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MCL coexpression mm9:211: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000181!1.20e-08!5;CL:0000417!1.20e-08!5;CL:0000668!1.20e-08!5;CL:0000412!1.20e-08!5;CL:0000182!1.20e-08!5
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002107!3.44e-29!22;UBERON:0007499!3.44e-29!22;UBERON:0006925!3.44e-29!22;UBERON:0009497!3.44e-29!22;UBERON:0000015!3.44e-29!22;UBERON:0002423!3.44e-29!22;UBERON:0006235!3.44e-29!22;UBERON:0008835!3.44e-29!22;UBERON:0003894!3.44e-29!22;UBERON:0004161!3.44e-29!22;UBERON:0008836!3.44e-29!22;UBERON:0009854!1.00e-27!23;UBERON:0009856!1.00e-27!23;UBERON:0002365!3.76e-25!25;UBERON:0002330!3.76e-25!25;UBERON:0005172!8.79e-17!49;UBERON:0005173!8.79e-17!49;UBERON:0002417!8.79e-17!49;UBERON:0000916!8.79e-17!49;UBERON:0003104!1.90e-12!61;UBERON:0009142!1.90e-12!61;UBERON:0005256!4.96e-12!45;UBERON:0003914!2.44e-11!47;UBERON:0009569!4.11e-11!66;UBERON:0003929!4.42e-09!55;UBERON:0005177!1.89e-08!79;UBERON:0002368!5.53e-08!60;UBERON:0004921!5.83e-08!114;UBERON:0001007!1.02e-07!116;UBERON:0001555!1.02e-07!116;UBERON:0007026!1.02e-07!116;UBERON:0004119!1.74e-07!118;UBERON:0000925!1.74e-07!118;UBERON:0006595!1.74e-07!118;UBERON:0002530!4.63e-07!65;UBERON:0000490!6.80e-07!66;UBERON:0002100!8.12e-07!90
|tfbs_overrepresentation_for_novel_motifs=0.515529,0.00410746,0.728967,0.349251,0.583983,0.375236,0.260823,0.823006,0.447161,0.00651839,0.058307,0.0703742,0.824565,0.0803677,0.417765,0,0.181863,1.10569,0.0219362,0.00882429,0.602659,0.285306,0.274124,0.83903,0.101074,0.0925036,0.322089,0.414175,0.295887,0.0229187,0.0448989,0.24825,0.18985,0.256257,0.040001,0.00119992,0.00451793,0.520947,0.431027,0.0417929,0.200539,0.17646,0.945329,0.658424,0.137084,0.329715,0.135497,0.0547326,0.562277,0.0551802,0.171222,0.105162,0.400161,0.352629,0.366252,0.0834375,1.15223,0.232739,0.0954774,0.281271,0.234502,0.109786,0.0959606,0.164496,0.297184,1.05559,0.477375,0.788774,0.654013,0.653981,0.0824089,1.13178,0.00934995,1.01803,0.000428747,0.0109354,0.0811141,0.405602,0.222945,0.190275,0.0797817,0.1927,0.715974,0.241579,0.303733,1.47216e-06,7.97601,0.0229891,0.138179,0.941399,0.536923,0.307432,1.31685,0.386793,0.0581172,0.358256,0.39942,0.259153,0.135636,0.0732502,0.174367,0.248056,0.339171,0.17158,0.509637,0.176029,0.208361,0.19722,0.0766307,0.0720256,0.109842,0.340541,0.620554,0.0601818,1.34096,0.0910418,0.00312853,0.355948,1.02955,0.307968,0.397177,0.152285,0.642404,0.404363,0.590426,0.225416,0.964938,0.25244,1.1983,0.22387,0.326211,0.336418,0.451368,0.30026,0.561842,1.05685,0.854146,0.707421,0.519224,2.88875,0.911155,0.481349,0.668927,0.255543,0.167066,2.60525,0.425589,1.25879,0.124145,0.0335534,0.0241889,4.78781e-06,0.353849,0.118078,0.0890431,0.418931,1.15602,1.34182,3.77663,0.0295616,0.527409,0.303098,0.225714,0.262999,0.495286,0.290114,0.1724,0.897275,0.000716212
