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MCL coexpression mm9:341: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002100!4.96e-13!90;UBERON:0000466!8.07e-11!79;UBERON:0005177!8.50e-11!79;UBERON:0005256!9.96e-11!45;UBERON:0003104!3.48e-09!61;UBERON:0009142!3.48e-09!61;UBERON:0002365!4.39e-09!25;UBERON:0002330!4.39e-09!25;UBERON:0004119!1.23e-08!118;UBERON:0000925!1.23e-08!118;UBERON:0006595!1.23e-08!118;UBERON:0001264!1.53e-08!12;UBERON:0001007!6.60e-08!116;UBERON:0001555!6.60e-08!116;UBERON:0007026!6.60e-08!116;UBERON:0009854!1.31e-07!23;UBERON:0009856!1.31e-07!23;UBERON:0000160!1.84e-07!31;UBERON:0005409!2.08e-07!47;UBERON:0002107!2.36e-07!22;UBERON:0007499!2.36e-07!22;UBERON:0006925!2.36e-07!22;UBERON:0009497!2.36e-07!22;UBERON:0000015!2.36e-07!22;UBERON:0002423!2.36e-07!22;UBERON:0006235!2.36e-07!22;UBERON:0008835!2.36e-07!22;UBERON:0003894!2.36e-07!22;UBERON:0004161!2.36e-07!22;UBERON:0008836!2.36e-07!22;UBERON:0004921!2.44e-07!114
|ontology_enrichment_uberon=UBERON:0002100!4.96e-13!90;UBERON:0000466!8.07e-11!79;UBERON:0005177!8.50e-11!79;UBERON:0005256!9.96e-11!45;UBERON:0003104!3.48e-09!61;UBERON:0009142!3.48e-09!61;UBERON:0002365!4.39e-09!25;UBERON:0002330!4.39e-09!25;UBERON:0004119!1.23e-08!118;UBERON:0000925!1.23e-08!118;UBERON:0006595!1.23e-08!118;UBERON:0001264!1.53e-08!12;UBERON:0001007!6.60e-08!116;UBERON:0001555!6.60e-08!116;UBERON:0007026!6.60e-08!116;UBERON:0009854!1.31e-07!23;UBERON:0009856!1.31e-07!23;UBERON:0000160!1.84e-07!31;UBERON:0005409!2.08e-07!47;UBERON:0002107!2.36e-07!22;UBERON:0007499!2.36e-07!22;UBERON:0006925!2.36e-07!22;UBERON:0009497!2.36e-07!22;UBERON:0000015!2.36e-07!22;UBERON:0002423!2.36e-07!22;UBERON:0006235!2.36e-07!22;UBERON:0008835!2.36e-07!22;UBERON:0003894!2.36e-07!22;UBERON:0004161!2.36e-07!22;UBERON:0008836!2.36e-07!22;UBERON:0004921!2.44e-07!114
|tfbs_overrepresentation_for_novel_motifs=0.724006,0.100083,0.658724,0.420313,0.175792,0.1439,0.588187,0.208045,0.22468,2.05171,0.516461,0.195161,0.660997,1.14547,0.0526745,0,0.945709,0.0434258,0.359583,0.146315,0.269699,0.0815567,1.7887,0.04574,0.677459,0.23172,0.169642,0.924618,1.29406,0.228725,0.148148,0.444875,0.374265,0.748679,0.759337,0.201664,0.636935,1.06955,0.0323669,1.53283,0.0448336,0.46125,0.139408,0.0534679,1.88647,1.30506,0.296243,0.500261,0.0457624,0.234067,0.345732,0.251452,0.595411,0.569522,0.585246,0.217101,0.0698305,1.04484,0.803833,0.617128,0.427748,0.717069,0.0998898,0.33663,0.639273,1.71984,0.710311,1.04299,0.423773,0.901202,0.612461,0.0194586,3.13863,0.615662,1.08627,1.01146,0.139945,0.287424,0.413185,0.0804202,0.220498,0.977212,0.25741,0.197096,0.512157,4.75232,0.10317,0.22906,0.300065,1.20106,0.775527,0.516553,0.455893,0.0485175,0.876965,0.110313,0.0798092,0.458317,0.296442,1.39155,0.154241,0.444635,0.553884,0.346214,0.34536,0.899914,1.02179,0.164518,0.995592,1.44667,0.106955,0.555481,0.0809652,0.524791,0.78216,0.383607,1.17366,0.426065,0.361025,0.150171,0.620583,0.319864,0.233041,0.286725,0.833329,0.416312,0.209158,0.450055,0.7089,0.415597,0.53872,0.130779,0.68148,0.226858,0.802533,0.435267,0.369821,0.152256,0.75625,1.56412,1.1699,0.714696,0.241832,0.45388,0.340119,0.461959,0.298675,1.52485,0.116859,1.09044,0.642185,4.15062,0.570933,0.517221,1.19997,0.645175,1.29828,0.459789,0.109473,0.369409,0.765175,0.511402,0.416689,1.15652,0.337452,0.220885,0.152947,0.194075,0.0576766
