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MCL coexpression mm9:233: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.360069300129636,0.885764903252032,0.940095963022424,0.324525627689665,0.254722434166292,0.383936593057231,0.252071962936197,0,0,0,0.108474404877635,0.0558041721483835,0,0,0.0959499323579933,0.100783889465809,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.545454304287177,0.408692801612187,0.311127917657318,0.930038297778725,0.484176860335644,0.534984022513845,0,0,0,0,0,0,0,0,0,0.200034908790818,0.364439294176354,0.37002711790928,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0753494505378687,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.100004302423367,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.13336176105449,0.167389851124624,0.0983461768813133,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0236264046620649,0.0543101607623745,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0331417600494206,0,0,0,0,0,0,0,0,0,0,0,0,0.0681778550615498,0.211728719351586,0.105986777695408,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0115846497345053,0,0.0208870423994129,0.0200223090406663,0.037610243787174,0.0588625755917643,0.0764305931706906,0.0486365415729897,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0043154;negative regulation of caspase activity;0.0249801416016453;12633!GO:0030693;caspase activity;0.0416153195043072;12633!GO:0003697;single-stranded DNA binding;0.0416153195043072;109019!GO:0043281;regulation of caspase activity;0.0483632233160235;12633!
|ontology_enrichment_celltype=CL:0000838!6.29e-29!12;CL:0000084!9.91e-27!11;CL:0000827!9.91e-27!11;CL:0000542!1.73e-26!13;CL:0000051!1.73e-26!13;CL:0000988!9.05e-24!32;CL:0002032!9.05e-24!32;CL:0000037!9.05e-24!32;CL:0000566!9.05e-24!32;CL:0000837!9.05e-24!32;CL:0000791!1.09e-22!9;CL:0000789!1.09e-22!9;CL:0002420!1.09e-22!9;CL:0002419!1.09e-22!9;CL:0000790!1.09e-22!9;CL:0002242!5.34e-21!16;CL:0000624!2.54e-20!8;CL:0000738!1.34e-19!17;CL:0002087!1.34e-19!17;CL:0002031!5.48e-17!25;CL:0002320!6.14e-17!46;CL:0000134!6.14e-17!46;CL:0000893!1.09e-15!6;CL:0002489!1.09e-15!6;CL:0000898!1.09e-15!6;CL:0000809!1.09e-15!6;CL:0000810!1.09e-15!6;CL:0000895!1.09e-15!6;CL:0000808!1.09e-15!6;CL:0000894!1.09e-15!6;CL:0000806!1.09e-15!6;CL:0000807!1.09e-15!6;CL:0000805!1.09e-15!6;CL:0002425!1.09e-15!6;CL:0002436!1.09e-15!6;CL:0002427!1.09e-15!6;CL:0002428!1.09e-15!6;CL:0002429!1.09e-15!6;CL:0002433!1.09e-15!6;CL:0002431!1.09e-15!6;CL:0002432!1.09e-15!6;CL:0000219!1.00e-13!54;CL:0000034!1.60e-11!97;CL:0000723!2.84e-09!91;CL:0000048!2.84e-09!91
|ontology_enrichment_disease=DOID:0060100!1.02e-08!3;DOID:4045!1.02e-08!3
|ontology_enrichment_uberon=UBERON:0002384!6.14e-17!46;UBERON:0002370!1.03e-14!23;UBERON:0000974!1.03e-14!23;UBERON:0004807!1.03e-14!23;UBERON:0005058!1.03e-14!23;UBERON:0003351!1.03e-14!23;UBERON:0009113!1.03e-14!23;UBERON:0003295!1.03e-14!23;UBERON:0009722!1.03e-14!23;UBERON:0005562!1.03e-14!23;UBERON:0007690!1.03e-14!23;UBERON:0006562!5.54e-14!24;UBERON:0003408!5.54e-14!24;UBERON:0001557!5.54e-14!24;UBERON:0001042!5.54e-14!24;UBERON:0008814!5.54e-14!24;UBERON:0009145!5.54e-14!24;UBERON:0000072!4.09e-12!27;UBERON:0002193!1.06e-11!48;UBERON:0002405!1.06e-11!48;UBERON:0002390!3.50e-11!45;UBERON:0003061!3.50e-11!45;UBERON:0004177!4.38e-11!29;UBERON:0005057!4.38e-11!29;UBERON:0000077!3.25e-10!35;UBERON:0000063!1.04e-08!35;UBERON:0007811!2.15e-08!36;UBERON:0000065!4.82e-07!41;UBERON:0001004!8.19e-07!42;UBERON:0000490!8.87e-07!66
}}

