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MCL coexpression mm9:167: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0518754608656755,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.110544086345426,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.588334799715528,0.715946473805753,0.549175539886958,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.381011483184416,0.520631700011211,0.383962049647022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.675734860560353,0.704029662940908,0.591309463360446,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0042163;interleukin-12 beta subunit binding;0.030616041290685;16159!GO:0008917;lipopolysaccharide N-acetylglucosaminyltransferase activity;0.030616041290685;108105!GO:0005143;interleukin-12 receptor binding;0.030616041290685;16159!GO:0019972;interleukin-12 binding;0.030616041290685;16159!GO:0043514;interleukin-12 complex;0.030616041290685;16159!GO:0004704;NF-kappaB-inducing kinase activity;0.030616041290685;56532!GO:0006955;immune response;0.030616041290685;16159,20302,14961!
|ontology_enrichment_celltype=CL:0000049!5.08e-15!19;CL:0000988!7.70e-12!32;CL:0002032!7.70e-12!32;CL:0000037!7.70e-12!32;CL:0000566!7.70e-12!32;CL:0000837!7.70e-12!32;CL:0000557!1.00e-10!7;CL:0002320!1.58e-10!46;CL:0000134!1.58e-10!46;CL:0000034!2.81e-09!97;CL:0000213!5.27e-09!1;CL:0002078!5.27e-09!1;CL:0000115!5.27e-09!1;CL:0002262!5.27e-09!1;CL:1000398!5.27e-09!1;CL:0000945!6.33e-09!1;CL:0000236!6.33e-09!1;CL:0000826!6.33e-09!1;CL:0000219!6.94e-09!54
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!1.58e-10!46;UBERON:0002394!5.27e-09!1;UBERON:0001281!5.27e-09!1;UBERON:0000353!5.27e-09!1;UBERON:0003497!5.27e-09!1;UBERON:0003909!5.27e-09!1;UBERON:0003928!5.27e-09!1;UBERON:0003835!5.27e-09!1;UBERON:0003513!5.27e-09!1;UBERON:0001280!5.27e-09!1;UBERON:0004647!5.27e-09!1;UBERON:0002294!5.27e-09!1;UBERON:0001173!5.27e-09!1;UBERON:0004912!5.27e-09!1;UBERON:0005171!5.27e-09!1
}}

