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MCL coexpression mm9:2063: Difference between revisions

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{{MCL_coexpression_mm9
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of polarity of embryonic epithelium;0.0082178272064866;14238!GO:0007164;establishment of tissue polarity;0.0082178272064866;14238!GO:0001736;establishment of planar polarity;0.0082178272064866;14238!GO:0001738;morphogenesis of a polarized epithelium;0.0106831753684326;14238!GO:0048566;embryonic gut development;0.0106831753684326;14238!GO:0048565;gut development;0.0123267408097299;14238!GO:0048568;embryonic organ development;0.0217185433314289;14238!GO:0030198;extracellular matrix organization and biogenesis;0.0292760094231085;14238!GO:0003713;transcription coactivator activity;0.0310451250022827;14238!GO:0003702;RNA polymerase II transcription factor activity;0.0312277433846491;14238!GO:0043062;extracellular structure organization and biogenesis;0.0369802224291897;14238!GO:0002009;morphogenesis of an epithelium;0.0421163644332438;14238!GO:0003712;transcription cofactor activity;0.0429855576954684;14238!GO:0016563;transcription activator activity;0.0480229277379061;14238!GO:0008134;transcription factor binding;0.0480229277379061;14238!GO:0045892;negative regulation of transcription, 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|gostat_on_MCL_coexpression=GO:0042249;establishment of polarity of embryonic epithelium;0.0082178272064866;14238!GO:0007164;establishment of tissue polarity;0.0082178272064866;14238!GO:0001736;establishment of planar polarity;0.0082178272064866;14238!GO:0001738;morphogenesis of a polarized epithelium;0.0106831753684326;14238!GO:0048566;embryonic gut development;0.0106831753684326;14238!GO:0048565;gut development;0.0123267408097299;14238!GO:0048568;embryonic organ development;0.0217185433314289;14238!GO:0030198;extracellular matrix organization and biogenesis;0.0292760094231085;14238!GO:0003713;transcription coactivator activity;0.0310451250022827;14238!GO:0003702;RNA polymerase II transcription factor activity;0.0312277433846491;14238!GO:0043062;extracellular structure organization and biogenesis;0.0369802224291897;14238!GO:0002009;morphogenesis of an epithelium;0.0421163644332438;14238!GO:0003712;transcription cofactor activity;0.0429855576954684;14238!GO:0016563;transcription activator activity;0.0480229277379061;14238!GO:0008134;transcription factor binding;0.0480229277379061;14238!GO:0045892;negative regulation of transcription, DNA-dependent;0.0480229277379061;14238!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002048!2.09e-11!14;UBERON:0000117!2.09e-11!14;UBERON:0000171!2.09e-11!14;UBERON:0000170!2.09e-11!14;UBERON:0005597!2.09e-11!14;UBERON:0000118!2.09e-11!14;UBERON:0005153!6.07e-09!17;UBERON:0005178!4.21e-08!17;UBERON:0005181!4.21e-08!17;UBERON:0002224!4.21e-08!17;UBERON:0000915!4.21e-08!17;UBERON:0008947!4.21e-08!17;UBERON:0003258!4.21e-08!17;UBERON:0002346!3.09e-07!64;UBERON:0003075!3.09e-07!64;UBERON:0007284!3.09e-07!64
