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MCL coexpression mm9:99: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000181!5.19e-29!5;CL:0000417!5.19e-29!5;CL:0000668!5.19e-29!5;CL:0000412!5.19e-29!5;CL:0000182!5.19e-29!5;CL:0000215!4.26e-08!3;CL:0000223!3.56e-07!20;CL:0000213!6.93e-07!1;CL:0002078!6.93e-07!1;CL:0000115!6.93e-07!1;CL:0002262!6.93e-07!1;CL:1000398!6.93e-07!1
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002107!9.56e-20!22;UBERON:0007499!9.56e-20!22;UBERON:0006925!9.56e-20!22;UBERON:0009497!9.56e-20!22;UBERON:0000015!9.56e-20!22;UBERON:0002423!9.56e-20!22;UBERON:0006235!9.56e-20!22;UBERON:0008835!9.56e-20!22;UBERON:0003894!9.56e-20!22;UBERON:0004161!9.56e-20!22;UBERON:0008836!9.56e-20!22;UBERON:0009854!7.64e-19!23;UBERON:0009856!7.64e-19!23;UBERON:0002365!2.97e-17!25;UBERON:0002330!2.97e-17!25;UBERON:0005256!4.23e-09!45;UBERON:0003914!1.15e-08!47;UBERON:0005631!2.18e-08!3;UBERON:0000478!2.18e-08!3;UBERON:0000158!2.18e-08!3;UBERON:0005172!2.90e-08!49;UBERON:0005173!2.90e-08!49;UBERON:0002417!2.90e-08!49;UBERON:0000916!2.90e-08!49;UBERON:0003929!3.09e-07!55;UBERON:0000305!6.09e-07!1;UBERON:0002394!6.93e-07!1;UBERON:0001281!6.93e-07!1;UBERON:0000353!6.93e-07!1;UBERON:0003497!6.93e-07!1;UBERON:0003909!6.93e-07!1;UBERON:0003928!6.93e-07!1;UBERON:0003835!6.93e-07!1;UBERON:0003513!6.93e-07!1;UBERON:0001280!6.93e-07!1;UBERON:0004647!6.93e-07!1;UBERON:0002294!6.93e-07!1;UBERON:0001173!6.93e-07!1;UBERON:0004912!6.93e-07!1;UBERON:0005171!6.93e-07!1
|tfbs_overrepresentation_for_novel_motifs=0.206593,0.023945,0.23953,0.313695,1.329,0.355988,0.177565,0.782573,0.385666,0.216219,0.213631,0.435646,0.131646,0.512174,0.893948,0,0.934718,0.423988,0.903563,0.356979,0.0507993,0.133811,0.195102,0.115501,0.697444,0.605738,0.108173,0.422167,0.0133195,0.234598,0.245244,0.328274,0.534874,0.09279,0.0158914,0.849249,0.190687,0.424764,0.724187,0.0704566,0.334666,0.393319,0.669124,0.331247,0.21844,0.101595,0.654683,0.475573,1.13476,0.163363,0.174972,0.475404,0.148483,0.26945,0.602169,0.350736,0.382905,0.142514,0.297701,0.105256,0.299048,0.17101,0.581903,0.162991,0.226819,0.208204,0.452056,0.376656,0.122612,0.743665,0.0341744,0.20721,0.171425,0.66823,0.333809,0.336714,0.179134,0.105179,0.51098,0.354369,0.152938,0.412948,0.169175,0.0762618,0.0561997,0.154099,0.169589,0.930792,0.118872,0.506671,0.54691,0.461135,0.626018,0.98321,0.332204,0.0304483,0.23763,0.351932,0.421535,0.28758,0.129423,0.327857,0.251397,0.175618,0.345063,0.0811196,0.748785,0.187963,0.670961,0.0948445,0.19104,0.539585,0.491695,0.0595484,0.190394,0.163274,0.201055,0.120694,0.630673,0.253812,0.101104,0.141948,0.246301,0.104446,0.22338,0.51915,0.0966174,0.337317,0.146904,0.205353,0.505314,0.106336,0.131866,0.384854,0.203285,0.377513,1.3412,0.397809,0.518294,0.833302,0.480276,0.896025,0.062864,0.620435,0.333229,0.564862,0.664878,0.79667,0.0382201,0.478311,0.103237,0.0618664,0.571809,0.594166,0.817784,0.113074,0.478255,0.645814,0.121439,0.0762312,0.179903,0.451063,0.829648,0.568993,0.164058,0.216925,0.080998,0.0308834,0.335981
