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MCL coexpression mm9:509: Difference between revisions

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{{MCL_coexpression_mm9
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acid binding;0.000132674954062797;66882,73681,72567,53379,70439,67958,20823,51796,209003,320586!GO:0003723;RNA binding;0.00116200650109324;53379,20823,67958,51796,209003!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00116200650109324;66882,72567,66580,53379,20823,67958,51796,320586,24061!GO:0016070;RNA metabolic process;0.00116200650109324;66882,72567,66580,53379,67958,20823,51796,320586!GO:0006396;RNA processing;0.00217965357397562;53379,20823,67958,51796!GO:0010467;gene expression;0.00289657235911795;66882,72567,66580,53379,67958,20823,51796,320586!GO:0044237;cellular metabolic process;0.00473553114394023;66882,73681,72567,66580,53379,20823,67958,51796,228005,320586,24061!GO:0043283;biopolymer metabolic process;0.00655461103996711;66882,72567,66580,53379,20823,67958,51796,320586,24061!GO:0043170;macromolecule metabolic process;0.00767170497479986;66882,72567,66580,53379,20823,67958,51796,228005,320586,24061!GO:0044238;primary metabolic process;0.0244127424594363;66882,72567,66580,53379,20823,67958,51796,228005,320586,24061!GO:0030529;ribonucleoprotein 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|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001048!6.99e-11!134;UBERON:0000153!5.61e-10!43;UBERON:0004177!6.88e-09!29;UBERON:0005057!6.88e-09!29;UBERON:0007811!6.34e-08!36;UBERON:0001041!1.68e-07!80;UBERON:0002370!6.07e-07!23;UBERON:0000974!6.07e-07!23;UBERON:0004807!6.07e-07!23;UBERON:0005058!6.07e-07!23;UBERON:0003351!6.07e-07!23;UBERON:0009113!6.07e-07!23;UBERON:0003295!6.07e-07!23;UBERON:0009722!6.07e-07!23;UBERON:0005562!6.07e-07!23;UBERON:0007690!6.07e-07!23;UBERON:0000077!6.43e-07!35;UBERON:0000065!8.24e-07!41
|tfbs_overrepresentation_for_novel_motifs=0.6379,0.284621,0.589984,0.25808,0.123731,0.269875,1.63878,0.237242,0.251553,0.928871,0.831817,0.336042,0.876414,0.939225,0.419678,0,1.31449,0.118546,0.215337,0.465097,0.176628,0.554623,1.67324,0.122718,1.13761,0.992246,0.0554034,0.287195,2.10391,0.145734,0.275529,0.624931,0.373899,0.397142,1.34707,0.850523,0.725394,0.885722,0.662669,0.581324,0.121091,0.279796,0.145909,1.35349,0.314995,1.28656,0.457618,0.300372,0.112678,0.474834,1.28025,1.04423,0.321327,0.759566,0.776306,0.952972,0.163199,0.325117,0.190698,1.69149,0.606104,1.06252,0.26973,1.25819,0.974413,0.541429,0.908031,1.25063,0.60172,1.10561,0.555733,0.246154,2.07063,0.808562,2.07384,0.37844,0.702638,0.447339,0.590017,0.179738,0.530081,1.34858,0.411949,0.227715,1.66599,0.620777,0.0697055,0.611818,0.462057,1.41118,0.975915,0.702809,0.636995,0.127646,1.59997,0.601346,0.233568,0.639644,0.457849,0.842735,0.111186,0.624668,0.742871,0.514993,1.27935,1.39895,0.569344,0.804983,0.539826,1.60173,0.218949,0.744577,0.180573,0.841652,0.982794,0.119923,1.09124,0.26114,0.53175,0.108794,0.813766,0.484912,0.995764,0.446521,1.03573,0.593478,0.353461,0.630607,0.906557,0.129636,0.726634,0.702495,0.877862,0.375176,1.0039,0.012643,0.231086,0.280962,0.955897,1.77738,1.3796,0.91261,0.393303,0.634793,0.508066,0.766765,0.460443,1.73788,0.232952,1.86228,0.0377782,1.85187,0.761071,1.0355,1.73629,0.839715,0.405736,0.143092,0.222538,0.652913,0.96517,0.697256,0.593895,0.21719,0.50503,0.367885,0.356446,0.33468,0.559027
