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MCL coexpression mm9:2285: Difference between revisions

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{{MCL_coexpression_mm9
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protein nuclear translocation;0.0103613104695119;20742!GO:0007182;common-partner SMAD protein phosphorylation;0.0103613104695119;20742!GO:0000060;protein import into nucleus, translocation;0.0103613104695119;20742!GO:0051016;barbed-end actin filament capping;0.0103613104695119;20742!GO:0051693;actin filament capping;0.0103613104695119;20742!GO:0030835;negative regulation of actin filament depolymerization;0.0103613104695119;20742!GO:0030834;regulation of actin filament depolymerization;0.0103613104695119;20742!GO:0030042;actin filament depolymerization;0.0103613104695119;20742!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0103613104695119;20742!GO:0051261;protein depolymerization;0.0103613104695119;20742!GO:0032535;regulation of cellular component size;0.0103613104695119;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0103613104695119;20742!GO:0030832;regulation of actin filament length;0.0103613104695119;20742!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0103613104695119;20742!GO:0033043;regulation of organelle organization and biogenesis;0.0103613104695119;20742!GO:0051129;negative regulation of cellular component organization and biogenesis;0.0103613104695119;20742!GO:0008154;actin polymerization and/or depolymerization;0.0114727313157225;20742!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0124606609567986;20742!GO:0051128;regulation of cellular component organization and biogenesis;0.0132346150534941;20742!GO:0006606;protein import into nucleus;0.0132346150534941;20742!GO:0051170;nuclear import;0.0132346150534941;20742!GO:0017038;protein import;0.0141844678085296;20742!GO:0051248;negative regulation of protein metabolic process;0.0144157363054078;20742!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0160498730802243;20742!GO:0006913;nucleocytoplasmic transport;0.017440757894382;20742!GO:0051169;nuclear transport;0.017440757894382;20742!GO:0005516;calmodulin binding;0.0193230539474992;20742!GO:0030036;actin cytoskeleton organization and biogenesis;0.0268175094505013;20742!GO:0030029;actin filament-based process;0.027742251155691;20742!GO:0006605;protein targeting;0.0305557077375409;20742!GO:0051246;regulation of protein metabolic process;0.0361761124552217;20742!GO:0003779;actin binding;0.0368740754944393;20742!GO:0007167;enzyme linked receptor protein signaling pathway;0.0393027962194675;20742!GO:0009892;negative regulation of metabolic process;0.0465301202933373;20742!GO:0008092;cytoskeletal protein 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|gostat_on_MCL_coexpression=GO:0007184;SMAD protein nuclear translocation;0.0103613104695119;20742!GO:0007182;common-partner SMAD protein phosphorylation;0.0103613104695119;20742!GO:0000060;protein import into nucleus, translocation;0.0103613104695119;20742!GO:0051016;barbed-end actin filament capping;0.0103613104695119;20742!GO:0051693;actin filament capping;0.0103613104695119;20742!GO:0030835;negative regulation of actin filament depolymerization;0.0103613104695119;20742!GO:0030834;regulation of actin filament depolymerization;0.0103613104695119;20742!GO:0030042;actin filament depolymerization;0.0103613104695119;20742!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0103613104695119;20742!GO:0051261;protein depolymerization;0.0103613104695119;20742!GO:0032535;regulation of cellular component size;0.0103613104695119;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0103613104695119;20742!GO:0030832;regulation of actin filament length;0.0103613104695119;20742!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0103613104695119;20742!GO:0033043;regulation of organelle organization and biogenesis;0.0103613104695119;20742!GO:0051129;negative regulation of cellular component organization and biogenesis;0.0103613104695119;20742!GO:0008154;actin polymerization and/or depolymerization;0.0114727313157225;20742!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0124606609567986;20742!GO:0051128;regulation of cellular component organization and biogenesis;0.0132346150534941;20742!GO:0006606;protein import into nucleus;0.0132346150534941;20742!GO:0051170;nuclear import;0.0132346150534941;20742!GO:0017038;protein import;0.0141844678085296;20742!GO:0051248;negative regulation of protein metabolic process;0.0144157363054078;20742!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0160498730802243;20742!GO:0006913;nucleocytoplasmic transport;0.017440757894382;20742!GO:0051169;nuclear transport;0.017440757894382;20742!GO:0005516;calmodulin binding;0.0193230539474992;20742!GO:0030036;actin cytoskeleton organization and biogenesis;0.0268175094505013;20742!GO:0030029;actin filament-based process;0.027742251155691;20742!GO:0006605;protein targeting;0.0305557077375409;20742!GO:0051246;regulation of protein metabolic process;0.0361761124552217;20742!GO:0003779;actin binding;0.0368740754944393;20742!GO:0007167;enzyme linked receptor protein signaling pathway;0.0393027962194675;20742!GO:0009892;negative regulation of metabolic process;0.0465301202933373;20742!GO:0008092;cytoskeletal protein binding;0.0465301202933373;20742!
|ontology_enrichment_celltype=CL:0002563!1.89e-07!9;CL:0002251!1.89e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!1.45e-22!31;UBERON:0005409!2.02e-22!47;UBERON:0000344!6.84e-12!15;UBERON:0001242!1.98e-10!13;UBERON:0000060!1.98e-10!13;UBERON:0001262!1.98e-10!13;UBERON:0004786!1.98e-10!13;UBERON:0001007!1.57e-08!116;UBERON:0001555!1.57e-08!116;UBERON:0007026!1.57e-08!116;UBERON:0004119!2.22e-08!118;UBERON:0000925!2.22e-08!118;UBERON:0006595!2.22e-08!118;UBERON:0004921!1.16e-07!114;UBERON:0003350!1.89e-07!9;UBERON:0004808!1.89e-07!9;UBERON:0001277!1.89e-07!9
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.801438,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.162942,0.755749,0.790506,0.37041,0.81685,1.2551,0,1.02248,0.473993,0.928768,0.24402,0.570433,1.71244,0.815872,1.20979,0.620553,0.846564,0.342316,0.727368,0.535752,0.790816,0.711848,1.12823,0.471365,0.318879,0.503207,0.30022,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,1.04032,0.504971,0.0986756,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,1.40995,1.2746,1.29252,0.82458,0.549352,1.82858,0.882473,0.822375,1.10737,0.885556,1.02399,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.205546,1.32691,0.323563,0.310084,2.34289,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.11855,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,1.34553,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,1.79716,1.51002,0.476467,0.143825,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,0.485304,0.293812,0.184289,1.27621,1.87995,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,1.16191,0.788782,2.03331
|tfbs_overrepresentation_jaspar=MA0003.1;0.600426,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;0.0809287,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;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;0.266382,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;1.29714,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;3.96212,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;0.00221226,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;2.56224,MA0078.1;0.891476,MA0081.1;0.621611,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;0.582815,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;1.56822,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;0.783305,MA0101.1;4.90831,MA0103.1;0.540576,MA0105.1;4.16446,MA0106.1;0.899777,MA0107.1;3.34176,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;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,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;1.91256,MA0139.1;0.365453,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;0.608454,MA0146.1;2.82479,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.856416,MA0035.2;0.788288,MA0039.2;0.0959929,MA0138.2;0.951653,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;0.211985,MA0065.2;0.212467,MA0150.1;1.61189,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;0.728853,MA0155.1;1.21457,MA0156.1;2.32242,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;1.32296,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;1.90618,MA0102.2;1.8929,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 18:17, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:137155026..137155042,-p1@Elf3
Mm9::chr2:132771764..132771778,-p3@Fermt1
Mm9::chr2:132771788..132771802,-p2@Fermt1
Mm9::chr2:132771819..132771830,-p10@Fermt1