}}

Latest revision as of 14:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126957832..126957840,-p@chr10:126957832..126957840
-
Mm9::chr10:68567689..68567694,+p@chr10:68567689..68567694
+
Mm9::chr10:68682076..68682094,+p7@Rhobtb1
Mm9::chr10:68682195..68682203,+p19@Rhobtb1
Mm9::chr10:7500063..7500075,+p1@ENSMUST00000147230
p1@uc007eim.1
Mm9::chr10:93536784..93536789,+p@chr10:93536784..93536789
+
Mm9::chr11:115885278..115885291,-p4@Gm12657
p4@Gm6421
p4@Gm6749
p4@Gm7194
p4@Gm7227
p4@H3f3a
p4@H3f3b
p4@H3f3c
Mm9::chr11:60749121..60749133,+p@chr11:60749121..60749133
+
Mm9::chr11:69870356..69870397,+p@chr11:69870356..69870397
+
Mm9::chr11:8449222..8449247,-p@chr11:8449222..8449247
-
Mm9::chr12:105392056..105392101,-p1@Serpina3c
Mm9::chr13:113126137..113126150,+p@chr13:113126137..113126150
+
Mm9::chr13:34720187..34720194,-p@chr13:34720187..34720194
-
Mm9::chr13:53076382..53076393,-p2@Nfil3
Mm9::chr13:53076396..53076452,-p1@Nfil3
Mm9::chr13:75844995..75845009,+p3@Ell2
Mm9::chr14:45938205..45938221,-p1@Ero1l
Mm9::chr14:60059409..60059419,+p9@Cab39l
Mm9::chr14:70731115..70731135,-p14@Slc39a14
Mm9::chr14:70731248..70731254,-p13@Slc39a14
Mm9::chr14:70731265..70731284,-p7@Slc39a14
Mm9::chr14:70731296..70731315,-p8@Slc39a14
Mm9::chr14:70731321..70731330,-p9@Slc39a14
Mm9::chr15:75771423..75771445,+p2@Zfp623
Mm9::chr15:84753870..84753881,+p2@Nup50
Mm9::chr16:11365866..11365871,-p@chr16:11365866..11365871
-
Mm9::chr16:37868270..37868289,+p3@Lrrc58
Mm9::chr16:78266194..78266225,-p@chr16:78266194..78266225
-
Mm9::chr16:78302020..78302049,+p3@Cxadr
Mm9::chr16:90738467..90738483,+p7@Mrap
Mm9::chr16:92399058..92399087,-p@chr16:92399058..92399087
-
Mm9::chr16:95923706..95923717,+p6@Ets2
Mm9::chr17:23813627..23813651,-p@chr17:23813627..23813651
-
Mm9::chr17:26643089..26643111,-p@chr17:26643089..26643111
-
Mm9::chr17:26643117..26643133,-p@chr17:26643117..26643133
-
Mm9::chr17:26643323..26643340,-p@chr17:26643323..26643340
-
Mm9::chr17:26644573..26644604,-p2@Dusp1
Mm9::chr17:71096223..71096230,-p@chr17:71096223..71096230
-
Mm9::chr17:71351737..71351744,-p5@Myl12a
Mm9::chr17:71351828..71351932,-p3@Myl12a
Mm9::chr18:46901166..46901178,-p@chr18:46901166..46901178
-
Mm9::chr18:9485342..9485347,-p@chr18:9485342..9485347
-
Mm9::chr19:27410018..27410024,+p@chr19:27410018..27410024
+
Mm9::chr19:39421834..39421838,+p@chr19:39421834..39421838
+
Mm9::chr19:39585310..39585313,+p2@Cyp2c39
Mm9::chr19:39585334..39585345,+p1@Cyp2c39
