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MCL coexpression mm9:728: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0005409!2.19e-16!47;UBERON:0000160!1.86e-14!31;UBERON:0004119!5.67e-14!118;UBERON:0000925!5.67e-14!118;UBERON:0006595!5.67e-14!118;UBERON:0001007!3.39e-13!116;UBERON:0001555!3.39e-13!116;UBERON:0007026!3.39e-13!116;UBERON:0004921!2.75e-12!114;UBERON:0000344!3.73e-09!15;UBERON:0001242!4.13e-08!13;UBERON:0000060!4.13e-08!13;UBERON:0001262!4.13e-08!13;UBERON:0004786!4.13e-08!13;UBERON:0004923!1.71e-07!24
|ontology_enrichment_uberon=UBERON:0005409!2.19e-16!47;UBERON:0000160!1.86e-14!31;UBERON:0004119!5.67e-14!118;UBERON:0000925!5.67e-14!118;UBERON:0006595!5.67e-14!118;UBERON:0001007!3.39e-13!116;UBERON:0001555!3.39e-13!116;UBERON:0007026!3.39e-13!116;UBERON:0004921!2.75e-12!114;UBERON:0000344!3.73e-09!15;UBERON:0001242!4.13e-08!13;UBERON:0000060!4.13e-08!13;UBERON:0001262!4.13e-08!13;UBERON:0004786!4.13e-08!13;UBERON:0004923!1.71e-07!24
|tfbs_overrepresentation_for_novel_motifs=0.860199,0.883225,0.297937,0.945937,0.200163,0.373426,0.458558,0.392928,0.816027,0.771958,1.071,0.447169,0.785818,0.470194,0.214197,0,0.656089,0.19356,0.736624,0.786777,0.26524,0.60924,0.469335,0.198877,0.304728,0.496413,0.709649,0.392919,0.67135,0.572447,0.379806,0.754912,0.560002,0.31333,0.214608,0.102262,2.32607,0.443753,0.498354,0.143746,0.196807,0.38461,0.307718,0.215898,0.434259,0.923221,0.578773,1.05036,0.479635,1.25738,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.695271,0.435119,0.68053,0.47505,0.735292,0.531188,0.854737,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.128829,0.155003,0.944464,0.320434,0.623453,0.646602,0.567793,0.718494,0.74114,0.406536,1.61386,0.529804,0.119727,0.830765,2.41237,0.182066,0.271714,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.950022,0.892226,0.388243,0.770215,0.57902,0.50528,0.184103,0.754637,0.87698,0.639679,0.638654,0.999084,0.696857,0.403887,1.37632,1.35258,0.315128,0.878738,0.743427,0.421988,1.12221,0.195318,0.409202,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,1.17725,0.760818,1.04463,0.59809,0.86025,0.353344,1.01535,0.48999,1.14365,0.142597,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,2.45403,0.580497,0.129005,0.895708,0.911723,0.489108,0.976367,0.523103,0.224422,0.319291,0.876739,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.18312,0.445669,0.809881
|tfbs_overrepresentation_for_novel_motifs=0.860199,0.883225,0.297937,0.945937,0.200163,0.373426,0.458558,0.392928,0.816027,0.771958,1.071,0.447169,0.785818,0.470194,0.214197,0,0.656089,0.19356,0.736624,0.786777,0.26524,0.60924,0.469335,0.198877,0.304728,0.496413,0.709649,0.392919,0.67135,0.572447,0.379806,0.754912,0.560002,0.31333,0.214608,0.102262,2.32607,0.443753,0.498354,0.143746,0.196807,0.38461,0.307718,0.215898,0.434259,0.923221,0.578773,1.05036,0.479635,1.25738,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.695271,0.435119,0.68053,0.47505,0.735292,0.531188,0.854737,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.128829,0.155003,0.944464,0.320434,0.623453,0.646602,0.567793,0.718494,0.74114,0.406536,1.61386,0.529804,0.119727,0.830765,2.41237,0.182066,0.271714,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.950022,0.892226,0.388243,0.770215,0.57902,0.50528,0.184103,0.754637,0.87698,0.639679,0.638654,0.999084,0.696857,0.403887,1.37632,1.35258,0.315128,0.878738,0.743427,0.421988,1.12221,0.195318,0.409202,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,1.17725,0.760818,1.04463,0.59809,0.86025,0.353344,1.01535,0.48999,1.14365,0.142597,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,2.45403,0.580497,0.129005,0.895708,0.911723,0.489108,0.976367,0.523103,0.224422,0.319291,0.876739,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.18312,0.445669,0.809881
|tfbs_overrepresentation_jaspar=MA0003.1;1.53513,MA0004.1;0.946922,MA0006.1;0.210471,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;0.795745,MA0017.1;0.658116,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;1.17347,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;1.82935,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;1.21025,MA0056.1;0,MA0057.1;0.216209,MA0058.1;0.752621,MA0059.1;0.777514,MA0060.1;0.446031,MA0061.1;0.16896,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.484739,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;1.10611,MA0074.1;0.451832,MA0076.1;0.696577,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;1.39028,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.642324,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;1.26149,MA0105.1;0.304995,MA0106.1;0.543967,MA0107.1;0.237082,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.342068,MA0113.1;0.516916,MA0114.1;0.167085,MA0115.1;0.878749,MA0116.1;0.210297,MA0117.1;0.846964,MA0119.1;1.44977,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;0.598671,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;1.26076,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.976447,MA0145.1;1.46364,MA0146.1;0.642452,MA0147.1;1.01679,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;0.314778,MA0035.2;0.44524,MA0039.2;1.66029,MA0138.2;0.590987,MA0002.2;0.123715,MA0137.2;0.713675,MA0104.2;0.828906,MA0047.2;0.495607,MA0112.2;0.663994,MA0065.2;0.163769,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.862467,MA0155.1;1.12565,MA0156.1;0.694831,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.550545,MA0160.1;0.378276,MA0161.1;0,MA0162.1;2.22848,MA0163.1;1.31067,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;0.937792,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;0.981631,MA0442.1;0
}}
}}

