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MCL coexpression mm9:1244: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001008!7.78e-16!19;UBERON:0006554!6.56e-15!18;UBERON:0000489!1.61e-14!21;UBERON:0002113!3.54e-11!14;UBERON:0003918!3.54e-11!14;UBERON:0011143!3.54e-11!14;UBERON:0005095!3.54e-11!14;UBERON:0007687!3.54e-11!14;UBERON:0000474!2.16e-10!9;UBERON:0003134!2.41e-09!8;UBERON:0005156!2.85e-08!26;UBERON:0000990!2.85e-08!26;UBERON:0003102!4.60e-08!22;UBERON:0002102!5.92e-08!7;UBERON:0004710!5.92e-08!7;UBERON:0005419!5.92e-08!7;UBERON:0005417!5.92e-08!7;UBERON:0005729!5.92e-08!7;UBERON:0003100!6.63e-08!11;UBERON:0004175!1.94e-07!9;UBERON:0003133!8.13e-07!24
|ontology_enrichment_uberon=UBERON:0001008!7.78e-16!19;UBERON:0006554!6.56e-15!18;UBERON:0000489!1.61e-14!21;UBERON:0002113!3.54e-11!14;UBERON:0003918!3.54e-11!14;UBERON:0011143!3.54e-11!14;UBERON:0005095!3.54e-11!14;UBERON:0007687!3.54e-11!14;UBERON:0000474!2.16e-10!9;UBERON:0003134!2.41e-09!8;UBERON:0005156!2.85e-08!26;UBERON:0000990!2.85e-08!26;UBERON:0003102!4.60e-08!22;UBERON:0002102!5.92e-08!7;UBERON:0004710!5.92e-08!7;UBERON:0005419!5.92e-08!7;UBERON:0005417!5.92e-08!7;UBERON:0005729!5.92e-08!7;UBERON:0003100!6.63e-08!11;UBERON:0004175!1.94e-07!9;UBERON:0003133!8.13e-07!24
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.346849,0.550971,1.55624,0.247459,0.7141,0.594834,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.442204,0.426133,0.108444,0.657163,0.345236,1.19059,2.7654,0.223823,0.572827,1.80527,0.181062,0.558142,0.960397,0.892985,0.204204,0.364821,0.144368,1.56842,0.629145,0.820134,0.752287,0.907317,0.56353,0.0995018,0.366415,0.161543,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,1.59383,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.253541,0.11437,1.156,0.599223,0.19692,0.589776,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.0539203,0.0610418,1.62034,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.810643,0.281222,0.685716,0.976308,0.775372,0.160254,2.38104,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,0.585058,0.435642,0.428007,1.21641,1.0885,0.431734,3.6575,1.33732,0.340765,0.247162,1.33416,0.858327,0.862623,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,5.17219,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,2.37427,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,1.94251,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.325363,1.10596,0.287383,0.678689,1.18867,0.71546,0.983048,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,1.60971,0.325308,0.63125,0.5667
|tfbs_overrepresentation_for_novel_motifs=0.491922,0.217198,0.464605,0.535892,0.346849,0.550971,1.55624,0.247459,0.7141,0.594834,0.599767,0.632897,0.247704,0.6581,0.364314,0,0.856992,0.338549,0.656199,0.442204,0.426133,0.108444,0.657163,0.345236,1.19059,2.7654,0.223823,0.572827,1.80527,0.181062,0.558142,0.960397,0.892985,0.204204,0.364821,0.144368,1.56842,0.629145,0.820134,0.752287,0.907317,0.56353,0.0995018,0.366415,0.161543,0.524258,0.77511,0.589246,0.0835644,0.397446,0.839084,0.714419,0.517905,1.10437,1.12205,0.66551,0.406788,0.619643,0.21472,1.59383,0.939962,0.724164,0.269393,0.827522,0.677043,0.869046,1.2599,1.61148,0.935192,1.46355,1.1311,0.253541,0.11437,1.156,0.599223,0.19692,0.589776,0.763395,0.922432,0.430551,0.254777,0.874787,0.722675,0.240896,1.03903,0.0539203,0.0610418,1.62034,0.780154,1.77427,1.33021,1.04409,0.973447,0.35304,0.810643,0.281222,0.685716,0.976308,0.775372,0.160254,2.38104,0.960112,1.08669,0.839694,0.838613,1.38336,0.8998,0.585058,0.435642,0.428007,1.21641,1.0885,0.431734,3.6575,1.33732,0.340765,0.247162,1.33416,0.858327,0.862623,1.16147,0.805995,0.688501,0.762461,1.39185,0.926209,5.17219,0.966541,1.25836,0.356163,1.06946,0.52828,1.2285,0.679647,1.35909,0.106956,0.500709,2.37427,1.30952,2.14327,1.74232,1.26465,0.700956,0.971067,1.94251,0.564002,0.778321,2.10357,0.503174,0.348692,0.183562,0.325363,1.10596,0.287383,0.678689,1.18867,0.71546,0.983048,0.48935,0.500417,1.31911,1.03816,0.926663,0.482185,0.82857,1.60971,0.325308,0.63125,0.5667