Mm9::chr19:39585367..39585380,+p@chr19:39585367..39585380
+
Mm9::chr19:40265512..40265522,+p@chr19:40265512..40265522
+
Mm9::chr19:4059449..4059476,-p1@BC021614
Mm9::chr1:123224228..123224234,-p14@Insig2
Mm9::chr1:169173738..169173747,-p@chr1:169173738..169173747
-
Mm9::chr1:174095654..174095663,+p@chr1:174095654..174095663
+
Mm9::chr1:191684254..191684265,+p@chr1:191684254..191684265
+
Mm9::chr1:31006601..31006602,-p1@LOC100044742
p1@Ptp4a1
Mm9::chr1:31006722..31006725,-p14@LOC100044742
p14@Ptp4a1
Mm9::chr1:31006749..31006771,-p6@LOC100044742
p6@Ptp4a1
Mm9::chr1:31006862..31006883,-p7@LOC100044742
p7@Ptp4a1
Mm9::chr1:90456476..90456498,+p@chr1:90456476..90456498
+
Mm9::chr1:9535570..9535576,+p2@Rrs1
Mm9::chr2:104426232..104426235,+p@chr2:104426232..104426235
+
Mm9::chr2:152656146..152656153,-p7@Bcl2l1
Mm9::chr2:157392436..157392459,-p7@Blcap
Mm9::chr2:157943224..157943227,-p@chr2:157943224..157943227
-
Mm9::chr2:157943524..157943545,-p@chr2:157943524..157943545
-
Mm9::chr2:157944615..157944622,-p@chr2:157944615..157944622
-
Mm9::chr2:157944705..157944714,-p@chr2:157944705..157944714
-
Mm9::chr2:157945931..157945947,-p@chr2:157945931..157945947
-
Mm9::chr2:157953040..157953046,-p@chr2:157953040..157953046
-
Mm9::chr2:157972093..157972109,-p1@Tgm2
Mm9::chr2:164256745..164256756,-p@chr2:164256745..164256756
-
Mm9::chr2:164256761..164256773,-p@chr2:164256761..164256773
-
Mm9::chr2:19579682..19579699,+p2@Otud1
Mm9::chr2:30818619..30818669,+p@chr2:30818619..30818669
+
Mm9::chr2:32306888..32306899,-p6@Slc25a25
Mm9::chr2:32306916..32306990,-p1@Slc25a25
Mm9::chr2:32308704..32308710,-p@chr2:32308704..32308710
-
Mm9::chr2:35834246..35834262,+p@chr2:35834246..35834262
+
Mm9::chr2:3687911..3687936,+p@chr2:3687911..3687936
+
Mm9::chr2:3687945..3687954,+p@chr2:3687945..3687954
+
Mm9::chr3:107820349..107820359,-p@chr3:107820349..107820359
-
Mm9::chr3:145311674..145311692,-p@chr3:145311674..145311692
-
Mm9::chr3:153592594..153592603,-p@chr3:153592594..153592603
-
Mm9::chr3:79371669..79371686,-p4@Fnip2
Mm9::chr3:84445404..84445408,-p@chr3:84445404..84445408
-
Mm9::chr4:150122456..150122462,+p@chr4:150122456..150122462
+
Mm9::chr4:150229039..150229050,-p1@1700045H11Rik
Mm9::chr4:150240961..150240984,-p@chr4:150240961..150240984
-
Mm9::chr4:150241198..150241210,+p@chr4:150241198..150241210
+
Mm9::chr4:44085888..44085893,-p9@Gne
Mm9::chr4:45421750..45421779,-p2@Mcart1
Mm9::chr4:45495635..45495649,-p16@Shb
Mm9::chr4:63005684..63005691,+p@chr4:63005684..63005691
+
Mm9::chr5:116896716..116896749,-p2@Srrm4
Mm9::chr5:125870471..125870484,-p7@Ubc
Mm9::chr5:139960345..139960362,-p2@Zfand2a
Mm9::chr5:144166919..144166937,-p@chr5:144166919..144166937
-
Mm9::chr5:24606870..24606882,-p25@Prkag2
