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MCL coexpression mm9:1960: Difference between revisions

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{{MCL_coexpression_mm9
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protein nuclear translocation;0.023505369832511;20742!GO:0007182;common-partner SMAD protein phosphorylation;0.023505369832511;20742!GO:0016043;cellular component organization and biogenesis;0.023505369832511;20742,20479,224105!GO:0000060;protein import into nucleus, translocation;0.023505369832511;20742!GO:0046907;intracellular transport;0.023505369832511;20742,20479!GO:0051016;barbed-end actin filament capping;0.023505369832511;20742!GO:0006468;protein amino acid phosphorylation;0.023505369832511;20742,224105!GO:0030835;negative regulation of actin filament depolymerization;0.023505369832511;20742!GO:0016197;endosome transport;0.023505369832511;20479!GO:0051693;actin filament capping;0.023505369832511;20742!GO:0065008;regulation of biological quality;0.023505369832511;20742,224105!GO:0015031;protein transport;0.023505369832511;20742,20479!GO:0030834;regulation of actin filament depolymerization;0.023505369832511;20742!GO:0030042;actin filament depolymerization;0.023505369832511;20742!GO:0045184;establishment of protein localization;0.023505369832511;20742,20479!GO:0016310;phosphorylation;0.023505369832511;20742,224105!GO:0008104;protein localization;0.023505369832511;20742,20479!GO:0051649;establishment of cellular localization;0.023505369832511;20742,20479!GO:0051641;cellular localization;0.023505369832511;20742,20479!GO:0033036;macromolecule localization;0.023505369832511;20742,20479!GO:0008064;regulation of actin polymerization and/or depolymerization;0.023505369832511;20742!GO:0051261;protein depolymerization;0.023505369832511;20742!GO:0032535;regulation of cellular component size;0.023505369832511;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.023505369832511;20742!GO:0030832;regulation of actin filament length;0.023505369832511;20742!GO:0006793;phosphorus metabolic process;0.023505369832511;20742,224105!GO:0006796;phosphate metabolic process;0.023505369832511;20742,224105!GO:0046777;protein amino acid autophosphorylation;0.023505369832511;224105!GO:0051129;negative regulation of cellular component organization and biogenesis;0.023505369832511;20742!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.023505369832511;20742!GO:0033043;regulation of organelle organization and biogenesis;0.023505369832511;20742!GO:0016540;protein autoprocessing;0.023505369832511;224105!GO:0008154;actin polymerization and/or depolymerization;0.0260421011217123;20742!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0290580191680682;20742!GO:0051128;regulation of cellular component organization and biogenesis;0.0330672621854049;20742!GO:0006606;protein import into nucleus;0.0330672621854049;20742!GO:0051170;nuclear import;0.0330672621854049;20742!GO:0017038;protein import;0.0361372200379347;20742!GO:0016485;protein processing;0.0363069733211408;224105!GO:0051248;negative regulation of protein metabolic process;0.0364680038533275;20742!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0388782075728654;20742!GO:0005524;ATP binding;0.0388782075728654;20479,224105!GO:0001558;regulation of cell growth;0.0388782075728654;224105!GO:0043687;post-translational protein modification;0.0388782075728654;20742,224105!GO:0032559;adenyl ribonucleotide binding;0.0388782075728654;20479,224105!GO:0030554;adenyl nucleotide binding;0.0410937028247581;20479,224105!GO:0006913;nucleocytoplasmic transport;0.0410937028247581;20742!GO:0051169;nuclear transport;0.0410937028247581;20742!GO:0016049;cell growth;0.0410937028247581;224105!GO:0005516;calmodulin binding;0.0442380715621946;20742!GO:0008361;regulation of cell size;0.0442380715621946;224105!GO:0006464;protein modification process;0.0442380715621946;20742,224105!GO:0043412;biopolymer modification;0.0466962383095633;20742,224105!GO:0032553;ribonucleotide binding;0.0488271768818765;20479,224105!GO:0032555;purine ribonucleotide 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|gostat_on_MCL_coexpression=GO:0007184;SMAD protein nuclear translocation;0.023505369832511;20742!GO:0007182;common-partner SMAD protein phosphorylation;0.023505369832511;20742!GO:0016043;cellular component organization and biogenesis;0.023505369832511;20742,20479,224105!GO:0000060;protein import into nucleus, translocation;0.023505369832511;20742!GO:0046907;intracellular transport;0.023505369832511;20742,20479!GO:0051016;barbed-end actin filament capping;0.023505369832511;20742!GO:0006468;protein amino acid phosphorylation;0.023505369832511;20742,224105!GO:0030835;negative regulation of actin filament depolymerization;0.023505369832511;20742!GO:0016197;endosome transport;0.023505369832511;20479!GO:0051693;actin filament capping;0.023505369832511;20742!GO:0065008;regulation