|tfbs_overrepresentation_jaspar=MA0003.1;9.25704e-08,MA0004.1;0.0386778,MA0006.1;0.0378784,MA0007.1;0.0345391,MA0009.1;2.08166,MA0014.1;3.13941e-06,MA0017.1;0.0502375,MA0019.1;0.149481,MA0024.1;0.236337,MA0025.1;0.447626,MA0027.1;1.79005,MA0028.1;0.0424766,MA0029.1;1.84453,MA0030.1;1.19958,MA0031.1;0.586395,MA0038.1;0.638245,MA0040.1;2.12744,MA0041.1;0.226681,MA0042.1;0.0815934,MA0043.1;0.338401,MA0046.1;0.292762,MA0048.1;0.0144083,MA0050.1;0.189111,MA0051.1;0.3196,MA0052.1;0.281576,MA0055.1;0.493774,MA0056.1;0,MA0057.1;0.0589243,MA0058.1;0.0168932,MA0059.1;0.0190891,MA0060.1;0.0126569,MA0061.1;0.270678,MA0063.1;0,MA0066.1;1.03005,MA0067.1;0.541925,MA0068.1;0.0642225,MA0069.1;0.281822,MA0070.1;2.12269,MA0071.1;0.737734,MA0072.1;0.268765,MA0073.1;0.00526376,MA0074.1;0.917391,MA0076.1;0.0604222,MA0077.1;0.253476,MA0078.1;0.362007,MA0081.1;0.101777,MA0083.1;0.337793,MA0084.1;0.839097,MA0087.1;0.305237,MA0088.1;0.0203405,MA0089.1;0,MA0090.1;0.122189,MA0091.1;0.164036,MA0092.1;0.538284,MA0093.1;0.00911688,MA0095.1;0,MA0098.1;0,MA0100.1;0.23957,MA0101.1;0.0914866,MA0103.1;0.304736,MA0105.1;0.0116036,MA0106.1;0.116464,MA0107.1;0.143581,MA0108.2;0.489376,MA0109.1;0,MA0111.1;0.134063,MA0113.1;0.685781,MA0114.1;0.265007,MA0115.1;0.34055,MA0116.1;0.229776,MA0117.1;0.316023,MA0119.1;0.229463,MA0122.1;0.881488,MA0124.1;1.24138,MA0125.1;0.434239,MA0130.1;0,MA0131.1;0.450081,MA0132.1;0,MA0133.1;0,MA0135.1;0.366681,MA0136.1;0.27579,MA0139.1;0.393824,MA0140.1;0.514563,MA0141.1;0.0670014,MA0142.1;0.564251,MA0143.1;0.356668,MA0144.1;0.272495,MA0145.1;0.159807,MA0146.1;5.2053e-05,MA0147.1;0.00414162,MA0148.1;0.166966,MA0149.1;0.0218907,MA0062.2;0.0130139,MA0035.2;0.895877,MA0039.2;2.07995e-10,MA0138.2;0.142458,MA0002.2;0.59228,MA0137.2;0.571772,MA0104.2;0.00147001,MA0047.2;0.0921188,MA0112.2;0.0111014,MA0065.2;0.0543117,MA0150.1;0.323754,MA0151.1;0,MA0152.1;0.307642,MA0153.1;0.379811,MA0154.1;0.130725,MA0155.1;0.0172386,MA0156.1;0.0599368,MA0157.1;0.51621,MA0158.1;0,MA0159.1;0.0273428,MA0160.1;0.169842,MA0161.1;0,MA0162.1;5.77611e-07,MA0163.1;0.011278,MA0164.1;0.276219,MA0080.2;0.0530695,MA0018.2;0.0849176,MA0099.2;0.430062,MA0079.2;0,MA0102.2;0.888417,MA0258.1;0.233273,MA0259.1;0.00348176,MA0442.1;0
}}

Latest revision as of 14:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127435382..127435385,-p@chr10:127435382..127435385
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Mm9::chr10:24635298..24635299,-p@chr10:24635298..24635299
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Mm9::chr10:41405791..41405808,-p@chr10:41405791..41405808
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Mm9::chr10:87376350..87376367,+p@chr10:87376350..87376367
+
Mm9::chr11:120391390..120391415,+p@chr11:120391390..120391415
+
Mm9::chr11:16771803..16771819,+p@chr11:16771803..16771819
+
Mm9::chr13:36818295..36818314,-p@chr13:36818295..36818314
-
Mm9::chr15:75052967..75052978,+p@chr15:75052967..75052978
+
Mm9::chr17:30730479..30730484,-p@chr17:30730479..30730484
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Mm9::chr18:85040955..85040968,+p@chr18:85040955..85040968
+
Mm9::chr19:32024443..32024455,+p@chr19:32024443..32024455
+
