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MCL coexpression mm9:1102: Difference between revisions

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{{MCL_coexpression_mm9
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reticulum;0.0140907646314896;71853,14828,107513!GO:0044444;cytoplasmic part;0.0177715855052601;66111,71853,14828,107513!GO:0043022;ribosome binding;0.0177715855052601;14828!GO:0006983;ER overload response;0.0177715855052601;14828!GO:0016864;intramolecular oxidoreductase activity, transposing S-S bonds;0.0177715855052601;71853!GO:0003756;protein disulfide isomerase activity;0.0177715855052601;71853!GO:0016862;intramolecular oxidoreductase activity, interconverting keto- and enol-groups;0.0177715855052601;71853!GO:0043021;ribonucleoprotein binding;0.0258913450988841;14828!GO:0033554;cellular response to stress;0.0258913450988841;14828!GO:0006984;ER-nuclear signaling pathway;0.0258913450988841;14828!GO:0008320;protein transmembrane transporter activity;0.0258913450988841;66111!GO:0051716;cellular response to stimulus;0.0258913450988841;14828!GO:0005737;cytoplasm;0.0392027454275295;66111,71853,14828,107513!GO:0045454;cell redox homeostasis;0.0444489900098845;71853!GO:0016860;intramolecular oxidoreductase 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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000466!6.98e-13!79;UBERON:0002100!3.91e-12!90;UBERON:0005177!2.85e-10!79;UBERON:0001264!5.09e-09!12;UBERON:0002553!2.14e-08!39;UBERON:0000464!2.42e-08!57;UBERON:0003886!6.57e-08!38;UBERON:0005256!8.05e-08!45;UBERON:0002323!2.13e-07!37;UBERON:0004458!2.13e-07!37;UBERON:0003104!5.13e-07!61;UBERON:0009142!5.13e-07!61
|tfbs_overrepresentation_for_novel_motifs=1.11639,0.0418382,1.05921,0.480627,0.299217,0.495263,1.43443,0.594722,0.215218,0.478312,0.542749,0.575086,1.12363,1.46059,0.315771,0,1.86712,0.291368,0.19222,0.112498,0.374752,0.586604,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,2.46776,0.145661,0.50223,0.897561,0.289148,0.498917,0.316253,0.0235321,0.766323,1.40099,0.717242,1.21701,0.295233,0.507468,0.0742755,0.317766,0.822425,1.18381,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,2.69856,0.21183,1.02583,1.09164,1.55661,0.159969,0.166511,1.67636,0.859987,0.378988,0.610783,0.812889,0.663039,0.200155,0.975495,0.960306,0.164297,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.203879,0.913319,0.71485,0.79664,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,1.12953,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,1.13474,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,0.927167,1.04192,0.243291,0.619892,1.12411,1.57831,0.327731,0.435579,1.13413,1.25393,0.974632,0.864173,1.92222,0.767269,0.612377,0.278874,0.573477,0.433127
}}

Latest revision as of 16:23, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr12:17273377..17273407,+p1@Pdia6
Mm9::chr12:17273415..17273424,+p1@LOC100046302
p2@Pdia6
Mm9::chr13:38085980..38086053,-p1@Ssr1
Mm9::chr15:100246175..100246190,-p@chr15:100246175..100246190
-
Mm9::chr2:34627609..34627614,+p1@Hspa5
Mm9::chr9:89599731..89599742,-p@chr9:89599731..89599742
-
Mm9::chr9:89599745..89599851,-p1@Tmed3


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:0005783endoplasmic reticulum0.0140907646314896
GO:0044444cytoplasmic part0.0177715855052601
GO:0043022ribosome binding0.0177715855052601
GO:0006983ER overload response0.0177715855052601
GO:0016864intramolecular oxidoreductase activity, transposing S-S bonds0.0177715855052601
GO:0003756protein disulfide isomerase activity0.0177715855052601
GO:0016862intramolecular oxidoreductase activity, interconverting keto- and enol-groups0.0177715855052601
GO:0043021ribonucleoprotein binding0.0258913450988841
GO:0033554cellular response to stress0.0258913450988841
GO:0006984ER-nuclear signaling pathway0.0258913450988841
GO:0008320protein transmembrane transporter activity0.0258913450988841
GO:0051716cellular response to stimulus0.0258913450988841
GO:0005737cytoplasm0.0392027454275295
GO:0045454cell redox homeostasis0.0444489900098845
GO:0016860intramolecular oxidoreductase activity0.0444489900098845



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
immaterial anatomical entity6.98e-1379
trunk3.91e-1290
trunk region element2.85e-1079
pancreas5.09e-0912
anatomical cavity2.14e-0839
anatomical space2.42e-0857
body cavity precursor6.57e-0838
trunk mesenchyme8.05e-0845
body cavity2.13e-0737
body cavity or lining2.13e-0737
mesenchyme5.13e-0761
entire embryonic mesenchyme5.13e-0761


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)
MA0003.11.08574
MA0004.10.481116
MA0006.11.51462
MA0007.10.465969
MA0009.10.92425
MA0014.15.99891
MA0017.10.89657
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.11.55156
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.11.04397
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.801219
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.15.78191
MA0056.10
MA0057.10.376102
MA0058.11.00014
MA0059.11.02718
MA0060.12.67112
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.11.25994
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.0004304
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.598004
MA0089.10
MA0090.10.446539
MA0091.11.23749
MA0092.10.446857
MA0093.10.879104
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.488671
MA0106.10.677988
MA0107.10.342432
MA0108.21.8008
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.11.04809
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.0910975
MA0146.10.792204
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.967192
MA0035.20.573016
MA0039.24.43229
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.20.0910939
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.10.878466
MA0163.10.116706
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.22.82057
MA0102.21.65195
MA0258.10.246285
MA0259.12.06728
MA0442.10
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