|tfbs_overrepresentation_for_novel_motifs=0.724006,0.100083,0.658724,0.420313,0.175792,0.1439,0.588187,0.208045,0.22468,2.05171,0.516461,0.195161,0.660997,1.14547,0.0526745,0,0.945709,0.0434258,0.359583,0.146315,0.269699,0.0815567,1.7887,0.04574,0.677459,0.23172,0.169642,0.924618,1.29406,0.228725,0.148148,0.444875,0.374265,0.748679,0.759337,0.201664,0.636935,1.06955,0.0323669,1.53283,0.0448336,0.46125,0.139408,0.0534679,1.88647,1.30506,0.296243,0.500261,0.0457624,0.234067,0.345732,0.251452,0.595411,0.569522,0.585246,0.217101,0.0698305,1.04484,0.803833,0.617128,0.427748,0.717069,0.0998898,0.33663,0.639273,1.71984,0.710311,1.04299,0.423773,0.901202,0.612461,0.0194586,3.13863,0.615662,1.08627,1.01146,0.139945,0.287424,0.413185,0.0804202,0.220498,0.977212,0.25741,0.197096,0.512157,4.75232,0.10317,0.22906,0.300065,1.20106,0.775527,0.516553,0.455893,0.0485175,0.876965,0.110313,0.0798092,0.458317,0.296442,1.39155,0.154241,0.444635,0.553884,0.346214,0.34536,0.899914,1.02179,0.164518,0.995592,1.44667,0.106955,0.555481,0.0809652,0.524791,0.78216,0.383607,1.17366,0.426065,0.361025,0.150171,0.620583,0.319864,0.233041,0.286725,0.833329,0.416312,0.209158,0.450055,0.7089,0.415597,0.53872,0.130779,0.68148,0.226858,0.802533,0.435267,0.369821,0.152256,0.75625,1.56412,1.1699,0.714696,0.241832,0.45388,0.340119,0.461959,0.298675,1.52485,0.116859,1.09044,0.642185,4.15062,0.570933,0.517221,1.19997,0.645175,1.29828,0.459789,0.109473,0.369409,0.765175,0.511402,0.416689,1.15652,0.337452,0.220885,0.152947,0.194075,0.0576766
|tfbs_overrepresentation_jaspar=MA0003.1;3.56502,MA0004.1;0.135415,MA0006.1;1.13909,MA0007.1;0.39838,MA0009.1;0.467692,MA0014.1;0.824925,MA0017.1;0.482805,MA0019.1;0.315968,MA0024.1;1.92691,MA0025.1;0.677312,MA0027.1;2.06014,MA0028.1;4.83438,MA0029.1;0.411611,MA0030.1;0.417163,MA0031.1;0.387282,MA0038.1;0.65478,MA0040.1;0.478574,MA0041.1;0.0931678,MA0042.1;0.0865208,MA0043.1;0.552986,MA0046.1;0.499059,MA0048.1;1.06913,MA0050.1;0.481243,MA0051.1;1.24551,MA0052.1;0.485607,MA0055.1;0.268845,MA0056.1;0,MA0057.1;0.0707752,MA0058.1;0.0831725,MA0059.1;0.299763,MA0060.1;3.07493,MA0061.1;0.31638,MA0063.1;0,MA0066.1;0.223752,MA0067.1;0.78096,MA0068.1;0.0244109,MA0069.1;2.11422,MA0070.1;0.477443,MA0071.1;0.158881,MA0072.1;0.470071,MA0073.1;5.77707e-05,MA0074.1;0.19855,MA0076.1;2.45883,MA0077.1;0.451332,MA0078.1;0.262644,MA0081.1;0.332119,MA0083.1;0.552276,MA0084.1;1.09535,MA0087.1;0.513946,MA0088.1;1.18656,MA0089.1;0,MA0090.1;0.115519,MA0091.1;0.143375,MA0092.1;0.115696,MA0093.1;0.0584444,MA0095.1;0,MA0098.1;0,MA0100.1;0.190641,MA0101.1;1.58746,MA0103.1;0.235667,MA0105.1;0.27408,MA0106.1;0.740097,MA0107.1;1.2849,MA0108.2;0.334