|tfbs_overrepresentation_jaspar=MA0003.1;0.276983,MA0004.1;0.536396,MA0006.1;0.359699,MA0007.1;0.52077,MA0009.1;0.987341,MA0014.1;0.304529,MA0017.1;0.387481,MA0019.1;0.800946,MA0024.1;0.942716,MA0025.1;1.22395,MA0027.1;2.64231,MA0028.1;0.370592,MA0029.1;0.920529,MA0030.1;0.927235,MA0031.1;0.890871,MA0038.1;0.686534,MA0040.1;1.00009,MA0041.1;0.457338,MA0042.1;0.443591,MA0043.1;1.08567,MA0046.1;5.42469,MA0048.1;0.486223,MA0050.1;0.57678,MA0051.1;0.695779,MA0052.1;1.00829,MA0055.1;0.807132,MA0056.1;0,MA0057.1;2.76847,MA0058.1;0.436487,MA0059.1;0.449345,MA0060.1;0.275911,MA0061.1;0.307097,MA0063.1;0,MA0066.1;0.675169,MA0067.1;1.33603,MA0068.1;0.467569,MA0069.1;1.00864,MA0070.1;0.998765,MA0071.1;0.575909,MA0072.1;0.990133,MA0073.1;0.00140584,MA0074.1;0.638014,MA0076.1;0.407465,MA0077.1;0.968053,MA0078.1;1.73197,MA0081.1;0.473489,MA0083.1;1.08487,MA0084.1;1.66561,MA0087.1;1.04109,MA0088.1;0.358337,MA0089.1;0,MA0090.1;0.500693,MA0091.1;1.3559,MA0092.1;0.501022,MA0093.1;0.379257,MA0095.1;0,MA0098.1;0,MA0100.1;0.626021,MA0101.1;0.458688,MA0103.1;0.398766,MA0105.1;1.09694,MA0106.1;0.737893,MA0107.1;0.392331,MA0108.2;1.92698,MA0109.1;0,MA0111.1;0.515457,MA0113.1;0.708789,MA0114.1;0.304661,MA0115.1;1.08851,MA0116.1;0.359483,MA0117.1;1.05576,MA0119.1;0.459301,MA0122.1;1.07591,MA0124.1;1.28237,MA0125.1;1.20757,MA0130.1;0,MA0131.1;0.796279,MA0132.1;0,MA0133.1;0,MA0135.1;1.1226,MA0136.1;0.658622,MA0139.1;0.243463,MA0140.1;0.625902,MA0141.1;0.419361,MA0142.1;0.876028,MA0143.1;0.725672,MA0144.1;0.307873,MA0145.1;0.119202,MA0146.1;0.0392287,MA0147.1;0.320675,MA0148.1;0.553294,MA0149.1;0.464445,MA0062.2;0.204999,MA0035.2;0.630778,MA0039.2;0.0271858,MA0138.2;0.788113,MA0002.2;0.689262,MA0137.2;0.416331,MA0104.2;0.261255,MA0047.2;0.685741,MA0112.2;0.119197,MA0065.2;0.119561,MA0150.1;0.520653,MA0151.1;0,MA0152.1;0.685852,MA0153.1;2.56917,MA0154.1;1.49271,MA0155.1;0.132921,MA0156.1;0.406559,MA0157.1;0.843181,MA0158.1;0,MA0159.1;0.331229,MA0160.1;0.556423,MA0161.1;0,MA0162.1;0.0465447,MA0163.1;1.03138,MA0164.1;0.658997,MA0080.2;0.393257,MA0018.2;0.669032,MA0099.2;0.781628,MA0079.2;0.911432,MA0102.2;1.7182,MA0258.1;0.290587,MA0259.1;0.309517,MA0442.1;0
}}
}}

Revision as of 13:01, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:5636678..5636725,-p6@Esr1
Mm9::chr6:52190656..52190667,-p7@Hoxa10
Mm9::chr6:52190668..52190682,-p3@Hoxa10
Mm9::chr6:52195747..52195762,-p3@Hoxa11
Mm9::chr6:52195763..52195792,-p2@Hoxa11
Mm9::chr6:52195795..52195825,-p1@Hoxa11


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:0043565sequence-specific DNA binding0.00128041237870629
GO:0003700transcription factor activity0.00425779343150948
GO:0009653anatomical structure morphogenesis0.00745703692690638
GO:0045839negative regulation of mitosis0.00821737696392652
GO:0007389pattern specification process0.00916575112443743
GO:0006355regulation of transcription, DNA-dependent0.00916575112443743
GO:0006351transcription, DNA-dependent0.00916575112443743
GO:0032774RNA biosynthetic process0.00916575112443743
GO:0003677DNA binding0.00916575112443743
GO:0045449regulation of transcription0.00916575112443743
GO:0048856anatomical structure development0.00916575112443743
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00916575112443743
GO:0006350transcription0.00916575112443743
GO:0010468regulation of gene expression0.0093978923010452
GO:0031323regulation of cellular metabolic process0.00961506158071779