Latest revision as of 14:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:67000447..67000459,-p@chr10:67000447..67000459
-
Mm9::chr10:79622451..79622464,-p@chr10:79622451..79622464
-
Mm9::chr11:3005053..3005065,+p@chr11:3005053..3005065
+
Mm9::chr12:56567352..56567359,-p@chr12:56567352..56567359
-
Mm9::chr14:75579610..75579615,+p@chr14:75579610..75579615
+
Mm9::chr15:101096964..101096995,-p@chr15:101096964..101096995
-
Mm9::chr15:72979452..72979460,+p@chr15:72979452..72979460
+
Mm9::chr15:78603087..78603092,+p@chr15:78603087..78603092
+
Mm9::chr16:90283464..90283475,+p@chr16:90283464..90283475
+
Mm9::chr17:21587220..21587237,-p@chr17:21587220..21587237
-
Mm9::chr17:29631445..29631468,+p@chr17:29631445..29631468
+
Mm9::chr17:8068222..8068232,+p@chr17:8068222..8068232
+
Mm9::chr17:8068242..8068258,+p@chr17:8068242..8068258
+
Mm9::chr1:140033030..140033043,-p@chr1:140033030..140033043
-
Mm9::chr1:140072205..140072214,+p@chr1:140072205..140072214
+
Mm9::chr1:164501625..164501636,-p@chr1:164501625..164501636
-
Mm9::chr1:51535234..51535250,-p1@Obfc2a
Mm9::chr1:58770222..58770225,+p15@Cflar
Mm9::chr1:92953069..92953085,-p@chr1:92953069..92953085
-
Mm9::chr1:92959315..92959328,+p@chr1:92959315..92959328
+
Mm9::chr2:73323384..73323388,+p@chr2:73323384..73323388
+
Mm9::chr3:40550589..40550592,+p@chr3:40550589..40550592
+
Mm9::chr4:116793059..116793074,-p@chr4:116793059..116793074
-
Mm9::chr5:115939839..115939849,-p@chr5:115939839..115939849
-
Mm9::chr5:115939964..115939990,-p@chr5:115939964..115939990
-
Mm9::chr5:38611621..38611635,-p2@Zbtb49
Mm9::chr6:129183076..129183130,+p@chr6:129183076..129183130
+
Mm9::chr6:129187104..129187117,-p@chr6:129187104..129187117
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Mm9::chr6:129187277..129187288,+p@chr6:129187277..129187288
+
Mm9::chr6:129234454..129234459,-p@chr6:129234454..129234459
-
Mm9::chr7:108450534..108450596,-p1@Atg16l2
Mm9::chr7:31204698..31204711,+p@chr7:31204698..31204711
+
Mm9::chr7:97277849..97277866,-p@chr7:97277849..97277866
-
Mm9::chr8:23817098..23817104,+p@chr8:23817098..23817104
+
Mm9::chr9:44795249..44795263,-p@chr9:44795249..44795263
-
Mm9::chr9:44795268..44795283,-p@chr9:44795268..44795283
-


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:0043154negative regulation of caspase activity0.0249801416016453
GO:0030693caspase activity0.0416153195043072
GO:0003697single-stranded DNA binding0.0416153195043072
GO:0043281regulation of caspase activity0.0483632233160235



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>disease_data<br>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell6.29e-2912
T cell9.91e-2711
pro-T cell9.91e-2711
lymphocyte1.73e-2613
common lymphoid progenitor1.73e-2613
hematopoietic cell9.05e-2432
hematopoietic oligopotent progenitor cell9.05e-2432
hematopoietic stem cell9.05e-2432
angioblastic mesenchymal cell9.05e-2432
hematopoietic multipotent progenitor cell9.05e-2432
mature alpha-beta T cell1.09e-229
alpha-beta T cell1.09e-229
immature T cell1.09e-229
mature T cell1.09e-229
immature alpha-beta T cell1.09e-229
nucleate cell5.34e-2116
CD4-positive, alpha-beta T cell2.54e-208
leukocyte1.34e-1917
nongranular leukocyte1.34e-1917
hematopoietic lineage restricted progenitor cell5.48e-1725
connective tissue cell6.14e-1746
mesenchymal cell6.14e-1746
thymocyte1.09e-156
double negative thymocyte1.09e-156
naive T cell1.09e-156
double-positive, alpha-beta thymocyte1.09e-156
CD4-positive, alpha-beta thymocyte1.09e-156
naive thymus-derived CD4-positive, alpha-beta T cell1.09e-156
DN4 thymocyte1.09e-156
DN1 thymic pro-T cell1.09e-156
DN2 thymocyte1.09e-156
DN3 thymocyte1.09e-156
immature single positive thymocyte1.09e-156
early T lineage precursor1.09e-156
mature CD4 single-positive thymocyte1.09e-156
resting double-positive thymocyte1.09e-156
double-positive blast1.09e-156
CD69-positive double-positive thymocyte1.09e-156
CD69-positive, CD4-positive single-positive thymocyte1.09e-156
CD4-positive, CD8-intermediate double-positive thymocyte1.09e-156
CD24-positive, CD4 single-positive thymocyte1.09e-156
motile cell1.00e-1354
stem cell1.60e-1197
somatic stem cell2.84e-0991
multi fate stem cell2.84e-0991