|tfbs_overrepresentation_for_novel_motifs=0.641384,0.801438,0.612053,0.688265,0.483253,0.704257,0.803568,0.370124,0.993085,0.489964,0.755749,0.790506,0.37041,0.81685,0.502646,0,1.02248,0.473993,1.65947,0.24402,0.570433,0.197567,0.815872,0.481455,0.620553,0.846564,0.342316,0.727368,0.535752,0.790816,0.711848,2.54643,3.06215,0.318879,0.503207,1.04375,2.02937,0.786577,0.434783,1.82692,0.478558,0.717547,1.64392,0.504971,1.63233,0.675898,0.938241,0.744678,1.51493,0.539131,1.0041,0.875451,0.771943,1.2746,1.29252,0.82458,0.549352,0.776619,0.331485,0.822375,1.10737,0.885556,1.02399,0.992216,0.8366,1.03484,1.43193,1.78579,1.1025,1.63712,0.590754,0.377213,0.593145,1.32691,0.323563,0.310084,0.854076,0.926147,1.08947,0.575233,0.37865,1.04072,0.884013,0.362446,1.20828,3.90655,0.808001,4.98491,0.943446,1.94914,1.50286,1.21342,1.14153,0.490141,1.09896,1.05366,0.961641,1.14445,0.938512,0.264911,0.460566,1.12793,1.25667,1.00472,1.00361,0.717061,1.06633,0.740267,0.580757,0.57247,1.53136,1.25851,0.576517,0.7614,1.51002,2.08281,0.442329,0.692434,1.02384,0.456123,1.33244,0.970073,0.848526,0.925183,1.56496,1.09333,0.812403,1.13449,1.43038,0.493609,1.23918,0.680176,1.40022,0.839311,1.53196,0.569254,0.650785,0.719099,1.482,2.31884,1.91709,1.43673,0.861473,1.1391,0.996781,0.718046,0.941555,2.27909,1.57302,0.485304,0.293812,0.184289,1.27621,0.416214,0.838313,1.35996,0.87653,0.516549,0.63863,0.650472,1.49167,1.20739,1.09379,0.630949,0.993294,0.830321,0.459159,0.788782,0.0824127
|tfbs_overrepresentation_jaspar=MA0003.1;3.50387,MA0004.1;0.6888,MA0006.1;0.497533,MA0007.1;0.672186,MA0009.1;1.15569,MA0014.1;1.46333,MA0017.1;0.528196,MA0019.1;0.964875,MA0024.1;1.11019,MA0025.1;1.39562,MA0027.1;2.81824,MA0028.1;0.509589,MA0029.1;1.08753,MA0030.1;1.09438,MA0031.1;1.05719,MA0038.1;0.846479,MA0040.1;1.16866,MA0041.1;0.604221,MA0042.1;0.589368,MA0043.1;1.25564,MA0046.1;1.1929,MA0048.1;2.07944,MA0050.1;0.731539,MA0051.1;0.856094,MA0052.1;1.17701,MA0055.1;0.125758,MA0056.1;0,MA0057.1;1.29714,MA0058.1;0.581673,MA0059.1;0.59559,MA0060.1;0.403071,MA0061.1;0.438628,MA0063.1;0,MA0066.1;0.834648,MA0067.1;1.50873,MA0068.1;0.256913,MA0069.1;1.17737,MA0070.1;1.16732,MA0071.1;0.73062,MA0072.1;1.15853,MA0073.1;12.9526,MA0074.1;0.795862,MA0076.1;0.550092,MA0077.1;1.13603,MA0078.1;0.891476,MA0081.1;1.5065,MA0083.1;1.25482,MA0084.1;1.84013,MA0087.1;1.21037,MA0088.1;1.73268,MA0089.1;0,MA0090.1;0.650768,MA0091.1;0.703314,MA0092.1;0.651119,MA0093.1;0.519148,MA0095.1;0,MA0098.1;0,MA0100.1;1.84237,MA0101.1;0.605676,MA0103.1;0.540576,MA0105.1;0.313353,MA0106.1;0.899777,MA0107.1;0.533522,MA0108.2;0.989014,MA0109.1;0,MA0111.1;1.60035,MA0113.1;0.869608,MA0114.1;0.43587,MA0115.1;1.25852,MA0116.1;0.497293,MA0117.1;1.22527,MA0119.1;0.606338,MA0122.1;1.24573,MA0124.1;1.45461,MA0125.1;1.37907,MA0130.1;0,MA0131.1;0.960068,MA0132.1;0,MA0133.1;0,MA0135.1;1.29308,MA0136.1;0.817395,MA0139.1;0.957842,MA0140.1;0.78318,MA0141.1;0.563066,MA0142.1;1.04199,MA0143.1;0.887119,MA0144.1;0.439506,MA0145.1;1.14526,MA0146.1;0.313734,MA0147.1;0.453952,MA0148.1;0.706718,MA0149.1;0.611881,MA0062.2;0.319836,MA0035.2;0.788288,MA0039.2;2.41467,MA0138.2;3.59515,MA0002.2;0.368961,MA0137.2;0.559766,MA0104.2;0.386166,MA0047.2;0.845655,MA0112.2;1.14524,MA0065.2;0.212467,MA0150.1;0.67206,MA0151.1;0,MA0152.1;0.84577,MA0153.1;1.31015,MA0154.1;3.771,MA0155.1;0.230016,MA0156.1;0.549102,MA0157.1;1.0083,MA0158.1;0,MA0159.1;2.0472,MA0160.1;0.71003,MA0161.1;0,MA0162.1;0.346529,MA0163.1;0.327769,MA0164.1;0.817786,MA0080.2;2.27475,MA0018.2;0.828253,MA0099.2;0.944966,MA0079.2;6.78242,MA0102.2;4.08497,MA0258.1;0.419871,MA0259.1;0.441366,MA0442.1;0
}}

