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MCL coexpression mm9:1015: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0006346;methylation-dependent chromatin silencing;0.0478431093363871;17192!GO:0016581;NuRD complex;0.0478431093363871;17192!GO:0016573;histone acetylation;0.0478431093363871;17192!GO:0006473;protein amino acid acetylation;0.0478431093363871;17192!GO:0006342;chromatin silencing;0.0478431093363871;17192!GO:0031507;heterochromatin formation;0.0478431093363871;17192!GO:0045814;negative regulation of gene expression, epigenetic;0.0478431093363871;17192!
}}

Latest revision as of 16:15, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:128185557..128185594,+p1@Wibg
Mm9::chr10:79727687..79727778,+p1@Dazap1
Mm9::chr10:79862089..79862129,-p2@Mbd3
Mm9::chr10:79862134..79862173,-p3@Mbd3
Mm9::chr12:81744845..81744856,-p2@Erh
Mm9::chr17:57074836..57074927,-p1@Mllt1
Mm9::chr2:128793732..128793766,-p2@ENSMUST00000099385


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:0006346methylation-dependent chromatin silencing0.0478431093363871
GO:0016581NuRD complex0.0478431093363871
GO:0016573histone acetylation0.0478431093363871
GO:0006473protein amino acid acetylation0.0478431093363871
GO:0006342chromatin silencing0.0478431093363871
GO:0031507heterochromatin formation0.0478431093363871
GO:0045814negative regulation of gene expression, epigenetic0.0478431093363871



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
central nervous system2.04e-0873
nervous system2.14e-0875
ectoderm-derived structure2.17e-0795
ectoderm2.17e-0795
presumptive ectoderm2.17e-0795


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)
MA0003.15.34747
MA0004.11.20906
MA0006.11.51462
MA0007.10.465969
MA0009.10.92425
MA0014.14.01376
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.12.35736
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.11.01509
MA0043.11.02178
MA0046.10.960497
MA0048.13.27044
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.157978
MA0056.10
MA0057.10.756125
MA0058.11.00014
MA0059.10.397033
MA0060.10.656954
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.00223012
MA0074.10.580087
MA0076.12.5281
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.11.58083
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.11.51389
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.11.7399
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.631666
MA0146.11.15352
MA0147.12.95213
MA0148.10.49752
MA0149.10.411562
MA0062.22.20069
MA0035.20.573016
MA0039.21.72008
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.23.39864
MA0047.20.626803
MA0112.20.0910939
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.11.13804
MA0156.11.67246
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.15.32313
MA0163.13.21163
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.23.81329
MA0102.21.65195
MA0258.10.246285
MA0259.12.883
MA0442.10
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