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MCL coexpression mm9:1803: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004872!3.05e-07!33;UBERON:0000468!3.57e-07!333;UBERON:0005156!3.75e-07!26;UBERON:0000990!3.75e-07!26;UBERON:0004535!9.39e-07!23;UBERON:0001009!9.39e-07!23
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.087078,0.529553,0.603273,1.04755,0.618805,0.715644,0.812379,0.310789,0.115752,0.668936,0.702872,1.47559,0.728641,0.424775,0,0.930881,1.81635,0.283802,0.185796,0.489529,0.145201,0.727684,0.404661,0.537749,0.757752,0.274609,1.54767,0.456327,0.227599,0.626183,1.03545,0.395107,0.253145,0.425309,0.454919,0.384813,0.699032,0.947152,0.328675,0.401916,0.631725,0.134724,0.426986,0.4934,0.591277,0.847828,0.658142,0.370501,0.459555,0.912738,0.786094,0.627649,1.18062,1.19842,0.73621,3.05288,0.689304,0.26467,0.734051,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,0.257421,1.27178,3.68491,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.796301,1.1148,0.0793594,0.0882907,1.20595,0.852952,1.85284,1.40768,1.11989,1.04863,0.412897,0.937248,0.89388,0.806207,1.05152,0.848095,2.47367,3.64331,1.03517,1.16282,0.913356,0.91226,0.631253,0.97421,0.653843,0.499439,0.491483,0.550229,1.16464,0.495367,0.674448,1.41481,0.399936,0.0998646,1.47653,0.932233,0.380707,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,1.04166,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,0.566955,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,1.21592,0.133815,1.18223,0.343194,0.749664,2.82393,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,0.0513167
}}

Latest revision as of 17:31, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr4:43571258..43571293,-p11@Tln1
Mm9::chr6:34548518..34548529,+p9@Cald1
Mm9::chr6:34548530..34548587,+p1@Cald1
Mm9::chr6:34548595..34548606,+p8@Cald1
Mm9::chr6:34548615..34548626,+p11@Cald1


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:0030478actin cap0.00525180931773736
GO:0003779actin binding0.00525180931773736
GO:0008092cytoskeletal protein binding0.00657354137709317
GO:0007016cytoskeletal anchoring0.00657354137709317
GO:0007044cell-substrate junction assembly0.00657354137709317
GO:0030866cortical actin cytoskeleton organization and biogenesis0.0087640014480281
GO:0030865cortical cytoskeleton organization and biogenesis0.00903713359305485
GO:0030864cortical actin cytoskeleton0.00903713359305485
GO:0006940regulation of smooth muscle contraction0.0101557694197892
GO:0030863cortical cytoskeleton0.0101557694197892
GO:0007028cytoplasm organization and biogenesis0.0101557694197892
GO:0005856cytoskeleton0.0110612890703835
GO:0006939smooth muscle contraction0.0120992024380542
GO:0005925focal adhesion0.0120992024380542
GO:0044448cell cortex part0.0120992024380542
GO:0005924cell-substrate adherens junction0.0120992024380542
GO:0006937regulation of muscle contraction0.0120992024380542
GO:0001726ruffle0.0120992024380542
GO:0030055cell-matrix junction0.0120992024380542
GO:0005938cell cortex0.0154300466598971
GO:0043232intracellular non-membrane-bound organelle0.0174074266334173
GO:0043228non-membrane-bound organelle0.0174074266334173
GO:0005912adherens junction0.0174074266334173
GO:0016323basolateral plasma membrane0.0191386856223827
GO:0031252leading edge0.0199446936446966
GO:0003012muscle system process0.020164369857969
GO:0006936muscle contraction0.020164369857969
GO:0005200structural constituent of cytoskeleton0.0206127218757387
GO:0030036actin cytoskeleton organization and biogenesis0.0347652712330674
GO:0030029actin filament-based process0.035995992192866
GO:0015629actin cytoskeleton0.0400852403630016



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
splanchnic layer of lateral plate mesoderm3.05e-0733
multi-cellular organism3.57e-07333
reproductive structure3.75e-0726
reproductive system3.75e-0726
cardiovascular system9.39e-0723
circulatory system9.39e-0723


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)
MA0003.10.0185483
MA0004.10.603793
MA0006.10.419915
MA0007.10.587678
MA0009.11.06266
MA0014.10.0502051
MA0017.10.449113
MA0019.10.874061
MA0024.11.01759
MA0025.11.30092
MA0027.12.72141
MA0028.10.43138
MA0029.10.995171
MA0030.11.00195
MA0031.13.63693
MA0038.10.757669
MA0040.11.07552
MA0041.10.522007
MA0042.10.507715
MA0043.11.1618
MA0046.11.09955
MA0048.10.205696
MA0050.10.645342
MA0051.10.767098
MA0052.11.08379
MA0055.10.28842
MA0056.10
MA0057.10.192781
MA0058.10.50032
MA0059.10.513699
MA0060.12.4023
MA0061.10.364227
MA0063.10
MA0066.10.746072
MA0067.11.41352
MA0068.11.08757
MA0069.11.08414
MA0070.11.07418
MA0071.10.644448
MA0072.11.06547
MA0073.10.00450236
MA0074.10.708108
MA0076.10.470037
MA0077.11.04318
MA0078.11.88054
MA0081.10.53877
MA0083.11.16099
MA0084.11.74401
MA0087.11.11687
MA0088.12.0536
MA0089.10
MA0090.12.38058
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
MA0116.10.419688
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
MA0141.11.21195
MA0142.10.950155
MA0143.11.87173
MA0144.10.365053
MA0145.10.157686
MA0146.10.0604336
MA0147.10.378658
MA0148.11.50563
MA0149.12.25784
MA0062.20.254018
MA0035.20.700704
MA0039.20.489701
MA0138.20.861035
MA0002.20.299191
MA0137.22.09225
MA0104.20.315156
MA0047.20.75686
MA0112.20.157681
MA0065.20.158101
MA0150.10.587557
MA0151.10
MA0152.10.756973
MA0153.11.21594
MA0154.10.203217
MA0155.10.173445
MA0156.10.469089
MA0157.13.48755
MA0158.10
MA0159.10.389847
MA0160.10.624415
MA0161.10
MA0162.10.0699535
MA0163.10.230013
MA0164.12.90159
MA0080.20.455167
MA0018.20.739807
MA0099.20.854449
MA0079.20.0381166
MA0102.21.79669
MA0258.10.346619
MA0259.10.366802
MA0442.10
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