Revision as of 12:13, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:74945361..74945437,-p1@Cast
Mm9::chr18:23912236..23912260,+p5@Mapre2
Mm9::chr19:5560600..5560617,-p1@Ovol1
Mm9::chr2:24223085..24223140,+p3@Psd4
Mm9::chr4:55545337..55545357,-p1@Klf4
Mm9::chr5:75098978..75098991,-p4@Lnx1
Mm9::chr9:76414899..76414930,-p1@Fam83b
Mm9::chr9:76414933..76414938,-p2@Fam83b
Mm9::chrX:109812273..109812298,-p2@Pof1b
Mm9::chrX:7318414..7318447,-p2@Ccdc120


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:0030161calpain inhibitor activity0.0405925320326153
GO:0042787protein ubiquitination during ubiquitin-dependent protein catabolic process0.0405925320326153
GO:0000239pachytene0.0405925320326153
GO:0030163protein catabolic process0.0405925320326153
GO:0045892negative regulation of transcription, DNA-dependent0.0405925320326153
GO:0043285biopolymer catabolic process0.0405925320326153
GO:0000279M phase0.0405925320326153
GO:0016481negative regulation of transcription0.0405925320326153
GO:0007128meiotic prophase I0.0405925320326153
GO:0051324prophase0.0405925320326153
GO:0045934negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0405925320326153
GO:0032011ARF protein signal transduction0.0405925320326153
GO:0005086ARF guanyl-nucleotide exchange factor activity0.0405925320326153
GO:0030165PDZ domain binding0.0405925320326153
GO:0032012regulation of ARF protein signal transduction0.0405925320326153
GO:0022403cell cycle phase0.0405925320326153
GO:0009057macromolecule catabolic process0.0420435605551518
GO:0031324negative regulation of cellular metabolic process0.0420435605551518
GO:0009892negative regulation of metabolic process0.0491480804908414
GO:0008092cytoskeletal protein binding0.0491480804908414



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
gastrointestinal system2.19e-1647
intestine1.86e-1431
endoderm-derived structure5.67e-14118
endoderm5.67e-14118
presumptive endoderm5.67e-14118
digestive system3.39e-13116
digestive tract3.39e-13116
primitive gut3.39e-13116
subdivision of digestive tract2.75e-12114
mucosa3.73e-0915
intestinal mucosa4.13e-0813
anatomical wall4.13e-0813
wall of intestine4.13e-0813
gastrointestinal system mucosa4.13e-0813
organ component layer1.71e-0724


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)
MA0003.11.53513
MA0004.10.946922
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.10.795745
MA0017.10.658116
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.11.17347
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.11.82935
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.11.21025
MA0056.10
MA0057.10.216209
MA0058.10.752621
MA0059.10.777514
MA0060.10.446031
MA0061.10.16896
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.484739
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.11.10611
MA0074.10.451832
MA0076.10.696577
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.11.39028
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.642324
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.11.26149
MA0105.10.304995
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.167085
MA0115.10.878749
MA0116.10.210297
MA0117.10.846964
MA0119.11.44977
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.10.598671
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.11.26076
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.976447
MA0145.11.46364
MA0146.10.642452
MA0147.11.01679
MA0148.10.375491
MA0149.10.2978
MA0062.20.314778
MA0035.20.44524
MA0039.21.66029
MA0138.20.590987
MA0002.20.123715
MA0137.20.713675
MA0104.20.828906
MA0047.20.495607
MA0112.20.663994
MA0065.20.163769
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.862467
MA0155.11.12565
MA0156.10.694831
MA0157.10.642984
MA0158.10
MA0159.10.550545
MA0160.10.378276
MA0161.10
MA0162.12.22848
MA0163.11.31067
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.20.937792
MA0102.21.49914
MA0258.10.156336
MA0259.10.981631
MA0442.10
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