Uber Anatomy
Ontology termp-valuen
connective tissue6.14e-1746
thymus1.03e-1423
neck1.03e-1423
respiratory system epithelium1.03e-1423
hemolymphoid system gland1.03e-1423
pharyngeal epithelium1.03e-1423
thymic region1.03e-1423
pharyngeal gland1.03e-1423
entire pharyngeal arch endoderm1.03e-1423
thymus primordium1.03e-1423
early pharyngeal endoderm1.03e-1423
pharynx5.54e-1424
gland of gut5.54e-1424
upper respiratory tract5.54e-1424
chordate pharynx5.54e-1424
pharyngeal arch system5.54e-1424
pharyngeal region of foregut5.54e-1424
segment of respiratory tract4.09e-1227
hemolymphoid system1.06e-1148
immune system1.06e-1148
hematopoietic system3.50e-1145
blood island3.50e-1145
hemopoietic organ4.38e-1129
immune organ4.38e-1129
mixed endoderm/mesoderm-derived structure3.25e-1035
organ segment1.04e-0835
craniocervical region2.15e-0836
respiratory tract4.82e-0741
respiratory system8.19e-0742
unilaminar epithelium8.87e-0766

Disease
Ontology termp-valuen
musculoskeletal system cancer1.02e-083
muscle cancer1.02e-083


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)
MA0003.10.000935456
MA0004.10.468477
MA0006.10.578071
MA0007.10.0536384
MA0009.10.319708
MA0014.10.00180501
MA0017.10.0841017
MA0019.10.558564
MA0024.10.286848
MA0025.11.2713
MA0027.11.86664
MA0028.10.37014
MA0029.10.270957
MA0030.10.756624
MA0031.10.697945
MA0038.10.395619
MA0040.10.877597
MA0041.10.138104
MA0042.10.126435
MA0043.11.81052
MA0046.10.347468
MA0048.10.393553
MA0050.10.549684
MA0051.11.31659
MA0052.11.60045
MA0055.11.30542
MA0056.10
MA0057.10.0285887
MA0058.10.288373
MA0059.10.131258
MA0060.10.17896
MA0061.11.25335
MA0063.10
MA0066.10.11962
MA0067.11.47742
MA0068.10.706886
MA0069.10.335786
MA0070.10.328303
MA0071.10.547889
MA0072.10.321801
MA0073.10.361203
MA0074.10.332473
MA0076.10.741873
MA0077.10.823879
MA0078.10.148951
MA0081.10.631726
MA0083.13.70545
MA0084.10.910864
MA0087.10.360752
MA0088.10.271712
MA0089.10
MA0090.10.708046
MA0091.10.0641166
MA0092.11.09274
MA0093.10.390267
MA0095.10
MA0098.10
MA0100.10.654154
MA0101.10.929681
MA0103.10.229489
MA0105.10.406615
MA0106.10.153484
MA0107.11.01687
MA0108.21.12169
MA0109.10
MA0111.10.0518462
MA0113.10.137307
MA0114.10.109325
MA0115.10.398164
MA0116.10.34492
MA0117.10.372208
MA0119.10.0349497
MA0122.10.388118
MA0124.10.560604
MA0125.10.496324
MA0130.10
MA0131.10.551578
MA0132.10
MA0133.10
MA0135.10.425686
MA0136.11.19392
MA0139.10.127566
MA0140.11.0882
MA0141.12.02546
MA0142.12.72209
MA0143.10.880912
MA0144.10.237111
MA0145.10.124723
MA0146.10.00403676
MA0147.10.454096
MA0148.10.232527
MA0149.10.0363416
MA0062.21.12534
MA0035.20.323402
MA0039.20.0303508
MA0138.20.183173
MA0002.20.867732
MA0137.20.480594
MA0104.20.286392
MA0047.20.78783
MA0112.20.0127088
MA0065.20.0326101
MA0150.10.438025
MA0151.10
MA0152.10.125121
MA0153.10.43947
MA0154.10.148581
MA0155.10.00602147
MA0156.11.08302
MA0157.10.62294
MA0158.10
MA0159.10.486651
MA0160.10.235961
MA0161.10
MA0162.10.0572037
MA0163.10.00201546
MA0164.10.359295
MA0080.21.84097
MA0018.21.79088
MA0099.21.01567
MA0079.20.00136706
MA0102.22.20616
MA0258.10.0950215
MA0259.10.420519
MA0442.10
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