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MCL coexpression mm9:369: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000160!2.51e-14!31;UBERON:0005409!4.67e-14!47;UBERON:0005172!1.49e-12!49;UBERON:0005173!1.49e-12!49;UBERON:0002417!1.49e-12!49;UBERON:0000916!1.49e-12!49;UBERON:0002365!5.11e-12!25;UBERON:0002330!5.11e-12!25;UBERON:0005177!5.15e-12!79;UBERON:0004119!1.02e-11!118;UBERON:0000925!1.02e-11!118;UBERON:0006595!1.02e-11!118;UBERON:0009854!1.36e-11!23;UBERON:0009856!1.36e-11!23;UBERON:0001007!1.80e-11!116;UBERON:0001555!1.80e-11!116;UBERON:0007026!1.80e-11!116;UBERON:0002107!3.81e-11!22;UBERON:0007499!3.81e-11!22;UBERON:0006925!3.81e-11!22;UBERON:0009497!3.81e-11!22;UBERON:0000015!3.81e-11!22;UBERON:0002423!3.81e-11!22;UBERON:0006235!3.81e-11!22;UBERON:0008835!3.81e-11!22;UBERON:0003894!3.81e-11!22;UBERON:0004161!3.81e-11!22;UBERON:0008836!3.81e-11!22;UBERON:0004921!1.26e-10!114;UBERON:0000344!8.29e-10!15;UBERON:0002100!5.76e-09!90;UBERON:0009569!7.44e-09!66;UBERON:0001242!8.99e-09!13;UBERON:0000060!8.99e-09!13;UBERON:0001262!8.99e-09!13;UBERON:0004786!8.99e-09!13;UBERON:0003104!2.85e-08!61;UBERON:0009142!2.85e-08!61;UBERON:0000466!3.09e-08!79;UBERON:0004923!2.17e-07!24;UBERON:0005256!2.47e-07!45
|ontology_enrichment_uberon=UBERON:0000160!2.51e-14!31;UBERON:0005409!4.67e-14!47;UBERON:0005172!1.49e-12!49;UBERON:0005173!1.49e-12!49;UBERON:0002417!1.49e-12!49;UBERON:0000916!1.49e-12!49;UBERON:0002365!5.11e-12!25;UBERON:0002330!5.11e-12!25;UBERON:0005177!5.15e-12!79;UBERON:0004119!1.02e-11!118;UBERON:0000925!1.02e-11!118;UBERON:0006595!1.02e-11!118;UBERON:0009854!1.36e-11!23;UBERON:0009856!1.36e-11!23;UBERON:0001007!1.80e-11!116;UBERON:0001555!1.80e-11!116;UBERON:0007026!1.80e-11!116;UBERON:0002107!3.81e-11!22;UBERON:0007499!3.81e-11!22;UBERON:0006925!3.81e-11!22;UBERON:0009497!3.81e-11!22;UBERON:0000015!3.81e-11!22;UBERON:0002423!3.81e-11!22;UBERON:0006235!3.81e-11!22;UBERON:0008835!3.81e-11!22;UBERON:0003894!3.81e-11!22;UBERON:0004161!3.81e-11!22;UBERON:0008836!3.81e-11!22;UBERON:0004921!1.26e-10!114;UBERON:0000344!8.29e-10!15;UBERON:0002100!5.76e-09!90;UBERON:0009569!7.44e-09!66;UBERON:0001242!8.99e-09!13;UBERON:0000060!8.99e-09!13;UBERON:0001262!8.99e-09!13;UBERON:0004786!8.99e-09!13;UBERON:0003104!2.85e-08!61;UBERON:0009142!2.85e-08!61;UBERON:0000466!3.09e-08!79;UBERON:0004923!2.17e-07!24;UBERON:0005256!2.47e-07!45
|tfbs_overrepresentation_for_novel_motifs=0.403818,0.534014,0.364203,0.469866,0.458154,0.164217,0.644497,0.766372,0.0267199,0.243837,0.570169,0.218542,1.12096,0.23628,0.855559,0,1.01097,0.0539173,0.225105,0.794788,0.0932143,0.362751,0.235613,0.790844,0.37554,2.03034,0.0827016,1.01147,0.566523,0.487282,0.168752,0.476579,0.0529999,0.348165,0.498491,0.56272,0.413492,0.617803,0.159542,0.304085,0.0555312,0.512679,0.186867,0.232623,0.224221,1.42394,0.323935,1.0546,0.025795,0.573736,0.374992,0.760562,0.266413,1.4683,0.619345,0.677917,0.0837141,0.209397,0.194113,0.67439,0.459084,0.777251,0.862507,0.958213,1.99405,1.03267,0.745869,1.08074,0.455021,0.938231,1.13692,0.792871,0.392313,0.650163,0.0701313,1.98208,0.34796,0.314806,0.444191,0.0954455,0.79827,1.04303,0.283653