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MCL coexpression mm9:2139: Difference between revisions

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{{MCL_coexpression_mm9
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binding;0.0132224404946697;52589!GO:0030130;clathrin coat of trans-Golgi network vesicle;0.0132224404946697;52589!GO:0012510;trans-Golgi network transport vesicle membrane;0.0132224404946697;52589!GO:0030660;Golgi-associated vesicle membrane;0.0132224404946697;52589!GO:0030658;transport vesicle membrane;0.0132224404946697;52589!GO:0030140;trans-Golgi network transport vesicle;0.0132224404946697;52589!GO:0030125;clathrin vesicle coat;0.0132224404946697;52589!GO:0030665;clathrin coated vesicle membrane;0.0133488477014198;52589!GO:0030133;transport vesicle;0.014233698148671;52589!GO:0030120;vesicle coat;0.014233698148671;52589!GO:0004114;3',5'-cyclic-nucleotide phosphodiesterase activity;0.014233698148671;18575!GO:0030662;coated vesicle membrane;0.014233698148671;52589!GO:0004112;cyclic-nucleotide phosphodiesterase activity;0.014233698148671;18575!GO:0005798;Golgi-associated vesicle;0.014233698148671;52589!GO:0030118;clathrin coat;0.0161288711390064;52589!GO:0030659;cytoplasmic vesicle membrane;0.0168978828051994;52589!GO:0044433;cytoplasmic vesicle part;0.018963696350062;52589!GO:0030117;membrane coat;0.018963696350062;52589!GO:0048475;coated membrane;0.018963696350062;52589!GO:0015631;tubulin binding;0.018963696350062;52589!GO:0012506;vesicle membrane;0.018963696350062;52589!GO:0008081;phosphoric diester hydrolase activity;0.0210057255474447;18575!GO:0000139;Golgi membrane;0.0213265492945545;52589!GO:0030136;clathrin-coated vesicle;0.0219159455711895;52589!GO:0030135;coated vesicle;0.0247265757976326;52589!GO:0005516;calmodulin binding;0.0292251395178627;18575!GO:0044431;Golgi apparatus part;0.0346942842544783;52589!GO:0016023;cytoplasmic membrane-bound vesicle;0.0473232041672845;52589!GO:0031988;membrane-bound 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|gostat_on_MCL_coexpression=GO:0030276;clathrin binding;0.0132224404946697;52589!GO:0030130;clathrin coat of trans-Golgi network vesicle;0.0132224404946697;52589!GO:0012510;trans-Golgi network transport vesicle membrane;0.0132224404946697;52589!GO:0030660;Golgi-associated vesicle membrane;0.0132224404946697;52589!GO:0030658;transport vesicle membrane;0.0132224404946697;52589!GO:0030140;trans-Golgi network transport vesicle;0.0132224404946697;52589!GO:0030125;clathrin vesicle coat;0.0132224404946697;52589!GO:0030665;clathrin coated vesicle membrane;0.0133488477014198;52589!GO:0030133;transport vesicle;0.014233698148671;52589!GO:0030120;vesicle coat;0.014233698148671;52589!GO:0004114;3',5'-cyclic-nucleotide phosphodiesterase activity;0.014233698148671;18575!GO:0030662;coated vesicle membrane;0.014233698148671;52589!GO:0004112;cyclic-nucleotide phosphodiesterase activity;0.014233698148671;18575!GO:0005798;Golgi-associated vesicle;0.014233698148671;52589!GO:0030118;clathrin coat;0.0161288711390064;52589!GO:0030659;cytoplasmic vesicle membrane;0.0168978828051994;52589!GO:0044433;cytoplasmic vesicle part;0.018963696350062;52589!GO:0030117;membrane coat;0.018963696350062;52589!GO:0048475;coated membrane;0.018963696350062;52589!GO:0015631;tubulin binding;0.018963696350062;52589!GO:0012506;vesicle membrane;0.018963696350062;52589!GO:0008081;phosphoric diester hydrolase activity;0.0210057255474447;18575!GO:0000139;Golgi membrane;0.0213265492945545;52589!GO:0030136;clathrin-coated vesicle;0.0219159455711895;52589!GO:0030135;coated vesicle;0.0247265757976326;52589!GO:0005516;calmodulin binding;0.0292251395178627;18575!GO:0044431;Golgi apparatus part;0.0346942842544783;52589!GO:0016023;cytoplasmic membrane-bound vesicle;0.0473232041672845;52589!GO:0031988;membrane-bound vesicle;0.0473926053613473;52589!
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|ontology_enrichment_uberon=UBERON:0010314!7.18e-12!92;UBERON:0002346!3.92e-09!64;UBERON:0003075!3.92e-09!64;UBERON:0007284!3.92e-09!64;UBERON:0004121!9.39e-08!95;UBERON:0000924!9.39e-08!95;UBERON:0006601!9.39e-08!95;UBERON:0010371!2.10e-07!73;UBERON:0001017!2.19e-07!73;UBERON:0001016!3.51e-07!75;UBERON:0000073!4.83e-07!54;UBERON:0003056!7.25e-07!49
|tfbs_overrepresentation_for_novel_motifs=0.641384,1.30284,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,1.76086,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,0.928768,0.683591,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,2.45781,0.727368,0.535752,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.30022,0.460474,0.786577,0.434783,0.40068,1.20358,0.717547,1.64392,0.504971,0.325217,0.675898,0.938241,0.744678,0.949442,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,1.58617,0.822375,1.10737,0.885556,0.39557,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.864765,0.834514,1.54107,0.926147,1.08947,1.40903,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.961641,1.14445,0.938512,2.07187,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,0.442329,0.692434,1.02384,0.456123,1.33244,0.970073,1.97652,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,1.70121,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,2.27239,0.830321,0.459159,0.788782,0.0824127
|tfbs_overrepresentation_jaspar=MA0003.1;0.331308,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.276754,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;3.65347,MA0042.1;2.45339,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;2.07944,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;0.251896,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.713436,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;0.552621,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;1.1032,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;0.605676,MA0103.1;1.33576,MA0105.1;0.841866,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;0.666525,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;1.24367,MA0117.1;1.22527,MA0119.1;1.47447,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;1.11951,MA0145.1;1.14526,MA0146.1;0.0944145,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;0.0220513,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;1.14524,MA0065.2;0.609584,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.728853,MA0155.1;0.230016,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;0.465802,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.10667,MA0163.1;0.0996272,MA0164.1;0.817786,MA0080.2;0.534538,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;0.109419,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 18:03, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:37664157..37664187,-p9@Ncald
Mm9::chr6:56311850..56311864,-p@chr6:56311850..56311864
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Mm9::chr6:56311867..56311885,-p@chr6:56311867..56311885
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Mm9::chr6:56312350..56312380,-p1@Pde1c