of biological quality;0.023505369832511;20742,224105!GO:0015031;protein transport;0.023505369832511;20742,20479!GO:0030834;regulation of actin filament depolymerization;0.023505369832511;20742!GO:0030042;actin filament depolymerization;0.023505369832511;20742!GO:0045184;establishment of protein localization;0.023505369832511;20742,20479!GO:0016310;phosphorylation;0.023505369832511;20742,224105!GO:0008104;protein localization;0.023505369832511;20742,20479!GO:0051649;establishment of cellular localization;0.023505369832511;20742,20479!GO:0051641;cellular localization;0.023505369832511;20742,20479!GO:0033036;macromolecule localization;0.023505369832511;20742,20479!GO:0008064;regulation of actin polymerization and/or depolymerization;0.023505369832511;20742!GO:0051261;protein depolymerization;0.023505369832511;20742!GO:0032535;regulation of cellular component size;0.023505369832511;20742!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.023505369832511;20742!GO:0030832;regulation of actin filament length;0.023505369832511;20742!GO:0006793;phosphorus metabolic process;0.023505369832511;20742,224105!GO:0006796;phosphate metabolic process;0.023505369832511;20742,224105!GO:0046777;protein amino acid autophosphorylation;0.023505369832511;224105!GO:0051129;negative regulation of cellular component organization and biogenesis;0.023505369832511;20742!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.023505369832511;20742!GO:0033043;regulation of organelle organization and biogenesis;0.023505369832511;20742!GO:0016540;protein autoprocessing;0.023505369832511;224105!GO:0008154;actin polymerization and/or depolymerization;0.0260421011217123;20742!GO:0007179;transforming growth factor beta receptor signaling pathway;0.0290580191680682;20742!GO:0051128;regulation of cellular component organization and biogenesis;0.0330672621854049;20742!GO:0006606;protein import into nucleus;0.0330672621854049;20742!GO:0051170;nuclear import;0.0330672621854049;20742!GO:0017038;protein import;0.0361372200379347;20742!GO:0016485;protein processing;0.0363069733211408;224105!GO:0051248;negative regulation of protein metabolic process;0.0364680038533275;20742!GO:0007178;transmembrane receptor protein serine/threonine kinase signaling pathway;0.0388782075728654;20742!GO:0005524;ATP binding;0.0388782075728654;20479,224105!GO:0001558;regulation of cell growth;0.0388782075728654;224105!GO:0043687;post-translational protein modification;0.0388782075728654;20742,224105!GO:0032559;adenyl ribonucleotide binding;0.0388782075728654;20479,224105!GO:0030554;adenyl nucleotide binding;0.0410937028247581;20479,224105!GO:0006913;nucleocytoplasmic transport;0.0410937028247581;20742!GO:0051169;nuclear transport;0.0410937028247581;20742!GO:0016049;cell growth;0.0410937028247581;224105!GO:0005516;calmodulin binding;0.0442380715621946;20742!GO:0008361;regulation of cell size;0.0442380715621946;224105!GO:0006464;protein modification process;0.0442380715621946;20742,224105!GO:0043412;biopolymer modification;0.0466962383095633;20742,224105!GO:0032553;ribonucleotide binding;0.0488271768818765;20479,224105!GO:0032555;purine ribonucleotide binding;0.0488271768818765;20479,224105!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005409!6.71e-18!47;UBERON:0000160!5.08e-16!31;UBERON:0004119!2.17e-15!118;UBERON:0000925!2.17e-15!118;UBERON:0006595!2.17e-15!118;UBERON:0001007!1.57e-14!116;UBERON:0001555!1.57e-14!116;UBERON:0007026!1.57e-14!116;UBERON:0004921!1.34e-13!114;UBERON:0004923!1.58e-09!24;UBERON:0000344!2.62e-09!15;UBERON:0001242!2.62e-08!13;UBERON:0000060!2.62e-08!13;UBERON:0001262!2.62e-08!13;UBERON:0004786!2.62e-08!13
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.801438,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.381467,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,1.65947,0.683591,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.906602,0.727368,1.32554,0.290745,0.711848,1.12823,0.471365,0.318879,0.503207,0.623685,0.460474,0.786577,0.434783,0.40068,0.478558,0.717547,0.544696,0.504971,0.325217,0.675898,0.938241,0.744678,0.49007,0.539131,1.0041,0.875451,0.282443,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,0.39557,0.992216,1.95203,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.98374,0.205546,1.32691,0.323563,0.310084,0.318792,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,0.377699,0.129654,0.290918,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,0.430015,0.409166,0.367176,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,1.70541,1.06633,0.740267,0.580757,0.57247,0.633483,1.25851,0.576517,0.7614,1.51002,0.476467,1.40021,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,2.55912,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.195549,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,0.653418,2.11223,0.79777,1.03606,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,4.04063
}}