Mm9::chr6:108610513..108610528,+p3@Bhlhe40
Mm9::chr6:108615910..108615920,+p@chr6:108615910..108615920
+
Mm9::chr6:133055217..133055226,+p2@2700089E24Rik
p2@LOC100504757
Mm9::chr6:134381878..134381885,+p@chr6:134381878..134381885
+
Mm9::chr6:34663162..34663174,-p@chr6:34663162..34663174
-
Mm9::chr6:37489714..37489726,+p3@Akr1d1
Mm9::chr6:66987201..66987214,-p3@Gadd45a
Mm9::chr7:117927007..117927010,+p@chr7:117927007..117927010
+
Mm9::chr7:117928643..117928649,-p@chr7:117928643..117928649
-
Mm9::chr7:121912395..121912405,+p17@Insc
Mm9::chr7:53998349..53998350,-p1@Saa1
Mm9::chr7:54007202..54007205,+p1@Saa2
Mm9::chr7:56133428..56133464,-p@chr7:56133428..56133464
-
Mm9::chr7:56133492..56133522,-p@chr7:56133492..56133522
-
Mm9::chr8:120195160..120195171,-p6@Sdr42e1
Mm9::chr8:120195401..120195423,-p5@Sdr42e1
Mm9::chr8:120195426..120195455,-p3@Sdr42e1
Mm9::chr8:121965297..121965318,+p@chr8:121965297..121965318
+
Mm9::chr8:129115814..129115826,-p@chr8:129115814..129115826
-
Mm9::chr8:13037372..13037390,+p2@F10
Mm9::chr8:28370867..28370890,+p2@Eif4ebp1
Mm9::chr8:28370901..28370934,+p@chr8:28370901..28370934
+
Mm9::chr8:28371895..28371905,+p@chr8:28371895..28371905
+
Mm9::chr8:73155530..73155539,-p1@Gdf15
Mm9::chr8:73156318..73156360,-p2@Gdf15
Mm9::chr8:93908591..93908609,+p@chr8:93908591..93908609
+
Mm9::chr8:96703705..96703761,+p@chr8:96703705..96703761
+
Mm9::chr8:96718705..96718711,-p@chr8:96718705..96718711
-
Mm9::chr9:106149758..106149790,-p4@Alas1
Mm9::chr9:34926720..34926729,-p@chr9:34926720..34926729
-
Mm9::chr9:66368117..66368149,-p15@Usp3
Mm9::chr9:72538851..72538854,-p@chr9:72538851..72538854
-
Mm9::chr9:75257089..75257143,-p2@Mapk6
Mm9::chr9:92144587..92144591,+p7@Plscr1
Mm9::chrX:33868415..33868436,+p2@Lonrf3


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:0006953acute-phase response0.019018767241927



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 cell5.19e-295
endopolyploid cell5.19e-295
parenchymal cell5.19e-295
polyploid cell5.19e-295
hepatocyte5.19e-295
barrier cell4.26e-083
endodermal cell3.56e-0720
lining cell6.93e-071
meso-epithelial cell6.93e-071
endothelial cell6.93e-071
endothelial cell of sinusoid6.93e-071
endothelial cell of hepatic sinusoid6.93e-071

Uber Anatomy
Ontology termp-valuen
liver9.56e-2022
epithelial sac9.56e-2022
digestive gland9.56e-2022
epithelium of foregut-midgut junction9.56e-2022
anatomical boundary9.56e-2022
hepatobiliary system9.56e-2022
foregut-midgut junction9.56e-2022
hepatic diverticulum9.56e-2022
liver primordium9.56e-2022
septum transversum9.56e-2022
liver bud9.56e-2022
digestive tract diverticulum7.64e-1923
sac7.64e-1923
exocrine gland2.97e-1725
exocrine system2.97e-1725
trunk mesenchyme4.23e-0945
epithelial tube1.15e-0847
