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MCL coexpression mm9:1754: Difference between revisions

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{{MCL_coexpression_mm9
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protein complex;7.43800709243691e-06;76709,11867!GO:0015629;actin cytoskeleton;0.00317974803201679;76709,11867!GO:0003779;actin binding;0.00344285277496116;76709,11867!GO:0008092;cytoskeletal protein binding;0.00467999406256131;76709,11867!GO:0042995;cell projection;0.00467999406256131;76709,11867!GO:0044430;cytoskeletal part;0.00796575140518601;76709,11867!GO:0030833;regulation of actin filament polymerization;0.00923299553872398;76709!GO:0030041;actin filament polymerization;0.0125585240120914;76709!GO:0005856;cytoskeleton;0.0125585240120914;76709,11867!GO:0005925;focal adhesion;0.0125585240120914;76709!GO:0005924;cell-substrate adherens junction;0.0125585240120914;76709!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0125585240120914;76709!GO:0032535;regulation of cellular component size;0.0125585240120914;76709!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0125585240120914;76709!GO:0030832;regulation of actin filament length;0.0125585240120914;76709!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0125585240120914;76709!GO:0033043;regulation of organelle organization and biogenesis;0.0125585240120914;76709!GO:0030055;cell-matrix junction;0.0125585240120914;76709!GO:0051258;protein polymerization;0.0129155680297958;76709!GO:0008154;actin polymerization and/or depolymerization;0.0129155680297958;76709!GO:0051128;regulation of cellular component organization and biogenesis;0.0164040819038522;76709!GO:0043232;intracellular non-membrane-bound organelle;0.0164040819038522;76709,11867!GO:0043228;non-membrane-bound organelle;0.0164040819038522;76709,11867!GO:0005912;adherens junction;0.0164040819038522;76709!GO:0043234;protein complex;0.0171839640313105;76709,11867!GO:0016323;basolateral plasma membrane;0.0173720377187782;76709!GO:0032991;macromolecular complex;0.0252617152944039;76709,11867!GO:0044446;intracellular organelle part;0.0321503276516958;76709,11867!GO:0044422;organelle 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|gostat_on_MCL_coexpression=GO:0005885;Arp2/3 protein complex;7.43800709243691e-06;76709,11867!GO:0015629;actin cytoskeleton;0.00317974803201679;76709,11867!GO:0003779;actin binding;0.00344285277496116;76709,11867!GO:0008092;cytoskeletal protein binding;0.00467999406256131;76709,11867!GO:0042995;cell projection;0.00467999406256131;76709,11867!GO:0044430;cytoskeletal part;0.00796575140518601;76709,11867!GO:0030833;regulation of actin filament polymerization;0.00923299553872398;76709!GO:0030041;actin filament polymerization;0.0125585240120914;76709!GO:0005856;cytoskeleton;0.0125585240120914;76709,11867!GO:0005925;focal adhesion;0.0125585240120914;76709!GO:0005924;cell-substrate adherens junction;0.0125585240120914;76709!GO:0008064;regulation of actin polymerization and/or depolymerization;0.0125585240120914;76709!GO:0032535;regulation of cellular component size;0.0125585240120914;76709!GO:0032956;regulation of actin cytoskeleton organization and