Latest revision as of 17:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:31717418..31717433,-p1@1700018A04Rik
Mm9::chr13:31717548..31717596,+p1@Foxf2
Mm9::chr13:31717597..31717613,+p2@Foxf2
Mm9::chr13:31717614..31717628,+p3@Foxf2


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:0042249establishment of polarity of embryonic epithelium0.0082178272064866
GO:0007164establishment of tissue polarity0.0082178272064866
GO:0001736establishment of planar polarity0.0082178272064866
GO:0001738morphogenesis of a polarized epithelium0.0106831753684326
GO:0048566embryonic gut development0.0106831753684326
GO:0048565gut development0.0123267408097299
GO:0048568embryonic organ development0.0217185433314289
GO:0030198extracellular matrix organization and biogenesis0.0292760094231085
GO:0003713transcription coactivator activity0.0310451250022827
GO:0003702RNA polymerase II transcription factor activity0.0312277433846491
GO:0043062extracellular structure organization and biogenesis0.0369802224291897
GO:0002009morphogenesis of an epithelium0.0421163644332438
GO:0003712transcription cofactor activity0.0429855576954684
GO:0016563transcription activator activity0.0480229277379061
GO:0008134transcription factor binding0.0480229277379061
GO:0045892negative regulation of transcription, DNA-dependent0.0480229277379061



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
lung2.09e-1114
respiratory tube2.09e-1114
respiration organ2.09e-1114
pair of lungs2.09e-1114
lung primordium2.09e-1114
lung bud2.09e-1114
epithelial bud6.07e-0917
thoracic cavity element4.21e-0817
thoracic segment organ4.21e-0817
thoracic cavity4.21e-0817
thoracic segment of trunk4.21e-0817
respiratory primordium4.21e-0817
endoderm of foregut4.21e-0817
neurectoderm3.09e-0764
neural plate3.09e-0764
presumptive neural plate3.09e-0764


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)
MA0003.13.50387
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.11.46333
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.12.07944
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.125758
MA0056.10
MA0057.11.29714
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.112.9526
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.11.5065
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.11.73268
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.11.84237
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.11.60035
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.957842
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.11.14526
MA0146.10.313734
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.22.41467
MA0138.23.59515
MA0002.20.368961
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.21.14524
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.13.771
MA0155.10.230016
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.12.0472
MA0160.10.71003
MA0161.10
MA0162.10.346529
MA0163.10.327769
MA0164.10.817786
MA0080.22.27475
MA0018.20.828253
MA0099.20.944966
MA0079.26.78242
MA0102.24.08497
MA0258.10.419871
MA0259.10.441366
MA0442.10
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