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:0030276clathrin binding0.0132224404946697
GO:0030130clathrin coat of trans-Golgi network vesicle0.0132224404946697
GO:0012510trans-Golgi network transport vesicle membrane0.0132224404946697
GO:0030660Golgi-associated vesicle membrane0.0132224404946697
GO:0030658transport vesicle membrane0.0132224404946697
GO:0030140trans-Golgi network transport vesicle0.0132224404946697
GO:0030125clathrin vesicle coat0.0132224404946697
GO:0030665clathrin coated vesicle membrane0.0133488477014198
GO:0030133transport vesicle0.014233698148671
GO:0030120vesicle coat0.014233698148671
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity0.014233698148671
GO:0030662coated vesicle membrane0.014233698148671
GO:0004112cyclic-nucleotide phosphodiesterase activity0.014233698148671
GO:0005798Golgi-associated vesicle0.014233698148671
GO:0030118clathrin coat0.0161288711390064
GO:0030659cytoplasmic vesicle membrane0.0168978828051994
GO:0044433cytoplasmic vesicle part0.018963696350062
GO:0030117membrane coat0.018963696350062
GO:0048475coated membrane0.018963696350062
GO:0015631tubulin binding0.018963696350062
GO:0012506vesicle membrane0.018963696350062
GO:0008081phosphoric diester hydrolase activity0.0210057255474447
GO:0000139Golgi membrane0.0213265492945545
GO:0030136clathrin-coated vesicle0.0219159455711895
GO:0030135coated vesicle0.0247265757976326
GO:0005516calmodulin binding0.0292251395178627
GO:0044431Golgi apparatus part0.0346942842544783
GO:0016023cytoplasmic membrane-bound vesicle0.0473232041672845
GO:0031988membrane-bound vesicle0.0473926053613473



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>


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)
MA0003.10.331308
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.276754
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.13.65347
MA0042.12.45339
MA0043.11.25564
MA0046.11.1929
MA0048.12.07944
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.713436
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.552621
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.1032
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.11.33576
MA0105.10.841866
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.11.24367
MA0117.11.22527
MA0119.11.47447
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.11.11951
MA0145.11.14526
MA0146.10.0944145
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.0220513
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.21.14524
MA0065.20.609584
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.728853
MA0155.10.230016
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.10667
MA0163.10.0996272
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.109419
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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