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MCL coexpression mm9:761: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002107!4.72e-25!22;UBERON:0007499!4.72e-25!22;UBERON:0006925!4.72e-25!22;UBERON:0009497!4.72e-25!22;UBERON:0000015!4.72e-25!22;UBERON:0002423!4.72e-25!22;UBERON:0006235!4.72e-25!22;UBERON:0008835!4.72e-25!22;UBERON:0003894!4.72e-25!22;UBERON:0004161!4.72e-25!22;UBERON:0008836!4.72e-25!22;UBERON:0009854!5.92e-24!23;UBERON:0009856!5.92e-24!23;UBERON:0002365!5.10e-22!25;UBERON:0002330!5.10e-22!25;UBERON:0005256!4.34e-12!45;UBERON:0003914!1.47e-11!47;UBERON:0005172!4.54e-11!49;UBERON:0005173!4.54e-11!49;UBERON:0002417!4.54e-11!49;UBERON:0000916!4.54e-11!49;UBERON:0003929!8.15e-10!55;UBERON:0002368!5.85e-09!60;UBERON:0003104!8.35e-09!61;UBERON:0009142!8.35e-09!61;UBERON:0002530!3.11e-08!65;UBERON:0000490!4.22e-08!66;UBERON:0009569!4.22e-08!66;UBERON:0005911!9.99e-08!69;UBERON:0000949!2.20e-07!72
|ontology_enrichment_uberon=UBERON:0002107!4.72e-25!22;UBERON:0007499!4.72e-25!22;UBERON:0006925!4.72e-25!22;UBERON:0009497!4.72e-25!22;UBERON:0000015!4.72e-25!22;UBERON:0002423!4.72e-25!22;UBERON:0006235!4.72e-25!22;UBERON:0008835!4.72e-25!22;UBERON:0003894!4.72e-25!22;UBERON:0004161!4.72e-25!22;UBERON:0008836!4.72e-25!22;UBERON:0009854!5.92e-24!23;UBERON:0009856!5.92e-24!23;UBERON:0002365!5.10e-22!25;UBERON:0002330!5.10e-22!25;UBERON:0005256!4.34e-12!45;UBERON:0003914!1.47e-11!47;UBERON:0005172!4.54e-11!49;UBERON:0005173!4.54e-11!49;UBERON:0002417!4.54e-11!49;UBERON:0000916!4.54e-11!49;UBERON:0003929!8.15e-10!55;UBERON:0002368!5.85e-09!60;UBERON:0003104!8.35e-09!61;UBERON:0009142!8.35e-09!61;UBERON:0002530!3.11e-08!65;UBERON:0000490!4.22e-08!66;UBERON:0009569!4.22e-08!66;UBERON:0005911!9.99e-08!69;UBERON:0000949!2.20e-07!72
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.227469,0.330161,0.394491,0.227651,0.40827,0.495658,0.448965,0.468136,0.133458,0.453212,0.484001,0.449446,0.507558,0.680035,0,0.696644,0.22065,0.134657,0.0703872,0.296085,0.403891,0.50668,1.20034,0.337218,0.534339,0.402559,0.428336,0.268347,0.0963992,0.414842,0.796599,0.218674,0.364174,0.242923,0.482999,0.210533,0.480503,0.559915,0.167387,0.637027,0.419787,0.371854,0.684206,0.317317,0.383899,0.618203,0.443479,0.904531,0.271021,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,1.39791,0.471658,0.12126,0.512521,0.776777,0.569793,0.492158,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.0512949,0.987652,0.116281,0.107966,0.735293,0.607043,0.759798,0.81171,0.152219,0.713779,1.39458,0.858535,0.873141,0.0176817,0.0211263,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.657661,0.188213,0.515495,0.871972,0.812053,0.618454,0.585565,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,1.11973,0.30446,0.297733,0.919252,0.921485,0.301014,0.458194,1.16629,0.633313,0.0259088,0.398075,0.697928,0.207304,0.993019,1.56109,0.536114,0.606154,1.22022,0.763454,1.25707,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,0.951467,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.098204,0.041769,0.938577,0.178329,0.526881,1.01974,0.561556,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,0.914544,0.669337,0.519673,0.209556,0.482466,0.00844742
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.227469,0.330161,0.394491,0.227651,0.40827,0.495658,0.448965,0.468136,0.133458,0.453212,0.484001,0.449446,0.507558,0.680035,0,0.696644,0.22065,0.134657,0.0703872,0.296085,0.403891,0.50668,1.20034,0.337218,0.534339,0.402559,0.428336,0.268347,0.0963992,0.414842,0.796599,0.218674,0.364174,0.242923,0.482999,0.210533,0.480503,0.559915,0.167387,0.637027,0.419787,0.371854,0.684206,0.317317,0.383899,0.618203,0.443479,0.904531,0.271021,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,1.39791,0.471658,0.12126,0.512521,0.776777,0.569793,0.492158,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.0512949,0.987652,0.116281,0.107966,0.735293,0.607043,0.759798,0.81171,0.152219,0.713779,1.39458,0.858535,0.873141,0.0176817,0.0211263,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.657661,0.188213,0.515495,0.871972,0.812053,0.618454,0.585565,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,1.11973,0.30446,0.297733,0.919252,0.921485,0.301014,0.458194,1.16629,0.633313,0.0259088,0.398075,0.697928,0.207304,0.993019,1.56109,0.536114,0.606154,1.22022,0.763454,1.25707,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,0.951467,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.098204,0.041769,0.938577,0.178329,0.526881,1.01974,0.561556,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,0.914544,0.669337,0.519673,0.209556,0.482466,0.00844742
|tfbs_overrepresentation_jaspar=MA0003.1;0.00143485,MA0004.1;0.394951,MA0006.1;0.238555,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.00813637,MA0017.1;0.726051,MA0019.1;1.551,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.24786,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.865043,MA0042.1;0.837668,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.0824771,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.692644,MA0056.1;0,MA0057.1;0.0745664,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.9744,MA0061.1;0.194456,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.077274,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;2.9934e-06,MA0074.1;1.22546,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.0492918,MA0089.1;0,MA0090.1;0.362551,MA0091.1;1.04993,MA0092.1;0.362847,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.109964,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;1.59789,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.19245,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.143341,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.0543321,MA0146.1;0.0548413,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;0.113962,MA0035.2;1.21101,MA0039.2;0.000502396,MA0138.2;0.630612,MA0002.2;0.447007,MA0137.2;0.287486,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;0.200175,MA0065.2;0.44341,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.276788,MA0155.1;0.0631765,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.0143037,MA0163.1;0.0600297,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;2.50341e-07,MA0102.2;1.5442,MA0258.1;0.533988,MA0259.1;0.196451,MA0442.1;0
}}
}}

