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MCL coexpression mm9:1092: Difference between revisions

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{{MCL_coexpression_mm9
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cell fate determination;0.00427327014737304;21385!GO:0042693;muscle cell fate commitment;0.00427327014737304;21385!GO:0048738;cardiac muscle development;0.0128198104421191;21385!GO:0007569;cell aging;0.0138881279789624;21385!GO:0030879;mammary gland development;0.0170930805894921;21385!GO:0001709;cell fate determination;0.0170930805894921;21385!GO:0007568;aging;0.0170930805894921;21385!GO:0003007;heart morphogenesis;0.0181613981263354;21385!GO:0042692;muscle cell differentiation;0.0299128910316112;21385!GO:0048732;gland development;0.0316221990905605;21385!GO:0045165;cell fate commitment;0.038847910430664;21385!GO:0014706;striated muscle development;0.0434449131649592;21385!GO:0000122;negative regulation of transcription from RNA polymerase II promoter;0.0454034953158385;21385!GO:0016564;transcription repressor activity;0.0454034953158385;21385!GO:0007517;muscle development;0.0454034953158385;21385!GO:0007507;heart development;0.0454034953158385;21385!GO:0045892;negative regulation of transcription, 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|gostat_on_MCL_coexpression=GO:0007521;muscle cell fate determination;0.00427327014737304;21385!GO:0042693;muscle cell fate commitment;0.00427327014737304;21385!GO:0048738;cardiac muscle development;0.0128198104421191;21385!GO:0007569;cell aging;0.0138881279789624;21385!GO:0030879;mammary gland development;0.0170930805894921;21385!GO:0001709;cell fate determination;0.0170930805894921;21385!GO:0007568;aging;0.0170930805894921;21385!GO:0003007;heart morphogenesis;0.0181613981263354;21385!GO:0042692;muscle cell differentiation;0.0299128910316112;21385!GO:0048732;gland development;0.0316221990905605;21385!GO:0045165;cell fate commitment;0.038847910430664;21385!GO:0014706;striated muscle development;0.0434449131649592;21385!GO:0000122;negative regulation of transcription from RNA polymerase II promoter;0.0454034953158385;21385!GO:0016564;transcription repressor activity;0.0454034953158385;21385!GO:0007517;muscle development;0.0454034953158385;21385!GO:0007507;heart development;0.0454034953158385;21385!GO:0045892;negative regulation of transcription, DNA-dependent;0.0470059716211034;21385!
|ontology_enrichment_celltype=CL:0000107!3.45e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002048!3.63e-10!14;UBERON:0000117!3.63e-10!14;UBERON:0000171!3.63e-10!14;UBERON:0000170!3.63e-10!14;UBERON:0005597!3.63e-10!14;UBERON:0000118!3.63e-10!14;UBERON:0000468!4.57e-10!333;UBERON:0005157!1.29e-09!20;UBERON:0000464!2.10e-08!57;UBERON:0002113!4.08e-08!14;UBERON:0003918!4.08e-08!14;UBERON:0011143!4.08e-08!14;UBERON:0005095!4.08e-08!14;UBERON:0007687!4.08e-08!14;UBERON:0001008!6.12e-08!19;UBERON:0005153!9.85e-08!17;UBERON:0005177!1.11e-07!79;UBERON:0000010!1.19e-07!11;UBERON:0006554!1.31e-07!18;UBERON:0005178!1.41e-07!17;UBERON:0005181!1.41e-07!17;UBERON:0002224!1.41e-07!17;UBERON:0000915!1.41e-07!17;UBERON:0008947!1.41e-07!17;UBERON:0003258!1.41e-07!17;UBERON:0002410!3.45e-07!9;UBERON:0000922!3.62e-07!320;UBERON:0009569!5.62e-07!66
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.161863,0.411716,0.480627,0.299217,0.495263,1.43443,0.206208,1.15776,1.7494,1.34037,0.575086,0.206435,0.599731,1.53029,0,0.795315,0.291368,2.38602,0.112498,0.374752,2.02657,0.598814,0.29769,1.89054,0.62766,0.184473,1.28465,0.344372,0.145661,0.50223,0.897561,0.289148,0.166577,2.33037,0.0235321,0.279977,0.57142,0.258564,0.230656,0.295233,0.507468,0.932136,0.317766,3.80125,0.469348,0.714592,1.31862,0.478447,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,0.611537,1.09164,0.507615,0.159969,0.498755,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,1.72681,0.975495,4.20174,0.164297,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.708155,0.237542,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,1.10097,1.02459,0.380122,2.31879,1.27206,0.293461,1.12953,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,3.16844,1.00568,2.07207,1.16374,0.620831,1.29374,0.0806013,0.446555,1.26843,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,1.13988,0.300961,0.452587,1.38961,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,1.13413,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.763807,0.573477,15.215
}}