189,MA0109.1;0,MA0111.1;0.123589,MA0113.1;0.247414,MA0114.1;0.899025,MA0115.1;0.555491,MA0116.1;2.12475,MA0117.1;1.30637,MA0119.1;0.312977,MA0122.1;0.544387,MA0124.1;0.731064,MA0125.1;0.662359,MA0130.1;0,MA0131.1;0.839673,MA0132.1;0,MA0133.1;0,MA0135.1;0.585739,MA0136.1;0.2124,MA0139.1;0.957166,MA0140.1;0.190563,MA0141.1;0.0753473,MA0142.1;0.979417,MA0143.1;0.259584,MA0144.1;0.912796,MA0145.1;0.0996878,MA0146.1;1.02174,MA0147.1;0.618817,MA0148.1;0.145271,MA0149.1;0.0966891,MA0062.2;8.45539,MA0035.2;0.193764,MA0039.2;0.54209,MA0138.2;0.306125,MA0002.2;0.398735,MA0137.2;0.93004,MA0104.2;0.716451,MA0047.2;0.231108,MA0112.2;0.0410681,MA0065.2;0.0413739,MA0150.1;0.126483,MA0151.1;0,MA0152.1;0.231185,MA0153.1;0.600798,MA0154.1;0.0811709,MA0155.1;0.0533867,MA0156.1;0.525036,MA0157.1;0.348973,MA0158.1;0,MA0159.1;0.0409628,MA0160.1;0.450623,MA0161.1;0,MA0162.1;2.73975,MA0163.1;0.161704,MA0164.1;0.61003,MA0080.2;0.0641137,MA0018.2;0.626252,MA0099.2;0.301184,MA0079.2;0.153696,MA0102.2;1.14642,MA0258.1;0.0286458,MA0259.1;1.77851,MA0442.1;0
}}
}}

Revision as of 11:35, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:116135416..116135452,-p1@Srp68
Mm9::chr12:60230744..60230805,+p3@Ctage5
Mm9::chr13:73741583..73741594,+p3@Clptm1l
Mm9::chr16:11134590..11134605,-p4@Txndc11
Mm9::chr16:38562934..38562974,+p1@Tmem39a
Mm9::chr1:13579798..13579985,-p1@Tram1
Mm9::chr1:75432577..75432588,+p2@Gmppa
Mm9::chr2:143836938..143836972,-p1@Rrbp1
Mm9::chr3:115710258..115710314,-p1@Slc30a7
Mm9::chr3:58329035..58329050,+p@chr3:58329035..58329050
+
Mm9::chr3:58329639..58329650,-p3@Serp1
Mm9::chr3:58329664..58329683,-p1@Serp1
Mm9::chr3:58329690..58329710,-p2@Serp1
Mm9::chr5:115608144..115608168,-p1@Mlec
Mm9::chr5:130698198..130698260,+p1@0610007L01Rik
Mm9::chr5:31171996..31172037,+p1@Tmem214
Mm9::chr6:88468729..88468751,-p2@Sec61a1
Mm9::chr8:26830514..26830525,+p3@Ppapdc1b
Mm9::chr8:26830526..26830571,+p1@Ppapdc1b
Mm9::chr9:103965379..103965476,-p1@Uba5
Mm9::chr9:35018762..35018809,+p1@Srpr
Mm9::chr9:35018814..35018833,+p2@Srpr
Mm9::chr9:65908002..65908080,+p1@Ppib


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:0048500signal recognition particle0.00597732630773684
GO:0005786signal recognition particle, endoplasmic reticulum targeting0.00597732630773684
GO:0005783endoplasmic reticulum0.00597732630773684
GO:0065002intracellular protein transport across a membrane0.0260779050019175
GO:0005047signal recognition particle binding0.0260779050019175
GO:0005789endoplasmic reticulum membrane0.0315120351101235
GO:0042175nuclear envelope-endoplasmic reticulum network0.0315120351101235
GO:0005785signal recognition particle receptor complex0.0315120351101235
GO:0044432endoplasmic reticulum part0.0315120351101235
GO:0006886intracellular protein transport0.0400770095428246
GO:00083127S RNA binding0.0400770095428246
GO:0005791rough endoplasmic reticulum0.0400770095428246
GO:0030867rough endoplasmic reticulum membrane0.0400770095428246



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
