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MCL coexpression mm9:651: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_celltype=CL:0000791!1.63e-30!9;CL:0000789!1.63e-30!9;CL:0002420!1.63e-30!9;CL:0002419!1.63e-30!9;CL:0000790!1.63e-30!9;CL:0000624!4.14e-27!8;CL:0000084!1.04e-24!11;CL:0000827!1.04e-24!11;CL:0000838!1.57e-22!12;CL:0000893!8.08e-21!6;CL:0002489!8.08e-21!6;CL:0000898!8.08e-21!6;CL:0000809!8.08e-21!6;CL:0000810!8.08e-21!6;CL:0000895!8.08e-21!6;CL:0000808!8.08e-21!6;CL:0000894!8.08e-21!6;CL:0000806!8.08e-21!6;CL:0000807!8.08e-21!6;CL:0000805!8.08e-21!6;CL:0002425!8.08e-21!6;CL:0002436!8.08e-21!6;CL:0002427!8.08e-21!6;CL:0002428!8.08e-21!6;CL:0002429!8.08e-21!6;CL:0002433!8.08e-21!6;CL:0002431!8.08e-21!6;CL:0002432!8.08e-21!6;CL:0000542!1.10e-20!13;CL:0000051!1.10e-20!13;CL:0002242!1.55e-16!16;CL:0000738!1.78e-15!17;CL:0002087!1.78e-15!17;CL:0002031!7.11e-15!25;CL:0000988!3.46e-11!32;CL:0002032!3.46e-11!32;CL:0000037!3.46e-11!32;CL:0000566!3.46e-11!32;CL:0000837!3.46e-11!32;CL:0002320!3.47e-07!46;CL:0000134!3.47e-07!46
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!1.08e-44!29;UBERON:0005057!1.08e-44!29;UBERON:0002370!2.08e-41!23;UBERON:0000974!2.08e-41!23;UBERON:0004807!2.08e-41!23;UBERON:0005058!2.08e-41!23;UBERON:0003351!2.08e-41!23;UBERON:0009113!2.08e-41!23;UBERON:0003295!2.08e-41!23;UBERON:0009722!2.08e-41!23;UBERON:0005562!2.08e-41!23;UBERON:0007690!2.08e-41!23;UBERON:0006562!1.51e-39!24;UBERON:0003408!1.51e-39!24;UBERON:0001557!1.51e-39!24;UBERON:0001042!1.51e-39!24;UBERON:0008814!1.51e-39!24;UBERON:0009145!1.51e-39!24;UBERON:0000077!2.09e-36!35;UBERON:0000072!8.57e-35!27;UBERON:0002193!2.17e-34!48;UBERON:0002405!2.17e-34!48;UBERON:0002390!1.59e-33!45;UBERON:0003061!1.59e-33!45;UBERON:0000063!4.31e-26!35;UBERON:0007811!2.83e-25!36;UBERON:0000065!8.65e-22!41;UBERON:0001004!3.42e-21!42;UBERON:0000153!1.27e-20!43;UBERON:0003081!2.03e-15!87;UBERON:0003929!2.15e-15!55;UBERON:0002368!7.83e-14!60;UBERON:0001041!8.25e-14!80;UBERON:0002530!1.64e-12!65;UBERON:0000490!2.86e-12!66;UBERON:0000064!9.18e-12!99;UBERON:0005911!1.37e-11!69;UBERON:0000949!5.73e-11!72;UBERON:0000926!4.76e-10!120;UBERON:0004120!4.76e-10!120;UBERON:0006603!4.76e-10!120;UBERON:0004921!1.54e-08!114;UBERON:0001007!2.52e-08!116;UBERON:0001555!2.52e-08!116;UBERON:0007026!2.52e-08!116;UBERON:0004119!4.06e-08!118;UBERON:0000925!4.06e-08!118;UBERON:0006595!4.06e-08!118;UBERON:0002384!3.47e-07!46
}}

Latest revision as of 15:40, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:46171532..46171533,-p@chr11:46171532..46171533
-
Mm9::chr14:54218500..54218530,+p1@uc007tss.1
Mm9::chr14:54254496..54254506,+p1@ENSMUST00000103658
Mm9::chr14:54303268..54303275,+p1@ENSMUST00000103663
Mm9::chr14:54336355..54336381,+p1@ENSMUST00000103666
Mm9::chr14:54357978..54357982,+p1@ENSMUST00000171355
Mm9::chr14:54426138..54426147,+p2@ENSMUST00000103672
p2@uc007tto.1
Mm9::chr14:54843637..54843647,+p@chr14:54843637..54843647
+
Mm9::chr1:60825052..60825056,+p@chr1:60825052..60825056
+
Mm9::chr1:60828457..60828460,+p@chr1:60828457..60828460
+
Mm9::chr5:123439251..123439261,+p9@ENSMUST00000148466
p9@uc008zmw.1