|tfbs_overrepresentation_jaspar=MA0003.1;0.729668,MA0004.1;0.258473,MA0006.1;0.817804,MA0007.1;1.27649,MA0009.1;0.649874,MA0014.1;0.37055,MA0017.1;0.150118,MA0019.1;1.2076,MA0024.1;0.608636,MA0025.1;0.873493,MA0027.1;2.275,MA0028.1;2.65933,MA0029.1;0.588275,MA0030.1;0.594419,MA0031.1;0.561217,MA0038.1;0.992094,MA0040.1;0.661716,MA0041.1;0.198922,MA0042.1;0.189008,MA0043.1;0.74191,MA0046.1;0.683926,MA0048.1;0.289404,MA0050.1;0.290354,MA0051.1;0.388883,MA0052.1;0.669354,MA0055.1;0.14835,MA0056.1;0,MA0057.1;0.489127,MA0058.1;0.541281,MA0059.1;0.563468,MA0060.1;1.47333,MA0061.1;1.11472,MA0063.1;0,MA0066.1;0.371389,MA0067.1;0.981551,MA0068.1;0.0266408,MA0069.1;0.669676,MA0070.1;0.660488,MA0071.1;0.289658,MA0072.1;0.652465,MA0073.1;5.04981e-06,MA0074.1;0.340281,MA0076.1;2.17293,MA0077.1;0.632005,MA0078.1;0.418168,MA0081.1;0.605506,MA0083.1;0.741151,MA0084.1;1.30392,MA0087.1;0.699999,MA0088.1;0.857785,MA0089.1;0,MA0090.1;1.2186,MA0091.1;0.269175,MA0092.1;0.231323,MA0093.1;0.444403,MA0095.1;0,MA0098.1;0,MA0100.1;0.330364,MA0101.1;1.72541,MA0103.1;0.157724,MA0105.1;0.170132,MA0106.1;0.425111,MA0107.1;1.45792,MA0108.2;0.50131,MA0109.1;0,MA0111.1;0.679612,MA0113.1;0.400008,MA0114.1;0.0981613,MA0115.1;0.744589,MA0116.1;0.131762,MA0117.1;0.713754,MA0119.1;0.200349,MA0122.1;0.732707,MA0124.1;0.929684,MA0125.1;0.857794,MA0130.1;0,MA0131.1;2.08224,MA0132.1;0,MA0133.1;0,MA0135.1;0.77683,MA0136.1;0.357464,MA0139.1;0.231431,MA0140.1;0.330266,MA0141.1;0.171891,MA0142.1;0.547747,MA0143.1;0.414534,MA0144.1;1.11784,MA0145.1;0.370377,MA0146.1;0.458458,MA0147.1;0.349075,MA0148.1;0.271704,MA0149.1;0.204102,MA0062.2;2.60889,MA0035.2;0.33429,MA0039.2;0.945584,MA0138.2;1.18323,MA0002.2;0.0664561,MA0137.2;2.21956,MA0104.2;0.930677,MA0047.2;0.380343,MA0112.2;0.918188,MA0065.2;0.190247,MA0150.1;0.246295,MA0151.1;0,MA0152.1;0.380437,MA0153.1;0.792819,MA0154.1;0.283993,MA0155.1;0.0879017,MA0156.1;0.949678,MA0157.1;0.518122,MA0158.1;0,MA0159.1;0.365914,MA0160.1;0.274172,MA0161.1;0,MA0162.1;0.353984,MA0163.1;0.18727,MA0164.1;0.357779,MA0080.2;0.153997,MA0018.2;0.959515,MA0099.2;0.463355,MA0079.2;0.133151,MA0102.2;1.35579,MA0258.1;0.301988,MA0259.1;0.678628,MA0442.1;0
}}

Latest revision as of 15:25, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:20032267..20032298,+p1@Bclaf1
Mm9::chr10:30320468..30320507,-p1@Trmt11
Mm9::chr11:83286581..83286625,+p1@Taf15
Mm9::chr16:98303146..98303177,-p1@A630089N07Rik
Mm9::chr1:58449963..58449991,+p1@Bzw1
Mm9::chr2:139996264..139996305,-p1@Esf1
Mm9::chr2:69560854..69560897,+p1@Ppig
Mm9::chr2:69699642..69699692,+p1@Ssb
Mm9::chr2:75497310..75497323,+p1@Gm11847
p1@Hnrnpa3
p1@LOC100504930