,0.0973679,0.545133,0.646822,4.74073,0.0508374,0.327889,1.23935,0.811671,0.549603,0.487824,0.0597386,1.90152,0.580811,0.248387,2.12881,0.324141,0.909992,0.0493173,0.476334,0.58753,0.375488,0.978012,0.171895,1.08837,0.546657,0.664746,1.07708,0.393011,0.58915,0.318143,0.199544,0.818358,0.20155,1.12275,0.157255,0.390716,0.0478434,0.655146,0.919978,0.258253,0.314081,0.869916,0.447391,0.233251,1.21067,0.744444,0.478953,0.572132,0.896011,0.716744,0.251791,0.838892,0.542152,1.33798,0.17313,0.792231,1.60311,1.2081,0.750296,0.267427,0.48577,0.369214,0.513419,0.326451,1.56378,0.135184,1.22075,1.43712,0.487074,0.60483,0.331339,0.251095,0.680035,0.76234,0.0699281,0.127194,0.825084,0.801233,0.544365,0.447776,0.779273,0.366469,0.245542,0.410962,0.217399,0.660742
|tfbs_overrepresentation_for_novel_motifs=0.403818,0.534014,0.364203,0.469866,0.458154,0.164217,0.644497,0.766372,0.0267199,0.243837,0.570169,0.218542,1.12096,0.23628,0.855559,0,1.01097,0.0539173,0.225105,0.794788,0.0932143,0.362751,0.235613,0.790844,0.37554,2.03034,0.0827016,1.01147,0.566523,0.487282,0.168752,0.476579,0.0529999,0.348165,0.498491,0.56272,0.413492,0.617803,0.159542,0.304085,0.0555312,0.512679,0.186867,0.232623,0.224221,1.42394,0.323935,1.0546,0.025795,0.573736,0.374992,0.760562,0.266413,1.4683,0.619345,0.677917,0.0837141,0.209397,0.194113,0.67439,0.459084,0.777251,0.862507,0.958213,1.99405,1.03267,0.745869,1.08074,0.455021,0.938231,1.13692,0.792871,0.392313,0.650163,0.0701313,1.98208,0.34796,0.314806,0.444191,0.0954455,0.79827,1.04303,0.283653,0.0973679,0.545133,0.646822,4.74073,0.0508374,0.327889,1.23935,0.811671,0.549603,0.487824,0.0597386,1.90152,0.580811,0.248387,2.12881,0.324141,0.909992,0.0493173,0.476334,0.58753,0.375488,0.978012,0.171895,1.08837,0.546657,0.664746,1.07708,0.393011,0.58915,0.318143,0.199544,0.818358,0.20155,1.12275,0.157255,0.390716,0.0478434,0.655146,0.919978,0.258253,0.314081,0.869916,0.447391,0.233251,1.21067,0.744444,0.478953,0.572132,0.896011,0.716744,0.251791,0.838892,0.542152,1.33798,0.17313,0.792231,1.60311,1.2081,0.750296,0.267427,0.48577,0.369214,0.513419,0.326451,1.56378,0.135184,1.22075,1.43712,0.487074,0.60483,0.331339,0.251095,0.680035,0.76234,0.0699281,0.127194,0.825084,0.801233,0.544365,0.447776,0.779273,0.366469,0.245542,0.410962,0.217399,0.660742
|tfbs_overrepresentation_jaspar=MA0003.1;0.722674,MA0004.1;1.46848,MA0006.1;1.2715,MA0007.1;0.145624,MA0009.1;0.499857,MA0014.1;2.81063,MA0017.1;0.074682,MA0019.1;0.344318,MA0024.1;0.461433,MA0025.1;0.712532,MA0027.1;2.09948,MA0028.1;0.877038,MA0029.1;0.442582,MA0030.1;0.448261,MA0031.1;0.417663,MA0038.1;0.256813,MA0040.1;0.510947,MA0041.1;0.109446,MA0042.1;0.102161,MA0043.1;0.586618,MA0046.1;0.531807,MA0048.1;0.918228,MA0050.1;1.61773,MA0051.1;1.34069,MA0052.1;0.518112,MA0055.1;0.358275,MA0056.1;0,MA0057.1;0.577065,MA0058.1;1.10711,MA0059.1;0.105184,MA0060.1;1.28316,MA0061.1;0.0422754,MA0063.1;0,MA0066.1;0.248543,MA0067.1;0.817149,MA0068.1;0.00634922,MA0069.1;0.518414,MA0070.1;0.509795,MA0071.1;0.532153,MA0072.1;0.502282,MA0073.1;1.43461,MA0074.1;1.18432,MA0076.1;1.00481,MA0077.1;0.48317,MA0078.1;0.289095,MA0081.1;0.37696,MA0083.1;0.585897,MA0084