biogenesis;0.0125585240120914;76709!GO:0030832;regulation of actin filament length;0.0125585240120914;76709!GO:0051493;regulation of cytoskeleton organization and biogenesis;0.0125585240120914;76709!GO:0033043;regulation of organelle organization and biogenesis;0.0125585240120914;76709!GO:0030055;cell-matrix junction;0.0125585240120914;76709!GO:0051258;protein polymerization;0.0129155680297958;76709!GO:0008154;actin polymerization and/or depolymerization;0.0129155680297958;76709!GO:0051128;regulation of cellular component organization and biogenesis;0.0164040819038522;76709!GO:0043232;intracellular non-membrane-bound organelle;0.0164040819038522;76709,11867!GO:0043228;non-membrane-bound organelle;0.0164040819038522;76709,11867!GO:0005912;adherens junction;0.0164040819038522;76709!GO:0043234;protein complex;0.0171839640313105;76709,11867!GO:0016323;basolateral plasma membrane;0.0173720377187782;76709!GO:0032991;macromolecular complex;0.0252617152944039;76709,11867!GO:0044446;intracellular organelle part;0.0321503276516958;76709,11867!GO:0044422;organelle part;0.0321503276516958;76709,11867!GO:0030036;actin cytoskeleton organization and biogenesis;0.033046321710988;76709!GO:0030029;actin filament-based process;0.0342542506351467;76709!GO:0051246;regulation of protein metabolic process;0.0461734766919451;76709!
|ontology_enrichment_celltype=CL:0000219!1.68e-09!54;CL:0002320!3.38e-08!46;CL:0000134!3.38e-08!46;CL:0002371!1.45e-07!118;CL:0000738!3.37e-07!17;CL:0002087!3.37e-07!17;CL:0000988!7.92e-07!32;CL:0002032!7.92e-07!32;CL:0000037!7.92e-07!32;CL:0000566!7.92e-07!32;CL:0000837!7.92e-07!32
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.01e-09!48;UBERON:0002405!1.01e-09!48;UBERON:0002390!1.20e-08!45;UBERON:0003061!1.20e-08!45;UBERON:0002384!3.38e-08!46;UBERON:0002204!4.70e-08!32;UBERON:0004119!8.17e-08!118;UBERON:0000925!8.17e-08!118;UBERON:0006595!8.17e-08!118;UBERON:0005409!1.90e-07!47;UBERON:0001007!2.59e-07!116;UBERON:0001555!2.59e-07!116;UBERON:0007026!2.59e-07!116;UBERON:0000160!2.78e-07!31;UBERON:0004923!4.98e-07!24;UBERON:0004921!9.88e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.087078,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.310789,0.370407,0.668936,0.702872,0.300533,0.728641,0.424775,0,0.930881,0.397593,0.775038,0.545768,0.489529,0.145201,0.727684,0.404661,1.32977,0.757752,0.274609,0.641282,0.456327,0.645258,0.626183,1.03545,0.395107,0.253145,0.425309,0.454919,0.384813,0.699032,0.360612,0.328675,0.401916,0.631725,0.419293,1.09239,0.227872,0.591277,0.847828,0.658142,0.115788,0.459555,0.912738,1.84811,0.627649,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,1.76944,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.714607,0.686172,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,3.26667,0.0882907,0.227755,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,0.848095,0.20438,0.384901,1.03517,1.16282,0.913356,0.91226,1.52669,0.97421,0.653843,0.499439,1.23125,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.673306,0.607321,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.44142,1.39156,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.230371,0.416978,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.425122
}}

