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MCL coexpression mm9:614: Difference between revisions

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{{MCL_coexpression_mm9
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of transcription from RNA polymerase III promoter;0.013477236618638;20841!GO:0003709;RNA polymerase III transcription factor activity;0.013477236618638;20841!GO:0031932;TORC 2 complex;0.013477236618638;!GO:0006383;transcription from RNA polymerase III promoter;0.0303104929307956;20841!GO:0051896;regulation of protein kinase B signaling cascade;0.0372893614573972;!GO:0003704;specific RNA polymerase II transcription factor activity;0.0372893614573972;20841!GO:0008380;RNA splicing;0.0372893614573972;328110,56194!GO:0006397;mRNA processing;0.0493083604530968;328110,56194!GO:0043491;protein kinase B signaling 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|gostat_on_MCL_coexpression=GO:0006359;regulation of transcription from RNA polymerase III promoter;0.013477236618638;20841!GO:0003709;RNA polymerase III transcription factor activity;0.013477236618638;20841!GO:0031932;TORC 2 complex;0.013477236618638;!GO:0006383;transcription from RNA polymerase III promoter;0.0303104929307956;20841!GO:0051896;regulation of protein kinase B signaling cascade;0.0372893614573972;!GO:0003704;specific RNA polymerase II transcription factor activity;0.0372893614573972;20841!GO:0008380;RNA splicing;0.0372893614573972;328110,56194!GO:0006397;mRNA processing;0.0493083604530968;328110,56194!GO:0043491;protein kinase B signaling cascade;0.0493083604530968;!
|ontology_enrichment_celltype=CL:0000542!4.03e-07!13;CL:0000051!4.03e-07!13;CL:0000838!4.69e-07!12
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001048!1.49e-09!134;UBERON:0001004!4.34e-09!42;UBERON:0000153!6.05e-09!43;UBERON:0000065!9.27e-09!41;UBERON:0007811!4.82e-08!36;UBERON:0004177!7.37e-08!29;UBERON:0005057!7.37e-08!29;UBERON:0000077!1.16e-07!35;UBERON:0003408!5.22e-07!24;UBERON:0000475!9.79e-07!150
|tfbs_overrepresentation_for_novel_motifs=0.737036,0.409645,0.686572,0.303186,0.1565,0.315748,1.02601,0.303924,0.0967611,0.336879,0.939294,0.385627,0.0909495,1.05028,0.504927,0,0.587245,0.150639,0.0817508,0.33293,0.215242,0.447169,1.84784,0.471175,1.29598,0.432737,0.265362,0.334131,0.191143,0.0536593,0.321757,0.683831,0.891038,0.0658632,0.975762,0.0172637,0.438297,0.382372,0.126724,0.347926,0.153518,0.870859,0.0834993,0.508662,0.283915,0.293566,0.512146,0.34807,0.169751,0.19345,0.570705,1.15826,0.419161,0.82076,0.837732,1.06445,0.200484,0.977003,0.0716833,0.412262,0.664611,2.04847,0.104381,0.560059,0.424276,0.598412,0.970969,1.3158,0.660133,1.17005,0.650349,0.647992,1.98355,0.870406,0.51601,0.222652,0.0658238,0.50152,0.648171,0.624196,0.0952669,0.60374,0.464847,0.0868537,0.758319,0.842691,0.0395547,0.198381,0.516731,1.47691,1.03946