Latest revision as of 16:23, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:85644728..85644768,+p@chr11:85644728..85644768
+
Mm9::chr11:85645796..85645812,-p1@ENSMUST00000136117
p1@uc007krx.1
p1@uc007kry.1
Mm9::chr11:85646263..85646278,+p2@Tbx2
Mm9::chr11:85646303..85646329,+p1@Tbx2
Mm9::chr11:85646341..85646352,+p3@Tbx2
Mm9::chr11:85646427..85646451,+p4@Tbx2
Mm9::chr11:85646469..85646488,+p5@Tbx2


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:0007521muscle cell fate determination0.00427327014737304
GO:0042693muscle cell fate commitment0.00427327014737304
GO:0048738cardiac muscle development0.0128198104421191
GO:0007569cell aging0.0138881279789624
GO:0030879mammary gland development0.0170930805894921
GO:0001709cell fate determination0.0170930805894921
GO:0007568aging0.0170930805894921
GO:0003007heart morphogenesis0.0181613981263354
GO:0042692muscle cell differentiation0.0299128910316112
GO:0048732gland development0.0316221990905605
GO:0045165cell fate commitment0.038847910430664
GO:0014706striated muscle development0.0434449131649592
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0454034953158385
GO:0016564transcription repressor activity0.0454034953158385
GO:0007517muscle development0.0454034953158385
GO:0007507heart development0.0454034953158385
GO:0045892negative regulation of transcription, DNA-dependent0.0470059716211034



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
autonomic neuron3.45e-079

Uber Anatomy
Ontology termp-valuen
lung3.63e-1014
respiratory tube3.63e-1014
respiration organ3.63e-1014
pair of lungs3.63e-1014
lung primordium3.63e-1014
lung bud3.63e-1014
multi-cellular organism4.57e-10333
epithelial fold1.29e-0920
anatomical space2.10e-0857
kidney4.08e-0814
kidney mesenchyme4.08e-0814
upper urinary tract4.08e-0814
kidney rudiment4.08e-0814
kidney field4.08e-0814
renal system6.12e-0819
epithelial bud9.85e-0817
trunk region element1.11e-0779
peripheral nervous system1.19e-0711
urinary system structure1.31e-0718
thoracic cavity element1.41e-0717
thoracic segment organ1.41e-0717
thoracic cavity1.41e-0717
thoracic segment of trunk1.41e-0717
respiratory primordium1.41e-0717
endoderm of foregut1.41e-0717
autonomic nervous system3.45e-079
embryo3.62e-07320
subdivision of trunk5.62e-0766


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)
MA0003.13.65284
MA0004.10.481116
MA0006.10.837454
MA0007.11.17655
MA0009.10.92425
MA0014.10.222567
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.13.62248
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.157978
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.11.22438
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.152496
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.15.30337
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.13.18843
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
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.116.8711
MA0146.13.11443
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.21.72008
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.21.17226
MA0047.20.626803
MA0112.22.13872
MA0065.22.14244
MA0150.10.465855
MA0151.10
MA0152.11.5176
MA0153.11.07519
MA0154.11.29007
MA0155.12.94388
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.14.62777
MA0163.11.63182
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.23.46801
MA0102.21.65195
MA0258.11.27611
MA0259.10.26402
MA0442.10
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