extraembryonic membrane2.18e-083
extraembryonic structure2.18e-083
membranous layer2.18e-083
abdomen element2.90e-0849
abdominal segment element2.90e-0849
abdominal segment of trunk2.90e-0849
abdomen2.90e-0849
gut epithelium3.09e-0755
amnion6.09e-071
bile duct6.93e-071
hepatic sinusoid6.93e-071
parenchyma6.93e-071
abdomen blood vessel6.93e-071
sinusoid6.93e-071
digestive system duct6.93e-071
abdominal segment blood vessel6.93e-071
trunk blood vessel6.93e-071
liver parenchyma6.93e-071
liver lobule6.93e-071
biliary system6.93e-071
biliary tree6.93e-071
biliary bud6.93e-071
hepatic duct6.93e-071


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)
MA0003.10.523531
MA0004.10.844833
MA0006.10.0544567
MA0007.10.98155
MA0009.10.161496
MA0014.10.0547326
MA0017.12.38147
MA0019.10.137252
MA0024.10.127857
MA0025.10.807952
MA0027.11.31025
MA0028.10.606333
MA0029.10.506885
MA0030.12.6463
MA0031.11.06187
MA0038.10.128079
MA0040.10.0450463
MA0041.10.0416835
MA0042.10.189291
MA0043.11.36815
MA0046.10.749163
MA0048.10.0993964
MA0050.10.0430605
MA0051.10.0599561
MA0052.10.401802
MA0055.10.0690182
MA0056.10
MA0057.10.0451498
MA0058.10.513942
MA0059.10.751351
MA0060.10.509846
MA0061.10.276694
MA0063.10
MA0066.10.373876
MA0067.10.555058
MA0068.10.0142238
MA0069.10.710962
MA0070.11.50399
MA0071.11.35279
MA0072.11.03312
MA0073.10.12751
MA0074.11.16733
MA0076.10.27507
MA0077.10.339561
MA0078.10.08078
MA0081.10.169026
MA0083.10.909059
MA0084.10.418593
MA0087.10.207636
MA0088.10.0453681
MA0089.10
MA0090.10.657686
MA0091.11.45351
MA0092.10.860337
MA0093.11.2296
MA0095.10
MA0098.10
MA0100.10.606172
MA0101.10.0425596
MA0103.10.350836
MA0105.10.917734
MA0106.10.0862558
MA0107.10.094774
MA0108.24.03412
MA0109.10
MA0111.10.162511
MA0113.11.25927
MA0114.11.46691
MA0115.13.14185
MA0116.10.854759
MA0117.10.221259
MA0119.10.334143
MA0122.10.0681555
MA0124.10.481625
MA0125.10.121806
MA0130.10
MA0131.10.470614
MA0132.10
MA0133.10
MA0135.10.603223
MA0136.10.041645
MA0139.10.495374
MA0140.10.150624
MA0141.10.939885
MA0142.10.68005
MA0143.10.315434
MA0144.10.0920125
MA0145.10.548712
MA0146.10.116308
MA0147.10.710765
MA0148.10.940326
MA0149.10.000428647
MA0062.20.0948636
MA0035.21.12537
MA0039.20.000168838
MA0138.20.99285
MA0002.20.0202583
MA0137.20.134121
MA0104.20.317956
MA0047.21.81806
MA0112.20.978443
MA0065.20.321965
MA0150.11.22994
MA0151.10
MA0152.10.0546282
MA0153.10.635693
MA0154.10.0651347
MA0155.10.206424
MA0156.10.0171022
MA0157.10.353312
MA0158.10
MA0159.10.795482
MA0160.10.535232
MA0161.10
MA0162.10.000348395
MA0163.10.0149798
MA0164.10.335557
MA0080.20.0130104
MA0018.20.776944
MA0099.25.34259
MA0079.20.000267638
MA0102.24.09017
MA0258.10.212673
MA0259.10.625798
MA0442.10
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