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
mature alpha-beta T cell1.63e-309
alpha-beta T cell1.63e-309
immature T cell1.63e-309
mature T cell1.63e-309
immature alpha-beta T cell1.63e-309
CD4-positive, alpha-beta T cell4.14e-278
T cell1.04e-2411
pro-T cell1.04e-2411
lymphoid lineage restricted progenitor cell1.57e-2212
thymocyte8.08e-216
double negative thymocyte8.08e-216
naive T cell8.08e-216
double-positive, alpha-beta thymocyte8.08e-216
CD4-positive, alpha-beta thymocyte8.08e-216
naive thymus-derived CD4-positive, alpha-beta T cell8.08e-216
DN4 thymocyte8.08e-216
DN1 thymic pro-T cell8.08e-216
DN2 thymocyte8.08e-216
DN3 thymocyte8.08e-216
immature single positive thymocyte8.08e-216
early T lineage precursor8.08e-216
mature CD4 single-positive thymocyte8.08e-216
resting double-positive thymocyte8.08e-216
double-positive blast8.08e-216
CD69-positive double-positive thymocyte8.08e-216
CD69-positive, CD4-positive single-positive thymocyte8.08e-216
CD4-positive, CD8-intermediate double-positive thymocyte8.08e-216
CD24-positive, CD4 single-positive thymocyte8.08e-216
lymphocyte1.10e-2013
common lymphoid progenitor1.10e-2013
nucleate cell1.55e-1616
leukocyte1.78e-1517
nongranular leukocyte1.78e-1517
hematopoietic lineage restricted progenitor cell7.11e-1525
hematopoietic cell3.46e-1132
hematopoietic oligopotent progenitor cell3.46e-1132
hematopoietic stem cell3.46e-1132
angioblastic mesenchymal cell3.46e-1132
hematopoietic multipotent progenitor cell3.46e-1132
connective tissue cell3.47e-0746
mesenchymal cell3.47e-0746

Uber Anatomy
Ontology termp-valuen
hemopoietic organ1.08e-4429
immune organ1.08e-4429
thymus2.08e-4123
neck2.08e-4123
respiratory system epithelium2.08e-4123
hemolymphoid system gland2.08e-4123
pharyngeal epithelium2.08e-4123
thymic region2.08e-4123
pharyngeal gland2.08e-4123
entire pharyngeal arch endoderm2.08e-4123
thymus primordium2.08e-4123
early pharyngeal endoderm2.08e-4123
pharynx1.51e-3924
gland of gut1.51e-3924
upper respiratory tract1.51e-3924
chordate pharynx1.51e-3924
pharyngeal arch system1.51e-3924
pharyngeal region of foregut1.51e-3924
mixed endoderm/mesoderm-derived structure2.09e-3635
segment of respiratory tract8.57e-3527
hemolymphoid system2.17e-3448
immune system2.17e-3448
hematopoietic system1.59e-3345
blood island1.59e-3345
organ segment4.31e-2635
craniocervical region2.83e-2536
respiratory tract8.65e-2241
respiratory system3.42e-2142
anterior region of body1.27e-2043
lateral plate mesoderm2.03e-1587
gut epithelium2.15e-1555
endocrine gland7.83e-1460
foregut8.25e-1480
gland1.64e-1265
unilaminar epithelium2.86e-1266
organ part9.18e-1299
endo-epithelium1.37e-1169
endocrine system5.73e-1172
mesoderm4.76e-10120
mesoderm-derived structure4.76e-10120
presumptive mesoderm4.76e-10120
subdivision of digestive tract1.54e-08114
digestive system2.52e-08116
digestive tract2.52e-08116
primitive gut2.52e-08116
endoderm-derived structure4.06e-08118
endoderm4.06e-08118
presumptive endoderm4.06e-08118
connective tissue3.47e-0746


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)
MA0003.10.000402533
MA0004.10.330313
MA0006.10.547312
MA0007.10.316976
MA0009.10.743257
MA0014.10.144697
MA0017.10.598706
MA0019.11.39291
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.11.62787
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.11.34187
MA0042.10.703657
MA0043.10.837621
MA0046.10.778239
MA0048.10.054097
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.0494654
MA0056.10
MA0057.10.71676
MA0058.10.246908
MA0059.10.257372
MA0060.10.12537
MA0061.10.147394
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.418079
MA0069.10.76361
MA0070.10.75417
MA0071.10.955636
MA0072.10.745922
MA0073.10.999802
MA0074.10.419185
MA0076.10.223625
MA0077.10.724865
MA0078.10.502121
MA0081.10.760108
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.0293443
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.10.812369
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.216742
MA0105.10.0759118
MA0106.10.509454
MA0107.10.211681
MA0108.20.589413
MA0109.10
MA0111.10.312463
MA0113.12.10423
MA0114.10.145642
MA0115.10.84036
MA0116.11.64911
MA0117.10.808813
MA0119.10.733279
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.10.690248
MA0140.10.408417
MA0141.10.233109
MA0142.10.63775
MA0143.10.49828
MA0144.10.147954
MA0145.10.0329586
MA0146.10.00490019
MA0147.10.157258
MA0148.10.344843
MA0149.10.269772
MA0062.20.0791588
MA0035.20.412747
MA0039.20.143896
MA0138.20.555696
MA0002.20.699393
MA0137.20.230686
MA0104.20.11535
MA0047.20.46201
MA0112.20.313687
MA0065.20.905908
MA0150.11.53423
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.0529077
MA0155.10.354827
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.495113
MA0160.10.347545
MA0161.10
MA0162.10.219632
MA0163.10.0308606
MA0164.11.11611
MA0080.20.609443
MA0018.20.446948
MA0099.20.549696
MA0079.20.0743239
MA0102.21.45844
MA0258.10.421574
MA0259.10.14914
MA0442.10
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