trunk4.96e-1390
immaterial anatomical entity8.07e-1179
trunk region element8.50e-1179
trunk mesenchyme9.96e-1145
mesenchyme3.48e-0961
entire embryonic mesenchyme3.48e-0961
exocrine gland4.39e-0925
exocrine system4.39e-0925
endoderm-derived structure1.23e-08118
endoderm1.23e-08118
presumptive endoderm1.23e-08118
pancreas1.53e-0812
digestive system6.60e-08116
digestive tract6.60e-08116
primitive gut6.60e-08116
digestive tract diverticulum1.31e-0723
sac1.31e-0723
intestine1.84e-0731
gastrointestinal system2.08e-0747
liver2.36e-0722
epithelial sac2.36e-0722
digestive gland2.36e-0722
epithelium of foregut-midgut junction2.36e-0722
anatomical boundary2.36e-0722
hepatobiliary system2.36e-0722
foregut-midgut junction2.36e-0722
hepatic diverticulum2.36e-0722
liver primordium2.36e-0722
septum transversum2.36e-0722
liver bud2.36e-0722
subdivision of digestive tract2.44e-07114


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)
MA0003.13.56502
MA0004.10.135415
MA0006.11.13909
MA0007.10.39838
MA0009.10.467692
MA0014.10.824925
MA0017.10.482805
MA0019.10.315968
MA0024.11.92691
MA0025.10.677312
MA0027.12.06014
MA0028.14.83438
MA0029.10.411611
MA0030.10.417163
MA0031.10.387282
MA0038.10.65478
MA0040.10.478574
MA0041.10.0931678
MA0042.10.0865208
MA0043.10.552986
MA0046.10.499059
MA0048.11.06913
MA0050.10.481243
MA0051.11.24551
MA0052.10.485607
MA0055.10.268845
MA0056.10
MA0057.10.0707752
MA0058.10.0831725
MA0059.10.299763
MA0060.13.07493
MA0061.10.31638
MA0063.10
MA0066.10.223752
MA0067.10.78096
MA0068.10.0244109
MA0069.12.11422
MA0070.10.477443
MA0071.10.158881
MA0072.10.470071
MA0073.15.77707e-05
MA0074.10.19855
MA0076.12.45883
MA0077.10.451332
MA0078.10.262644
MA0081.10.332119
MA0083.10.552276
MA0084.11.09535
MA0087.10.513946
MA0088.11.18656
MA0089.10
MA0090.10.115519
MA0091.10.143375
MA0092.10.115696
MA0093.10.0584444
MA0095.10
MA0098.10
MA0100.10.190641
MA0101.11.58746
MA0103.10.235667
MA0105.10.27408
MA0106.10.740097
MA0107.11.2849
MA0108.20.334189
MA0109.10
MA0111.10.123589
MA0113.10.247414
MA0114.10.899025
MA0115.10.555491
MA0116.12.12475
MA0117.11.30637
MA0119.10.312977
MA0122.10.544387
MA0124.10.731064
MA0125.10.662359
MA0130.10
MA0131.10.839673
MA0132.10
MA0133.10
MA0135.10.585739
MA0136.10.2124
MA0139.10.957166
MA0140.10.190563
MA0141.10.0753473
MA0142.10.979417
MA0143.10.259584
MA0144.10.912796
MA0145.10.0996878
MA0146.11.02174
MA0147.10.618817
MA0148.10.145271
MA0149.10.0966891
MA0062.28.45539
MA0035.20.193764
MA0039.20.54209
MA0138.20.306125
MA0002.20.398735
MA0137.20.93004
MA0104.20.716451
MA0047.20.231108
MA0112.20.0410681
MA0065.20.0413739
MA0150.10.126483
MA0151.10
MA0152.10.231185
MA0153.10.600798
MA0154.10.0811709
MA0155.10.0533867
MA0156.10.525036
MA0157.10.348973
MA0158.10
MA0159.10.0409628
MA0160.10.450623
MA0161.10
MA0162.12.73975
MA0163.10.161704
MA0164.10.61003
MA0080.20.0641137
MA0018.20.626252
MA0099.20.301184
MA0079.20.153696
MA0102.21.14642
MA0258.10.0286458
MA0259.11.77851
MA0442.10
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