Latest revision as of 17:26, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:74283053..74283172,+p1@Arpc2
Mm9::chr5:145875118..145875144,+p2@Arpc1b
p2@Gm5637
Mm9::chr5:145875149..145875169,+p1@Arpc1b
p1@Gm5637
Mm9::chr6:117856915..117856940,+p10@Hnrnpf
Mm9::chr8:97856179..97856242,+p1@AA960436


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:0005885Arp2/3 protein complex7.43800709243691e-06
GO:0015629actin cytoskeleton0.00317974803201679
GO:0003779actin binding0.00344285277496116
GO:0008092cytoskeletal protein binding0.00467999406256131
GO:0042995cell projection0.00467999406256131
GO:0044430cytoskeletal part0.00796575140518601
GO:0030833regulation of actin filament polymerization0.00923299553872398
GO:0030041actin filament polymerization0.0125585240120914
GO:0005856cytoskeleton0.0125585240120914
GO:0005925focal adhesion0.0125585240120914
GO:0005924cell-substrate adherens junction0.0125585240120914
GO:0008064regulation of actin polymerization and/or depolymerization0.0125585240120914
GO:0032535regulation of cellular component size0.0125585240120914
GO:0032956regulation of actin cytoskeleton organization and biogenesis0.0125585240120914
GO:0030832regulation of actin filament length0.0125585240120914
GO:0051493regulation of cytoskeleton organization and biogenesis0.0125585240120914
GO:0033043regulation of organelle organization and biogenesis0.0125585240120914
GO:0030055cell-matrix junction0.0125585240120914
GO:0051258protein polymerization0.0129155680297958
GO:0008154actin polymerization and/or depolymerization0.0129155680297958
GO:0051128regulation of cellular component organization and biogenesis0.0164040819038522
GO:0043232intracellular non-membrane-bound organelle0.0164040819038522
GO:0043228non-membrane-bound organelle0.0164040819038522
GO:0005912adherens junction0.0164040819038522
GO:0043234protein complex0.0171839640313105
GO:0016323basolateral plasma membrane0.0173720377187782
GO:0032991macromolecular complex0.0252617152944039
GO:0044446intracellular organelle part0.0321503276516958
GO:0044422organelle part0.0321503276516958
GO:0030036actin cytoskeleton organization and biogenesis0.033046321710988
GO:0030029actin filament-based process0.0342542506351467
GO:0051246regulation of protein metabolic process0.0461734766919451



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>

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.01e-0948
immune system1.01e-0948
hematopoietic system1.20e-0845
blood island1.20e-0845
connective tissue3.38e-0846
musculoskeletal system4.70e-0832
endoderm-derived structure8.17e-08118
endoderm8.17e-08118
presumptive endoderm8.17e-08118
gastrointestinal system1.90e-0747
digestive system2.59e-07116
digestive tract2.59e-07116
primitive gut2.59e-07116
intestine2.78e-0731
organ component layer4.98e-0724
subdivision of digestive tract9.88e-07114


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)
MA0003.12.77888
MA0004.10.603793
MA0006.11.07705
MA0007.10.587678
MA0009.11.06266
MA0014.10.418772
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.12.87883
MA0029.10.995171
MA0030.11.00195
MA0031.10.965177
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.593503
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.28842
MA0056.10
MA0057.10.562607
MA0058.10.50032
MA0059.10.513699
MA0060.10.330907
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.10.197245
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.0176764
MA0074.10.708108
MA0076.12.06136
MA0077.11.04318
MA0078.10.801834
MA0081.11.33193
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.10.453686
MA0089.10
MA0090.10.566938
MA0091.10.617887
MA0092.10.567278
MA0093.10.440484
MA0095.10
MA0098.10
MA0100.10.695835
MA0101.10.523409
MA0103.10.460936
MA0105.10.248108
MA0106.10.809991
MA0107.10.454197
MA0108.20.897859
MA0109.10
MA0111.10.582193
MA0113.10.780358
MA0114.10.361633
MA0115.11.16466
MA0116.11.07655
MA0117.11.13165
MA0119.10.524046
MA0122.11.15196
MA0124.11.35963
MA0125.11.28445
MA0130.10
MA0131.10.869325
MA0132.10
MA0133.10
MA0135.11.19898
MA0136.10.729175
MA0139.10.8026
MA0140.10.695713
MA0141.10.482463
MA0142.10.950155
MA0143.10.797553
MA0144.10.365053
MA0145.11.48363
MA0146.11.74263
MA0147.10.378658
MA0148.10.621195
MA0149.10.529387
MA0062.25.63113
MA0035.20.700704
MA0039.22.75243
MA0138.20.861035
MA0002.20.809945
MA0137.20.479301
MA0104.20.845917
MA0047.20.75686
MA0112.20.47695
MA0065.20.477991
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.587595
MA0155.10.515751
MA0156.10.469089
MA0157.10.91689
MA0158.10
MA0159.11.01146
MA0160.10.624415
MA0161.10
MA0162.12.45609
MA0163.10.497328
MA0164.10.729558
MA0080.21.15331
MA0018.20.739807
MA0099.20.854449
MA0079.24.61124
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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