,0.763136,0.696137,0.16091,0.782777,0.360425,0.622881,0.698838,0.512384,0.0434558,0.438441,0.683562,0.803823,0.571268,0.57027,1.56637,0.627019,0.344504,0.63348,0.216685,0.261228,0.805555,0.626352,0.361667,1.04639,0.463309,0.479057,0.306448,1.43693,0.139554,0.875675,0.540309,0.434408,0.500675,1.09972,0.651709,0.403884,1.64843,2.22387,0.163147,0.787341,0.296885,0.940498,0.426575,1.06766,0.092963,0.274293,0.873625,1.01927,1.84381,1.44523,0.975592,0.445463,0.693891,0.564145,0.326684,0.515065,1.80426,0.276297,0.927992,0.445509,2.768,0.822286,0.747142,0.425729,0.901933,0.458393,0.178202,0.265096,0.274055,1.02862,0.757491,0.652135,0.25933,0.561023,0.418964,0.141416,0.384198,0.788879
|tfbs_overrepresentation_jaspar=MA0003.1;1.06346,MA0004.1;0.303605,MA0006.1;0.960584,MA0007.1;0.290695,MA0009.1;0.709264,MA0014.1;2.06593,MA0017.1;0.186015,MA0019.1;0.535691,MA0024.1;0.667197,MA0025.1;0.936082,MA0027.1;2.34178,MA0028.1;0.992869,MA0029.1;0.64639,MA0030.1;0.65267,MA0031.1;0.618697,MA0038.1;1.1047,MA0040.1;0.721328,MA0041.1;0.239557,MA0042.1;0.228771,MA0043.1;0.802848,MA0046.1;0.743934,MA0048.1;0.168666,MA0050.1;0.337476,MA0051.1;0.440863,MA0052.1;0.729105,MA0055.1;0.00695701,MA0056.1;0,MA0057.1;0.983678,MA0058.1;0.635024,MA0059.1;0.233271,MA0060.1;1.7211,MA0061.1;0.129002,MA0063.1;0,MA0066.1;0.422624,MA0067.1;1.04514,MA0068.1;1.43405,MA0069.1;0.729433,MA0070.1;0.720077,MA0071.1;0.336739,MA0072.1;0.711905,MA0073.1;0.486225,MA0074.1;1.01196,MA0076.1;1.73147,MA0077.1;0.691048,MA0078.1;0.471303,MA0081.1;0.252371,MA0083.1;0.802078,MA0084.1;1.3693,MA0087.1;0.760279,MA0088.1;0.459114,MA0089.1;0,MA0090.1;0.27428,MA0091.1;0.315003,MA0092.1;0.274547,MA0093.1;0.531567,MA0095.1;0,MA0098.1;0,MA0100.1;0.379666,MA0101.1;0.240622,MA0103.1;0.19444,MA0105.1;0.226879,MA0106.1;0.478503,MA0107.1;0.189625,MA0108.2;0.557195,MA0109.1;0,MA0111.1;0.78079,MA0113.1;0.452439,MA0114.1;0.400482,MA0115.1;0.805567,MA0116.1;0.959944,MA0117.1;0.774259,MA0119.1;0.241106,MA0122.1;0.793507,MA0124.1;0.992825,MA0125.1;0.920215,MA0130.1;0,MA0131.1;0.531427,MA0132.1;0,MA0133.1;0,MA0135.1;0.838263,MA0136.1;0.408073,MA0139.1;0.0883913,MA0140.1;0.379562,MA0141.1;0.210047,MA0142.1;0.604892,MA0143.1;0.467531,MA0144.1;0.129525,MA0145.1;0.0257706,MA0146.1;1.54841,MA0147.1;0.428193,MA0148.1;0.317692,MA0149.1;0.245177,MA0062.2;1.31267,MA0035.2;0.383789,MA0039.2;1.12665,MA0138.2;0.523978,MA0002.2;0.0901987,MA0137.2;0.207733,MA0104.2;0.670538,MA0047.2;0.431964,MA0112.2;1.15536,MA0065.2;1.15835,MA0150.1;0.290598,MA0151.1;0,MA0152.1;0.432062,MA0153.1;0.854464,MA0154.1;0.16541,MA0155.1;0.30272,MA0156.1;1.72768,MA0157.1;0.574484,MA0158.1;0,MA0159.1;0.876351,MA0160.1;0.320315,MA0161.1;0,MA0162.1;1.35924,MA0163.1;3.87586,MA0164.1;1.052,MA0080.2;1.06013,MA0018.2;1.07118,MA0099.2;0.518072,MA0079.2;5.43656,MA0102.2;1.42135,MA0258.1;0.756558,MA0259.1;0.408856,MA0442.1;0
}}