.1;1.1333,MA0087.1;0.546952,MA0088.1;0.376174,MA0089.1;0,MA0090.1;0.133736,MA0091.1;0.163657,MA0092.1;0.826612,MA0093.1;1.36217,MA0095.1;0,MA0098.1;0,MA0100.1;0.213782,MA0101.1;0.355777,MA0103.1;0.273906,MA0105.1;0.168725,MA0106.1;0.295186,MA0107.1;0.0769078,MA0108.2;0.363107,MA0109.1;0,MA0111.1;0.14244,MA0113.1;0.750951,MA0114.1;0.656298,MA0115.1;0.589161,MA0116.1;0.486423,MA0117.1;0.559943,MA0119.1;3.78386,MA0122.1;0.577888,MA0124.1;0.766819,MA0125.1;0.697415,MA0130.1;0,MA0131.1;0.340612,MA0132.1;0,MA0133.1;0,MA0135.1;0.619844,MA0136.1;0.236653,MA0139.1;1.50059,MA0140.1;0.2137,MA0141.1;0.301299,MA0142.1;0.40532,MA0143.1;0.285913,MA0144.1;1.03454,MA0145.1;0.876802,MA0146.1;1.02077,MA0147.1;0.708858,MA0148.1;0.496714,MA0149.1;0.113293,MA0062.2;1.22637,MA0035.2;0.620478,MA0039.2;5.43429,MA0138.2;0.334152,MA0002.2;0.10237,MA0137.2;2.10582,MA0104.2;0.826656,MA0047.2;0.256234,MA0112.2;0.0580443,MA0065.2;0.879925,MA0150.1;0.446676,MA0151.1;0,MA0152.1;0.256315,MA0153.1;0.635107,MA0154.1;1.22533,MA0155.1;0.0735373,MA0156.1;0.0836044,MA0157.1;0.378326,MA0158.1;0,MA0159.1;0.051085,MA0160.1;0.167661,MA0161.1;0,MA0162.1;0.950387,MA0163.1;0.0374936,MA0164.1;0.667063,MA0080.2;0.266721,MA0018.2;0.244112,MA0099.2;0.329046,MA0079.2;0.321474,MA0102.2;1.18455,MA0258.1;0.0367249,MA0259.1;1.47814,MA0442.1;0
}}
}}

Revision as of 11:38, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:120353209..120353235,+p1@Slc25a10
Mm9::chr11:120353243..120353263,+p3@Slc25a10
Mm9::chr11:96891239..96891311,+p1@Scrn2
Mm9::chr13:54167229..54167278,+p1@Sfxn1
Mm9::chr17:12868652..12868673,-p4@Slc22a1
Mm9::chr19:44144226..44144277,-p1@Erlin1
Mm9::chr19:44181916..44181931,-p2@Chuk
Mm9::chr1:133693960..133693995,+p1@Pm20d1
Mm9::chr1:13658820..13658853,+p1@Xkr9
Mm9::chr1:13659082..13659121,+p@chr1:13659082..13659121
+
Mm9::chr1:169280107..169280196,+p2@Aldh9a1
Mm9::chr1:169280315..169280365,+p1@Aldh9a1
Mm9::chr1:169280377..169280380,+p@chr1:169280377..169280380
+
Mm9::chr1:59030534..59030545,+p6@Stradb
Mm9::chr1:59030546..59030561,+p7@Stradb
Mm9::chr1:93339454..93339482,+p@chr1:93339454..93339482
+
Mm9::chr4:154937907..154937974,+p1@Nadk
Mm9::chr5:31223940..31223956,+p4@Khk
Mm9::chr5:31224198..31224239,+p2@Khk
Mm9::chr5:31224240..31224269,+p1@Khk
Mm9::chr6:137703123..137703129,+p2@Dera


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:0019145aminobutyraldehyde dehydrogenase activity0.0359392976497014
GO:0004139deoxyribose-phosphate aldolase activity0.0359392976497014
GO:0004454ketohexokinase activity0.0359392976497014
GO:0003951NAD+ kinase activity0.0461798253473553
GO:0030099myeloid cell differentiation0.0461798253473553
GO:0007252I-kappaB phosphorylation0.0461798253473553
GO:0008384IkappaB kinase activity0.0461798253473553
GO:0009264deoxyribonucleotide catabolic process0.0478757600170195
GO:0009437carnitine metabolic process0.0478757600170195



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
epithelial cell5.95e-0725

Uber Anatomy
Ontology termp-valuen
intestine2.51e-1431
gastrointestinal system4.67e-1447
abdomen element1.49e-1249
abdominal segment element1.49e-1249
abdominal segment of trunk1.49e-1249
abdomen1.49e-1249