Revision as of 12:16, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:24635378..24635387,-p@chr10:24635378..24635387
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Mm9::chr11:54937465..54937483,-p@chr11:54937465..54937483
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Mm9::chr12:105274041..105274062,-p@chr12:105274041..105274062
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Mm9::chr12:105576582..105576626,+p1@Serpina3k
Mm9::chr13:64208454..64208487,-p@chr13:64208454..64208487
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Mm9::chr1:90003409..90003415,+p2@Ugt1a6b
Mm9::chr4:60434820..60434827,-p1@Mup12
p1@Mup16
p1@Mup17
p1@Mup19
p1@Mup8
p1@Mup9
Mm9::chr7:74792456..74792469,+p7@Ttc23
Mm9::chr9:82994262..82994284,+p@chr9:82994262..82994284
+


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

no results for this coexpression

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
metabolising cell8.20e-295
endopolyploid cell8.20e-295
parenchymal cell8.20e-295
polyploid cell8.20e-295
hepatocyte8.20e-295
fibroblast6.88e-101
hepatic stellate cell6.88e-101
endodermal cell1.78e-0720

Uber Anatomy
Ontology termp-valuen
liver4.72e-2522
epithelial sac4.72e-2522
digestive gland4.72e-2522
epithelium of foregut-midgut junction4.72e-2522
anatomical boundary4.72e-2522
hepatobiliary system4.72e-2522
foregut-midgut junction4.72e-2522
hepatic diverticulum4.72e-2522
liver primordium4.72e-2522
septum transversum4.72e-2522
liver bud4.72e-2522
digestive tract diverticulum5.92e-2423
sac5.92e-2423
exocrine gland5.10e-2225
exocrine system5.10e-2225
trunk mesenchyme4.34e-1245
epithelial tube1.47e-1147
abdomen element4.54e-1149
abdominal segment element4.54e-1149
abdominal segment of trunk4.54e-1149
abdomen4.54e-1149
gut epithelium8.15e-1055
endocrine gland5.85e-0960
mesenchyme8.35e-0961
entire embryonic mesenchyme8.35e-0961
gland3.11e-0865
unilaminar epithelium4.22e-0866
subdivision of trunk4.22e-0866
endo-epithelium9.99e-0869
endocrine system2.20e-0772


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)
MA0003.10.00143485
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.00813637
MA0017.10.726051
MA0019.11.551
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.865043
MA0042.10.837668
MA0043.10.918718
MA0046.10.858391
MA0048.10.0824771
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.692644
MA0056.10
MA0057.10.0745664
MA0058.10.305206
MA0059.10.316585
MA0060.10.9744
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.12.9934e-06
MA0074.11.22546
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.0492918
MA0089.10
MA0090.10.362551
MA0091.11.04993
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.21.59789
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.0543321
MA0146.10.0548413
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.20.113962
MA0035.21.21101
MA0039.20.000502396
MA0138.20.630612
MA0002.20.447007
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.20.200175
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.276788
MA0155.10.0631765
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0143037
MA0163.10.0600297
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.22.50341e-07
MA0102.21.5442
MA0258.10.533988
MA0259.10.196451
MA0442.10
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