Latest revision as of 14:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:120053963..120053967,+p@chr10:120053963..120053967
+
Mm9::chr10:120061343..120061376,-p@chr10:120061343..120061376
-
Mm9::chr10:120065209..120065225,-p@chr10:120065209..120065225
-
Mm9::chr10:120123300..120123309,-p@chr10:120123300..120123309
-
Mm9::chr10:85456254..85456272,-p@chr10:85456254..85456272
-
Mm9::chr10:92606582..92606596,+p@chr10:92606582..92606596
+
Mm9::chr11:103126604..103126611,-p@chr11:103126604..103126611
-
Mm9::chr11:49947901..49947923,+p@chr11:49947901..49947923
+
Mm9::chr11:61819276..61819285,+p@chr11:61819276..61819285
+
Mm9::chr11:61819286..61819297,+p@chr11:61819286..61819297
+
Mm9::chr11:68259506..68259512,-p@chr11:68259506..68259512
-
Mm9::chr11:83462851..83462867,-p1@Ccl3
Mm9::chr11:86437788..86437799,-p@chr11:86437788..86437799
-
Mm9::chr12:106248215..106248231,-p3@4831426I19Rik
Mm9::chr12:106248233..106248269,-p1@4831426I19Rik
Mm9::chr12:70639175..70639180,+p@chr12:70639175..70639180
+
Mm9::chr12:70639273..70639286,+p@chr12:70639273..70639286
+
Mm9::chr12:88175517..88175560,-p@chr12:88175517..88175560
-
Mm9::chr13:75931975..75932008,+p@chr13:75931975..75932008
+
Mm9::chr13:81102365..81102383,+p3@ENSMUST00000153304
Mm9::chr13:83711147..83711168,-p@chr13:83711147..83711168
-
Mm9::chr14:33306049..33306071,+p@chr14:33306049..33306071
+
Mm9::chr14:56407552..56407566,-p4@Ripk3
Mm9::chr14:56407573..56407586,-p5@Ripk3
Mm9::chr14:56407596..56407630,-p3@Ripk3
Mm9::chr15:34012330..34012348,-p@chr15:34012330..34012348
-
Mm9::chr15:76020904..76020912,+p@chr15:76020904..76020912
+
Mm9::chr15:95717935..95717968,-p@chr15:95717935..95717968
-
Mm9::chr15:97652191..97652207,+p@chr15:97652191..97652207
+
Mm9::chr16:11442685..11442693,-p@chr16:11442685..11442693
-
Mm9::chr16:19760490..19760517,+p5@B3gnt5
Mm9::chr16:31234441..31234453,+p@chr16:31234441..31234453
+
Mm9::chr16:35983510..35983521,+p2@Kpna1
Mm9::chr16:3723356..3723384,-p@chr16:3723356..3723384
-
Mm9::chr16:3723593..3723595,+p@chr16:3723593..3723595
+
Mm9::chr16:43363174..43363181,-p@chr16:43363174..43363181
-
Mm9::chr17:27684275..27684282,-p@chr17:27684275..27684282
-
Mm9::chr17:34401472..34401509,+p3@H2-Ab1
Mm9::chr17:84385007..84385010,+p@chr17:84385007..84385010
+
Mm9::chr18:36033156..36033159,+p@chr18:36033156..36033159
+
Mm9::chr1:174452802..174452813,-p@chr1:174452802..174452813
-
Mm9::chr1:89077535..89077544,-p@chr1:89077535..89077544
-
Mm9::chr2:13332427..13332432,-p@chr2:13332427..13332432
-
Mm9::chr2:13332642..13332646,+p@chr2:13332642..13332646
+
Mm9::chr2:13495184..13495192,-p@chr2:13495184..13495192
-
Mm9::chr2:28379505..28379515,+p@chr2:28379505..28379515
+
Mm9::chr2:6130909..6130912,+p@chr2:6130909..6130912
+
Mm9::chr3:132318763..132318775,-p@chr3:132318763..132318775
-
Mm9::chr3:142680113..142680132,+p@chr3:142680113..142680132
+
Mm9::chr3:14870028..14870037,+p@chr3:14870028..14870037
+
Mm9::chr3:151785938..151785945,+p@chr3:151785938..151785945
+
Mm9::chr3:68495418..68495433,+p4@Il12a
Mm9::chr5:105928638..105928642,+p@chr5:105928638..105928642
+
Mm9::chr5:118927759..118927787,-p@chr5:118927759..118927787
-
Mm9::chr5:118927802..118927815,-p@chr5:118927802..118927815
-
Mm9::chr5:3501654..3501664,-p@chr5:3501654..3501664
-
Mm9::chr5:3501997..3502008,+p@chr5:3501997..3502008
+
Mm9::chr5:48722662..48722665,-p@chr5:48722662..48722665
-
Mm9::chr6:42299670..42299679,-p@chr6:42299670..42299679
-
Mm9::chr6:52775834..52775853,+p@chr6:52775834..52775853
+
Mm9::chr6:53660709..53660740,-p@chr6:53660709..53660740
-
Mm9::chr7:50808933..50808944,+p@chr7:50808933..50808944
+
Mm9::chr7:63097704..63097722,+p@chr7:63097704..63097722
+
Mm9::chr8:26309323..26309328,+p@chr8:26309323..26309328
+
Mm9::chr8:48760189..48760222,-p2@Ing2