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:0007184SMAD protein nuclear translocation0.0103613104695119
GO:0007182common-partner SMAD protein phosphorylation0.0103613104695119
GO:0000060protein import into nucleus, translocation0.0103613104695119
GO:0051016barbed-end actin filament capping0.0103613104695119
GO:0051693actin filament capping0.0103613104695119
GO:0030835negative regulation of actin filament depolymerization0.0103613104695119
GO:0030834regulation of actin filament depolymerization0.0103613104695119
GO:0030042actin filament depolymerization0.0103613104695119
GO:0008064regulation of actin polymerization and/or depolymerization0.0103613104695119
GO:0051261protein depolymerization0.0103613104695119
GO:0032535regulation of cellular component size0.0103613104695119
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0103613104695119
GO:0030832regulation of actin filament length0.0103613104695119
GO:0051493regulation of cytoskeleton organization and biogenesis0.0103613104695119
GO:0033043regulation of organelle organization and biogenesis0.0103613104695119
GO:0051129negative regulation of cellular component organization and biogenesis0.0103613104695119
GO:0008154actin polymerization and/or depolymerization0.0114727313157225
GO:0007179transforming growth factor beta receptor signaling pathway0.0124606609567986
GO:0051128regulation of cellular component organization and biogenesis0.0132346150534941
GO:0006606protein import into nucleus0.0132346150534941
GO:0051170nuclear import0.0132346150534941
GO:0017038protein import0.0141844678085296
GO:0051248negative regulation of protein metabolic process0.0144157363054078
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0160498730802243
GO:0006913nucleocytoplasmic transport0.017440757894382
GO:0051169nuclear transport0.017440757894382
GO:0005516calmodulin binding0.0193230539474992
GO:0030036actin cytoskeleton organization and biogenesis0.0268175094505013
GO:0030029actin filament-based process0.027742251155691
GO:0006605protein targeting0.0305557077375409
GO:0051246regulation of protein metabolic process0.0361761124552217
GO:0003779actin binding0.0368740754944393
GO:0007167enzyme linked receptor protein signaling pathway0.0393027962194675
GO:0009892negative regulation of metabolic process0.0465301202933373
GO:0008092cytoskeletal protein binding0.0465301202933373



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
intestinal epithelial cell1.89e-079
epithelial cell of alimentary canal1.89e-079


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)
MA0003.10.600426
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.0809287
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
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.11.29714
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.13.96212
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.713436
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.00221226
MA0074.10.795862
MA0076.10.550092
MA0077.12.56224
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.582815
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.11.56822
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.14.90831
MA0103.10.540576
MA0105.14.16446
MA0106.10.899777
MA0107.13.34176
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.11.91256
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.608454
MA0146.12.82479
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.856416
MA0035.20.788288
MA0039.20.0959929
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.20.212467
MA0150.11.61189
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.728853
MA0155.11.21457
MA0156.12.32242
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.10667
MA0163.10.0996272
MA0164.10.817786
MA0080.21.32296
MA0018.20.828253
MA0099.20.944966
MA0079.21.90618
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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