.03e-0712


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)
MA0003.10.79075
MA0004.11.20906
MA0006.10.837454
MA0007.11.17655
MA0009.10.92425
MA0014.10.425579
MA0017.10.89657
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.11.8892
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.11.0092
MA0056.10
MA0057.10.117936
MA0058.11.77195
MA0059.11.02718
MA0060.10.656954
MA0061.10.261749
MA0063.10
MA0066.12.54082
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.0890846
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.11.23749
MA0092.10.446857
MA0093.11.58083
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.920496
MA0105.10.488671
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
MA0115.11.0246
MA0116.14.14771
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.585936
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.11.05551
MA0146.10.493711
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.790799
MA0138.20.727395
MA0002.20.592533
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.24.21276
MA0065.20.633155
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.11.87278
MA0155.11.13804
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.10.127623
MA0163.10.519779
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.065018
MA0102.21.65195
MA0258.13.62897
MA0259.10.729797
MA0442.10
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