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:0042163interleukin-12 beta subunit binding0.030616041290685
GO:0008917lipopolysaccharide N-acetylglucosaminyltransferase activity0.030616041290685
GO:0005143interleukin-12 receptor binding0.030616041290685
GO:0019972interleukin-12 binding0.030616041290685
GO:0043514interleukin-12 complex0.030616041290685
GO:0004704NF-kappaB-inducing kinase activity0.030616041290685
GO:0006955immune response0.030616041290685



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>

Uber Anatomy
Ontology termp-valuen
connective tissue1.58e-1046
bile duct5.27e-091
hepatic sinusoid5.27e-091
parenchyma5.27e-091
abdomen blood vessel5.27e-091
sinusoid5.27e-091
digestive system duct5.27e-091
abdominal segment blood vessel5.27e-091
trunk blood vessel5.27e-091
liver parenchyma5.27e-091
liver lobule5.27e-091
biliary system5.27e-091
biliary tree5.27e-091
biliary bud5.27e-091
hepatic duct5.27e-091


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)
MA0003.10.00825124
MA0004.11.07667
MA0006.10.0617935
MA0007.10.127958
MA0009.10.160008
MA0014.10.00951416
MA0017.10.0344004
MA0019.10.923135
MA0024.10.136175
MA0025.10.312699
MA0027.11.61241
MA0028.10.00106303
MA0029.10.125003
MA0030.10.128331
MA0031.10.357432
MA0038.10.341749
MA0040.10.167138
MA0041.10.304752
MA0042.10.0205974
MA0043.10.218486
MA0046.10.180835
MA0048.10.00580163
MA0050.12.13218
MA0051.11.90241
MA0052.10.985598
MA0055.10.0175834
MA0056.10
MA0057.10.0387303
MA0058.10.896529
MA0059.10.961816
MA0060.10.0166702
MA0061.12.05702
MA0063.10
MA0066.10.323968
MA0067.10.397426
MA0068.10.764811
MA0069.10.512214
MA0070.10.166392
MA0071.10.187661
MA0072.11.50653
MA0073.10.975762
MA0074.10.501007
MA0076.10.0129767
MA0077.10.45654
MA0078.10.184832
MA0081.10.792892
MA0083.10.217977
MA0084.10.676467
MA0087.10.191005
MA0088.10.350597
MA0089.10
MA0090.10.230817
MA0091.10.158194
MA0092.10.406799
MA0093.11.12856
MA0095.10
MA0098.10
MA0100.10.25207
MA0101.12.52099
MA0103.10.0395929
MA0105.11.81928
MA0106.10.192185
MA0107.13.5896
MA0108.20.0821349
MA0109.10
MA0111.10.255258
MA0113.10.377765
MA0114.10.00946157
MA0115.10.220288
MA0116.11.93368
MA0117.10.199875
MA0119.10.168873
MA0122.10.609276
MA0124.10.35604
MA0125.10.300895
MA0130.10
MA0131.10.249858
MA0132.10
MA0133.10
MA0135.10.24238
MA0136.10.870411
MA0139.10.157976
MA0140.10.76358
MA0141.10.227314
MA0142.10.692661
MA0143.10.18103
MA0144.10.904887
MA0145.10.535863
MA0146.10.0779514
MA0147.10.390102
MA0148.10.0606046
MA0149.10.00459441
MA0062.20.0212847
MA0035.20.77919
MA0039.21.67064
MA0138.20.0683955
MA0002.22.24306
MA0137.20.563101
MA0104.20.309103
MA0047.20.340496
MA0112.20.0737238
MA0065.20.0452644
MA0150.13.67908
MA0151.10
MA0152.10.0371679
MA0153.10.253603
MA0154.12.1942
MA0155.10.0409939
MA0156.12.4209
MA0157.10.301137
MA0158.10
MA0159.10.609356
MA0160.10.836815
MA0161.10
MA0162.10.0108531
MA0163.10.00375361
MA0164.10.54994
MA0080.21.22313
MA0018.20.0330876
MA0099.213.3584
MA0079.20.000141631
MA0102.20.723908
MA0258.11.55283
MA0259.10.91617
MA0442.10
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