Latest revision as of 17:46, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:30097900..30097962,-p4@Spnb2
Mm9::chr11:30097993..30098009,-p9@Spnb2
Mm9::chr16:32079210..32079245,-p2@Pak2
Mm9::chr1:108693264..108693290,-p2@Vps4b


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 translocation0.023505369832511
GO:0007182common-partner SMAD protein phosphorylation0.023505369832511
GO:0016043cellular component organization and biogenesis0.023505369832511
GO:0000060protein import into nucleus, translocation0.023505369832511
GO:0046907intracellular transport0.023505369832511
GO:0051016barbed-end actin filament capping0.023505369832511
GO:0006468protein amino acid phosphorylation0.023505369832511
GO:0030835negative regulation of actin filament depolymerization0.023505369832511
GO:0016197endosome transport0.023505369832511
GO:0051693actin filament capping0.023505369832511
GO:0065008regulation of biological quality0.023505369832511
GO:0015031protein transport0.023505369832511
GO:0030834regulation of actin filament depolymerization0.023505369832511
GO:0030042actin filament depolymerization0.023505369832511
GO:0045184establishment of protein localization0.023505369832511
GO:0016310phosphorylation0.023505369832511
GO:0008104protein localization0.023505369832511
GO:0051649establishment of cellular localization0.023505369832511
GO:0051641cellular localization0.023505369832511
GO:0033036macromolecule localization0.023505369832511
GO:0008064regulation of actin polymerization and/or depolymerization0.023505369832511
GO:0051261protein depolymerization0.023505369832511
GO:0032535regulation of cellular component size0.023505369832511
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.023505369832511
GO:0030832regulation of actin filament length0.023505369832511
GO:0006793phosphorus metabolic process0.023505369832511
GO:0006796phosphate metabolic process0.023505369832511
GO:0046777protein amino acid autophosphorylation0.023505369832511
GO:0051129negative regulation of cellular component organization and biogenesis0.023505369832511
GO:0051493regulation of cytoskeleton organization and biogenesis0.023505369832511
GO:0033043regulation of organelle organization and biogenesis0.023505369832511
GO:0016540protein autoprocessing0.023505369832511
GO:0008154actin polymerization and/or depolymerization0.0260421011217123
GO:0007179transforming growth factor beta receptor signaling pathway0.0290580191680682
GO:0051128regulation of cellular component organization and biogenesis0.0330672621854049
GO:0006606protein import into nucleus0.0330672621854049
GO:0051170nuclear import0.0330672621854049
GO:0017038protein import0.0361372200379347
GO:0016485protein processing0.0363069733211408
GO:0051248negative regulation of protein metabolic process0.0364680038533275
GO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway0.0388782075728654
GO:0005524ATP binding0.0388782075728654
GO:0001558regulation of cell growth0.0388782075728654
GO:0043687post-translational protein modification0.0388782075728654
GO:0032559adenyl ribonucleotide binding0.0388782075728654
GO:0030554adenyl nucleotide binding0.0410937028247581
GO:0006913nucleocytoplasmic transport0.0410937028247581
GO:0051169nuclear transport0.0410937028247581
GO:0016049cell growth0.0410937028247581
GO:0005516calmodulin binding0.0442380715621946
GO:0008361regulation of cell size0.0442380715621946
GO:0006464protein modification process0.0442380715621946
GO:0043412biopolymer modification0.0466962383095633
GO:0032553ribonucleotide binding0.0488271768818765
GO:0032555purine ribonucleotide binding0.0488271768818765



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 system6.71e-1847
intestine5.08e-1631
endoderm-derived structure2.17e-15118
endoderm2.17e-15118
presumptive endoderm2.17e-15118
digestive system1.57e-14116
digestive tract1.57e-14116
primitive gut1.57e-14116
subdivision of digestive tract1.34e-13114
organ component layer1.58e-0924
mucosa2.62e-0915
intestinal mucosa2.62e-0813
anatomical wall2.62e-0813
wall of intestine2.62e-0813
gastrointestinal system mucosa2.62e-0813


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
MA0007.12.71944
MA0009.11.15569
MA0014.11.46333
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
MA0057.10.701847
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.363073
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.582815
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.11.3208
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.11.11164
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
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.11.95888
MA0145.11.14526
MA0146.11.07887
MA0147.10.453952
MA0148.10.706718
MA0149.14.94249
MA0062.22.34802
MA0035.20.788288
MA0039.20.731226
MA0138.20.951653
MA0002.20.368961
MA0137.21.37638
MA0104.20.386166
MA0047.20.845655
MA0112.20.211985
MA0065.21.14711
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.11.34071
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.11.16288
MA0163.10.327769
MA0164.10.817786
MA0080.21.32296
MA0018.20.828253
MA0099.20.944966
MA0079.21.30573
MA0102.21.8929
MA0258.10.419871
MA0259.10.441366
MA0442.10
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