Latest revision as of 15:36, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:66137306..66137345,+p1@Prpf39
Mm9::chr15:6658372..6658396,+p1@Rictor
Mm9::chr18:84758883..84758919,-p1@Zfp407
Mm9::chr19:3575708..3575756,-p1@Ppp6r3
Mm9::chr1:129765361..129765384,+p1@Rab3gap1
Mm9::chr2:119722948..119723028,+p1@Mga
Mm9::chr2:180436702..180436751,-p1@Dido1
Mm9::chr2:53050248..53050294,-p1@Prpf40a
Mm9::chr2:59963708..59963832,-p1@Baz2b
Mm9::chr5:33196834..33196897,-p1@C330019G07Rik
Mm9::chr7:117205217..117205246,+p1@Zfp143
Mm9::chrX:39265054..39265089,-p1@Thoc2


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:0006359regulation of transcription from RNA polymerase III promoter0.013477236618638
GO:0003709RNA polymerase III transcription factor activity0.013477236618638
GO:0031932TORC 2 complex0.013477236618638
GO:0006383transcription from RNA polymerase III promoter0.0303104929307956
GO:0051896regulation of protein kinase B signaling cascade0.0372893614573972
GO:0003704specific RNA polymerase II transcription factor activity0.0372893614573972
GO:0008380RNA splicing0.0372893614573972
GO:0006397mRNA processing0.0493083604530968
GO:0043491protein kinase B signaling cascade0.0493083604530968



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
lymphocyte4.03e-0713
common lymphoid progenitor4.03e-0713
lymphoid lineage restricted progenitor cell4.69e-0712

Uber Anatomy
Ontology termp-valuen
primordium1.49e-09134
respiratory system4.34e-0942
anterior region of body6.05e-0943
respiratory tract9.27e-0941
craniocervical region4.82e-0836
hemopoietic organ7.37e-0829
immune organ7.37e-0829
mixed endoderm/mesoderm-derived structure1.16e-0735
gland of gut5.22e-0724
organism subdivision9.79e-07150


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)
MA0003.11.06346
MA0004.10.303605
MA0006.10.960584
MA0007.10.290695
MA0009.10.709264
MA0014.12.06593
MA0017.10.186015
MA0019.10.535691
MA0024.10.667197
MA0025.10.936082
MA0027.12.34178
MA0028.10.992869
MA0029.10.64639
MA0030.10.65267
MA0031.10.618697
MA0038.11.1047
MA0040.10.721328
MA0041.10.239557
MA0042.10.228771
MA0043.10.802848
MA0046.10.743934
MA0048.10.168666
MA0050.10.337476
MA0051.10.440863
MA0052.10.729105
MA0055.10.00695701
MA0056.10
MA0057.10.983678
MA0058.10.635024
MA0059.10.233271
MA0060.11.7211
MA0061.10.129002
MA0063.10
MA0066.10.422624
MA0067.11.04514
MA0068.11.43405
MA0069.10.729433
MA0070.10.720077
MA0071.10.336739
MA0072.10.711905
MA0073.10.486225
MA0074.11.01196
MA0076.11.73147
MA0077.10.691048
MA0078.10.471303
MA0081.10.252371
MA0083.10.802078
MA0084.11.3693
MA0087.10.760279
MA0088.10.459114
MA0089.10
MA0090.10.27428
MA0091.10.315003
MA0092.10.274547
MA0093.10.531567
MA0095.10
MA0098.10
MA0100.10.379666
MA0101.10.240622
MA0103.10.19444
MA0105.10.226879
MA0106.10.478503
MA0107.10.189625
MA0108.20.557195
MA0109.10
MA0111.10.78079
MA0113.10.452439
MA0114.10.400482
MA0115.10.805567
MA0116.10.959944
MA0117.10.774259
MA0119.10.241106
MA0122.10.793507
MA0124.10.992825
MA0125.10.920215
MA0130.10
MA0131.10.531427
MA0132.10
MA0133.10
MA0135.10.838263
MA0136.10.408073
MA0139.10.0883913
MA0140.10.379562
MA0141.10.210047
MA0142.10.604892
MA0143.10.467531
MA0144.10.129525
MA0145.10.0257706
MA0146.11.54841
MA0147.10.428193
MA0148.10.317692
MA0149.10.245177
MA0062.21.31267
MA0035.20.383789
MA0039.21.12665
MA0138.20.523978
MA0002.20.0901987
MA0137.20.207733
MA0104.20.670538
MA0047.20.431964
MA0112.21.15536
MA0065.21.15835
MA0150.10.290598
MA0151.10
MA0152.10.432062
MA0153.10.854464
MA0154.10.16541
MA0155.10.30272
MA0156.11.72768
MA0157.10.574484
MA0158.10
MA0159.10.876351
MA0160.10.320315
MA0161.10
MA0162.11.35924
MA0163.13.87586
MA0164.11.052
MA0080.21.06013
MA0018.21.07118
MA0099.20.518072
MA0079.25.43656
MA0102.21.42135
MA0258.10.756558
MA0259.10.408856
MA0442.10
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