p1@LOC100505153
p1@LOC100505318
Mm9::chr4:134909041..134909072,-p1@Srrm1
Mm9::chr6:51419835..51419853,-p1@Hnrnpa2b1
p1@LOC100045191
Mm9::chr9:95412276..95412311,-p1@2610101N10Rik
Mm9::chrX:148450978..148451061,+p1@Smc1a
Mm9::chrX:46048227..46048272,+p1@Rbmx2


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:0003676nucleic acid binding0.000132674954062797
GO:0003723RNA binding0.00116200650109324
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00116200650109324
GO:0016070RNA metabolic process0.00116200650109324
GO:0006396RNA processing0.00217965357397562
GO:0010467gene expression0.00289657235911795
GO:0044237cellular metabolic process0.00473553114394023
GO:0043283biopolymer metabolic process0.00655461103996711
GO:0043170macromolecule metabolic process0.00767170497479986
GO:0044238primary metabolic process0.0244127424594363
GO:0030529ribonucleoprotein complex0.0418820546813995



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)
MA0003.10.729668
MA0004.10.258473
MA0006.10.817804
MA0007.11.27649
MA0009.10.649874
MA0014.10.37055
MA0017.10.150118
MA0019.11.2076
MA0024.10.608636
MA0025.10.873493
MA0027.12.275
MA0028.12.65933
MA0029.10.588275
MA0030.10.594419
MA0031.10.561217
MA0038.10.992094
MA0040.10.661716
MA0041.10.198922
MA0042.10.189008
MA0043.10.74191
MA0046.10.683926
MA0048.10.289404
MA0050.10.290354
MA0051.10.388883
MA0052.10.669354
MA0055.10.14835
MA0056.10
MA0057.10.489127
MA0058.10.541281
MA0059.10.563468
MA0060.11.47333
MA0061.11.11472
MA0063.10
MA0066.10.371389
MA0067.10.981551
MA0068.10.0266408
MA0069.10.669676
MA0070.10.660488
MA0071.10.289658
MA0072.10.652465
MA0073.15.04981e-06
MA0074.10.340281
MA0076.12.17293
MA0077.10.632005
MA0078.10.418168
MA0081.10.605506
MA0083.10.741151
MA0084.11.30392
MA0087.10.699999
MA0088.10.857785
MA0089.10
MA0090.11.2186
MA0091.10.269175
MA0092.10.231323
MA0093.10.444403
MA0095.10
MA0098.10
MA0100.10.330364
MA0101.11.72541
MA0103.10.157724
MA0105.10.170132
MA0106.10.425111
MA0107.11.45792
MA0108.20.50131
MA0109.10
MA0111.10.679612
MA0113.10.400008
MA0114.10.0981613
MA0115.10.744589
MA0116.10.131762
MA0117.10.713754
MA0119.10.200349
MA0122.10.732707
MA0124.10.929684
MA0125.10.857794
MA0130.10
MA0131.12.08224
MA0132.10
MA0133.10
MA0135.10.77683
MA0136.10.357464
MA0139.10.231431
MA0140.10.330266
MA0141.10.171891
MA0142.10.547747
MA0143.10.414534
MA0144.11.11784
MA0145.10.370377
MA0146.10.458458
MA0147.10.349075
MA0148.10.271704
MA0149.10.204102
MA0062.22.60889
MA0035.20.33429
MA0039.20.945584
MA0138.21.18323
MA0002.20.0664561
MA0137.22.21956
MA0104.20.930677
MA0047.20.380343
MA0112.20.918188
MA0065.20.190247
MA0150.10.246295
MA0151.10
MA0152.10.380437
MA0153.10.792819
MA0154.10.283993
MA0155.10.0879017
MA0156.10.949678
MA0157.10.518122
MA0158.10
MA0159.10.365914
MA0160.10.274172
MA0161.10
MA0162.10.353984
MA0163.10.18727
MA0164.10.357779
MA0080.20.153997
MA0018.20.959515
MA0099.20.463355
MA0079.20.133151
MA0102.21.35579
MA0258.10.301988
MA0259.10.678628
MA0442.10
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