Mm9::chr19:32024502..32024514,+p@chr19:32024502..32024514
+
Mm9::chr2:103294385..103294399,-p@chr2:103294385..103294399
-
Mm9::chr2:103294453..103294474,+p@chr2:103294453..103294474
+
Mm9::chr2:103294506..103294547,-p@chr2:103294506..103294547
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Mm9::chr2:103294708..103294737,-p@chr2:103294708..103294737
-
Mm9::chr2:103294775..103294782,-p@chr2:103294775..103294782
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Mm9::chr2:103294788..103294845,-p@chr2:103294788..103294845
-
Mm9::chr2:103294855..103294864,-p@chr2:103294855..103294864
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Mm9::chr2:103307899..103307946,-p@chr2:103307899..103307946
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Mm9::chr3:118787953..118787967,+p@chr3:118787953..118787967
+
Mm9::chr3:118887044..118887048,+p@chr3:118887044..118887048
+
Mm9::chr4:104526380..104526393,-p@chr4:104526380..104526393
-
Mm9::chr4:107777751..107777764,-p@chr4:107777751..107777764
-
Mm9::chr4:49557784..49557797,-p@chr4:49557784..49557797
-
Mm9::chr4:96309420..96309423,-p@chr4:96309420..96309423
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Mm9::chr5:123630695..123630707,-p@chr5:123630695..123630707
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Mm9::chr5:123631456..123631467,-p@chr5:123631456..123631467
-
Mm9::chr5:123631476..123631488,-p@chr5:123631476..123631488
-
Mm9::chr5:135599604..135599630,+p@chr5:135599604..135599630
+
Mm9::chr5:146820597..146820625,-p@chr5:146820597..146820625
-
Mm9::chr5:146820658..146820666,-p@chr5:146820658..146820666
-
Mm9::chr7:134415997..134416003,-p@chr7:134415997..134416003
-
Mm9::chr7:52729831..52729837,-p@chr7:52729831..52729837
-
Mm9::chr7:53984058..53984086,-p@chr7:53984058..53984086
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Mm9::chr7:53984116..53984135,-p@chr7:53984116..53984135
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Mm9::chr7:53984241..53984264,-p@chr7:53984241..53984264
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Mm9::chr7:53984353..53984360,-p@chr7:53984353..53984360
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Mm9::chr7:53984532..53984539,-p@chr7:53984532..53984539
-
Mm9::chr9:106354410..106354428,+p@chr9:106354410..106354428
+
Mm9::chr9:121823937..121823982,-p@chr9:121823937..121823982
-
Mm9::chr9:121824293..121824302,-p@chr9:121824293..121824302
-
Mm9::chrX:20134685..20134694,+p@chrX:20134685..20134694
+


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:0004462lactoylglutathione lyase activity0.00262970470607571
GO:0016846carbon-sulfur lyase activity0.0118310777801947



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 cell1.20e-085
endopolyploid cell1.20e-085
parenchymal cell1.20e-085
polyploid cell1.20e-085
hepatocyte1.20e-085

Uber Anatomy
Ontology termp-valuen
liver3.44e-2922
epithelial sac3.44e-2922
digestive gland3.44e-2922
epithelium of foregut-midgut junction3.44e-2922
anatomical boundary3.44e-2922
hepatobiliary system3.44e-2922
foregut-midgut junction3.44e-2922