GO:0005667transcription factor complex0.00961506158071779
GO:0019222regulation of metabolic process0.0097359320341928
GO:0016070RNA metabolic process0.00994272197671441
GO:0001759induction of an organ0.00997226994819038
GO:0010092specification of organ identity0.00997226994819038
GO:0009887organ morphogenesis0.00997226994819038
GO:0045168cell-cell signaling during cell fate commitment0.00997226994819038
GO:0031128induction0.00997226994819038
GO:0044451nucleoplasm part0.00997226994819038
GO:0005654nucleoplasm0.0105053104482289
GO:0010467gene expression0.0117982004492543
GO:0003676nucleic acid binding0.0122037722687037
GO:0032502developmental process0.0127500285248328
GO:0031981nuclear lumen0.0127500285248328
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0137472389941103
GO:0007088regulation of mitosis0.0142119381120271
GO:0031974membrane-enclosed lumen0.0142119381120271
GO:0043233organelle lumen0.0142119381120271
GO:0050794regulation of cellular process0.0149611027976701
GO:0050789regulation of biological process0.0200777394008583
GO:0001656metanephros development0.0201764519006285
GO:0005496steroid binding0.0201764519006285
GO:0003707steroid hormone receptor activity0.0201764519006285
GO:0004879ligand-dependent nuclear receptor activity0.0201764519006285
GO:0044428nuclear part0.0205358236401176
GO:0065007biological regulation0.0229268067524417
GO:0005634nucleus0.0238045419967062
GO:0043283biopolymer metabolic process0.025483047988348
GO:0001822kidney development0.027160817266496
GO:0001655urogenital system development0.0287305713925266
GO:0048513organ development0.0325860332208126
GO:0016049cell growth0.0327041000229519
GO:0045165cell fate commitment0.0340555540588183
GO:0008361regulation of cell size0.0352516481138001
GO:0005515protein binding0.0352516481138001
GO:0045786negative regulation of progression through cell cycle0.0371480088490407
GO:0043234protein complex0.03962013826808
GO:0048731system development0.0425824276148522
GO:0003002regionalization0.0443845586634856
GO:0043170macromolecule metabolic process0.0451761693242856
GO:0007067mitosis0.0482831052960478
GO:0000087M phase of mitotic cell cycle0.0482831052960478
GO:0000074regulation of progression through cell cycle0.0496525167121281
GO:0001501skeletal development0.0496525167121281



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>


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)
MA0003.10.276983
MA0004.10.536396
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.304529
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.370592
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.15.42469
MA0048.10.486223
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.807132
MA0056.10
MA0057.12.76847
MA0058.10.436487
MA0059.10.449345
MA0060.10.275911
MA0061.10.307097
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.10.575909
MA0072.10.990133
MA0073.10.00140584
MA0074.10.638014
MA0076.10.407465
MA0077.10.968053
MA0078.11.73197
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.358337
MA0089.10
MA0090.10.500693
MA0091.11.3559
MA0092.10.501022
MA0093.10.379257
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.11.09694
MA0106.10.737893
MA0107.10.392331
MA0108.21.92698
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.10.0392287
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.0271858
MA0138.20.788113
MA0002.20.689262
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.12.56917
MA0154.11.49271
MA0155.10.132921
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.331229
MA0160.10.556423
MA0161.10
MA0162.10.0465447
MA0163.11.03138
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.911432
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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