exocrine gland5.11e-1225
exocrine system5.11e-1225
trunk region element5.15e-1279
endoderm-derived structure1.02e-11118
endoderm1.02e-11118
presumptive endoderm1.02e-11118
digestive tract diverticulum1.36e-1123
sac1.36e-1123
digestive system1.80e-11116
digestive tract1.80e-11116
primitive gut1.80e-11116
liver3.81e-1122
epithelial sac3.81e-1122
digestive gland3.81e-1122
epithelium of foregut-midgut junction3.81e-1122
anatomical boundary3.81e-1122
hepatobiliary system3.81e-1122
foregut-midgut junction3.81e-1122
hepatic diverticulum3.81e-1122
liver primordium3.81e-1122
septum transversum3.81e-1122
liver bud3.81e-1122
subdivision of digestive tract1.26e-10114
mucosa8.29e-1015
trunk5.76e-0990
subdivision of trunk7.44e-0966
intestinal mucosa8.99e-0913
anatomical wall8.99e-0913
wall of intestine8.99e-0913
gastrointestinal system mucosa8.99e-0913
mesenchyme2.85e-0861
entire embryonic mesenchyme2.85e-0861
immaterial anatomical entity3.09e-0879
organ component layer2.17e-0724
trunk mesenchyme2.47e-0745


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)
MA0003.10.722674
MA0004.11.46848
MA0006.11.2715
MA0007.10.145624
MA0009.10.499857
MA0014.12.81063
MA0017.10.074682
MA0019.10.344318
MA0024.10.461433
MA0025.10.712532
MA0027.12.09948
MA0028.10.877038
MA0029.10.442582
MA0030.10.448261
MA0031.10.417663
MA0038.10.256813
MA0040.10.510947
MA0041.10.109446
MA0042.10.102161
MA0043.10.586618
MA0046.10.531807
MA0048.10.918228
MA0050.11.61773
MA0051.11.34069
MA0052.10.518112
MA0055.10.358275
MA0056.10
MA0057.10.577065
MA0058.11.10711
MA0059.10.105184
MA0060.11.28316
MA0061.10.0422754
MA0063.10
MA0066.10.248543
MA0067.10.817149
MA0068.10.00634922
MA0069.10.518414
MA0070.10.509795
MA0071.10.532153
MA0072.10.502282
MA0073.11.43461
MA0074.11.18432
MA0076.11.00481
MA0077.10.48317
MA0078.10.289095
MA0081.10.37696
MA0083.10.585897
MA0084.11.1333
MA0087.10.546952
MA0088.10.376174
MA0089.10
MA0090.10.133736
MA0091.10.163657
MA0092.10.826612
MA0093.11.36217
MA0095.10
MA0098.10
MA0100.10.213782
MA0101.10.355777
MA0103.10.273906
MA0105.10.168725
MA0106.10.295186
MA0107.10.0769078
MA0108.20.363107
MA0109.10
MA0111.10.14244
MA0113.10.750951
MA0114.10.656298
MA0115.10.589161
MA0116.10.486423
MA0117.10.559943
MA0119.13.78386
MA0122.10.577888
MA0124.10.766819
MA0125.10.697415
MA0130.10
MA0131.10.340612
MA0132.10
MA0133.10
MA0135.10.619844
MA0136.10.236653
MA0139.11.50059
MA0140.10.2137
MA0141.10.301299
MA0142.10.40532
MA0143.10.285913
MA0144.11.03454
MA0145.10.876802
MA0146.11.02077
MA0147.10.708858
MA0148.10.496714
MA0149.10.113293
MA0062.21.22637
MA0035.20.620478
MA0039.25.43429
MA0138.20.334152
MA0002.20.10237
MA0137.22.10582
MA0104.20.826656
MA0047.20.256234
MA0112.20.0580443
MA0065.20.879925
MA0150.10.446676
MA0151.10
MA0152.10.256315
MA0153.10.635107
MA0154.11.22533
MA0155.10.0735373
MA0156.10.0836044
MA0157.10.378326
MA0158.10
MA0159.10.051085
MA0160.10.167661
MA0161.10
MA0162.10.950387
MA0163.10.0374936
MA0164.10.667063
MA0080.20.266721
MA0018.20.244112
MA0099.20.329046
MA0079.20.321474
MA0102.21.18455
MA0258.10.0367249
MA0259.11.47814
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:369&oldid=2573764"