hepatic diverticulum3.44e-2922
liver primordium3.44e-2922
septum transversum3.44e-2922
liver bud3.44e-2922
digestive tract diverticulum1.00e-2723
sac1.00e-2723
exocrine gland3.76e-2525
exocrine system3.76e-2525
abdomen element8.79e-1749
abdominal segment element8.79e-1749
abdominal segment of trunk8.79e-1749
abdomen8.79e-1749
mesenchyme1.90e-1261
entire embryonic mesenchyme1.90e-1261
trunk mesenchyme4.96e-1245
epithelial tube2.44e-1147
subdivision of trunk4.11e-1166
gut epithelium4.42e-0955
trunk region element1.89e-0879
endocrine gland5.53e-0860
subdivision of digestive tract5.83e-08114
digestive system1.02e-07116
digestive tract1.02e-07116
primitive gut1.02e-07116
endoderm-derived structure1.74e-07118
endoderm1.74e-07118
presumptive endoderm1.74e-07118
gland4.63e-0765
unilaminar epithelium6.80e-0766
trunk8.12e-0790


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)
MA0003.19.25704e-08
MA0004.10.0386778
MA0006.10.0378784
MA0007.10.0345391
MA0009.12.08166
MA0014.13.13941e-06
MA0017.10.0502375
MA0019.10.149481
MA0024.10.236337
MA0025.10.447626
MA0027.11.79005
MA0028.10.0424766
MA0029.11.84453
MA0030.11.19958
MA0031.10.586395
MA0038.10.638245
MA0040.12.12744
MA0041.10.226681
MA0042.10.0815934
MA0043.10.338401
MA0046.10.292762
MA0048.10.0144083
MA0050.10.189111
MA0051.10.3196
MA0052.10.281576
MA0055.10.493774
MA0056.10
MA0057.10.0589243
MA0058.10.0168932
MA0059.10.0190891
MA0060.10.0126569
MA0061.10.270678
MA0063.10
MA0066.11.03005
MA0067.10.541925
MA0068.10.0642225
MA0069.10.281822
MA0070.12.12269
MA0071.10.737734
MA0072.10.268765
MA0073.10.00526376
MA0074.10.917391
MA0076.10.0604222
MA0077.10.253476
MA0078.10.362007
MA0081.10.101777
MA0083.10.337793
MA0084.10.839097
MA0087.10.305237
MA0088.10.0203405
MA0089.10
MA0090.10.122189
MA0091.10.164036
MA0092.10.538284
MA0093.10.00911688
MA0095.10
MA0098.10
MA0100.10.23957
MA0101.10.0914866
MA0103.10.304736
MA0105.10.0116036
MA0106.10.116464
MA0107.10.143581
MA0108.20.489376
MA0109.10
MA0111.10.134063
MA0113.10.685781
MA0114.10.265007
MA0115.10.34055
MA0116.10.229776
MA0117.10.316023
MA0119.10.229463
MA0122.10.881488
MA0124.11.24138
MA0125.10.434239
MA0130.10
MA0131.10.450081
MA0132.10
MA0133.10
MA0135.10.366681
MA0136.10.27579
MA0139.10.393824
MA0140.10.514563
MA0141.10.0670014
MA0142.10.564251
MA0143.10.356668
MA0144.10.272495
MA0145.10.159807
MA0146.15.2053e-05
MA0147.10.00414162
MA0148.10.166966
MA0149.10.0218907
MA0062.20.0130139
MA0035.20.895877
MA0039.22.07995e-10
MA0138.20.142458
MA0002.20.59228
MA0137.20.571772
MA0104.20.00147001
MA0047.20.0921188
MA0112.20.0111014
MA0065.20.0543117
MA0150.10.323754
MA0151.10
MA0152.10.307642
MA0153.10.379811
MA0154.10.130725
MA0155.10.0172386
MA0156.10.0599368
MA0157.10.51621
MA0158.10
MA0159.10.0273428
MA0160.10.169842
MA0161.10
MA0162.15.77611e-07
MA0163.10.011278
MA0164.10.276219
MA0080.20.0530695
MA0018.20.0849176
MA0099.20.430062
MA0079.20
MA0102.20.888417
MA0258.10.233273
MA0259.10.00348176
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:211&oldid=3072210"