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MCL coexpression mm9:1356: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.26438523863893,0.468475367262837,0.336524299153945,0.456820040387881,0.498498180126065,0.243454641582056,0.14385946390664,0,0,0,0,0.0558041721483835,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.445593382951438,0.546134170286936,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.100004302423367,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0685090053637401,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.059629779596053,0,0,0,0,0,0,0,0.0417740847988257,0.015947867244644,0.041718751492076,0.0588625755917643,0.0398944891531444,0.0480053095083702,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000791!3.40e-43!9;CL:0000789!3.40e-43!9;CL:0002420!3.40e-43!9;CL:0002419!3.40e-43!9;CL:0000790!3.40e-43!9;CL:0000624!2.48e-38!8;CL:0000084!3.86e-35!11;CL:0000827!3.86e-35!11;CL:0000838!4.07e-32!12;CL:0000542!1.47e-29!13;CL:0000051!1.47e-29!13;CL:0000893!3.81e-29!6;CL:0002489!3.81e-29!6;CL:0000898!3.81e-29!6;CL:0000809!3.81e-29!6;CL:0000810!3.81e-29!6;CL:0000895!3.81e-29!6;CL:0000808!3.81e-29!6;CL:0000894!3.81e-29!6;CL:0000806!3.81e-29!6;CL:0000807!3.81e-29!6;CL:0000805!3.81e-29!6;CL:0002425!3.81e-29!6;CL:0002436!3.81e-29!6;CL:0002427!3.81e-29!6;CL:0002428!3.81e-29!6;CL:0002429!3.81e-29!6;CL:0002433!3.81e-29!6;CL:0002431!3.81e-29!6;CL:0002432!3.81e-29!6;CL:0002242!8.54e-24!16;CL:0000738!2.52e-22!17;CL:0002087!2.52e-22!17;CL:0002031!3.78e-18!25;CL:0000988!7.41e-14!32;CL:0002032!7.41e-14!32;CL:0000037!7.41e-14!32;CL:0000566!7.41e-14!32;CL:0000837!7.41e-14!32;CL:0002320!3.52e-09!46;CL:0000134!3.52e-09!46;CL:0000219!1.36e-07!54
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!3.11e-32!23;UBERON:0000974!3.11e-32!23;UBERON:0004807!3.11e-32!23;UBERON:0005058!3.11e-32!23;UBERON:0003351!3.11e-32!23;UBERON:0009113!3.11e-32!23;UBERON:0003295!3.11e-32!23;UBERON:0009722!3.11e-32!23;UBERON:0005562!3.11e-32!23;UBERON:0007690!3.11e-32!23;UBERON:0006562!8.19e-31!24;UBERON:0003408!8.19e-31!24;UBERON:0001557!8.19e-31!24;UBERON:0001042!8.19e-31!24;UBERON:0008814!8.19e-31!24;UBERON:0009145!8.19e-31!24;UBERON:0004177!2.33e-29!29;UBERON:0005057!2.33e-29!29;UBERON:0000072!3.52e-27!27;UBERON:0000077!5.65e-24!35;UBERON:0002193!1.73e-22!48;UBERON:0002405!1.73e-22!48;UBERON:0002390!5.13e-21!45;UBERON:0003061!5.13e-21!45;UBERON:0000063!1.58e-20!35;UBERON:0007811!6.67e-20!36;UBERON:0000065!3.10e-17!41;UBERON:0001004!8.90e-17!42;UBERON:0000153!2.43e-16!43;UBERON:0003929!2.46e-12!55;UBERON:0002368!3.88e-11!60;UBERON:0002530!4.02e-10!65;UBERON:0000490!6.15e-10!66;UBERON:0003081!9.39e-10!87;UBERON:0005911!2.04e-09!69;UBERON:0001041!2.88e-09!80;UBERON:0002384!3.52e-09!46;UBERON:0000949!6.16e-09!72;UBERON:0000064!2.63e-08!99
}}

Latest revision as of 16:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr14:122397461..122397492,+p@chr14:122397461..122397492
+
Mm9::chr14:54838649..54838660,+p@chr14:54838649..54838660
+
Mm9::chr14:54838705..54838714,+p@chr14:54838705..54838714
+
Mm9::chr2:11589194..11589197,+p@chr2:11589194..11589197
+
Mm9::chr2:34816921..34816937,+p@chr2:34816921..34816937
+
Mm9::chr4:32438406..32438415,-p@chr4:32438406..32438415
-


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 cell3.40e-439
alpha-beta T cell3.40e-439
immature T cell3.40e-439
mature T cell3.40e-439
immature alpha-beta T cell3.40e-439
CD4-positive, alpha-beta T cell2.48e-388
T cell3.86e-3511
pro-T cell3.86e-3511
lymphoid lineage restricted progenitor cell4.07e-3212
lymphocyte1.47e-2913
common lymphoid progenitor1.47e-2913
thymocyte3.81e-296
double negative thymocyte3.81e-296
naive T cell3.81e-296
double-positive, alpha-beta thymocyte3.81e-296
CD4-positive, alpha-beta thymocyte3.81e-296
naive thymus-derived CD4-positive, alpha-beta T cell3.81e-296
DN4 thymocyte3.81e-296
DN1 thymic pro-T cell3.81e-296
DN2 thymocyte3.81e-296
DN3 thymocyte3.81e-296
immature single positive thymocyte3.81e-296
early T lineage precursor3.81e-296
mature CD4 single-positive thymocyte3.81e-296
resting double-positive thymocyte3.81e-296
double-positive blast3.81e-296
CD69-positive double-positive thymocyte3.81e-296
CD69-positive, CD4-positive single-positive thymocyte3.81e-296
CD4-positive, CD8-intermediate double-positive thymocyte3.81e-296
CD24-positive, CD4 single-positive thymocyte3.81e-296
nucleate cell8.54e-2416
leukocyte2.52e-2217
nongranular leukocyte2.52e-2217
hematopoietic lineage restricted progenitor cell3.78e-1825
hematopoietic cell7.41e-1432
hematopoietic oligopotent progenitor cell7.41e-1432
hematopoietic stem cell7.41e-1432
angioblastic mesenchymal cell7.41e-1432
hematopoietic multipotent progenitor cell7.41e-1432
connective tissue cell3.52e-0946
mesenchymal cell3.52e-0946
motile cell1.36e-0754

Uber Anatomy
Ontology termp-valuen
thymus3.11e-3223
neck3.11e-3223
respiratory system epithelium3.11e-3223
hemolymphoid system gland3.11e-3223
pharyngeal epithelium3.11e-3223
thymic region3.11e-3223
pharyngeal gland3.11e-3223
entire pharyngeal arch endoderm3.11e-3223
thymus primordium3.11e-3223
early pharyngeal endoderm3.11e-3223
pharynx8.19e-3124
gland of gut8.19e-3124
upper respiratory tract8.19e-3124
chordate pharynx8.19e-3124
pharyngeal arch system8.19e-3124
pharyngeal region of foregut8.19e-3124
hemopoietic organ2.33e-2929
immune organ2.33e-2929
segment of respiratory tract3.52e-2727
mixed endoderm/mesoderm-derived structure5.65e-2435
hemolymphoid system1.73e-2248
immune system1.73e-2248
hematopoietic system5.13e-2145
blood island5.13e-2145
organ segment1.58e-2035
craniocervical region6.67e-2036
respiratory tract3.10e-1741
respiratory system8.90e-1742
anterior region of body2.43e-1643
gut epithelium2.46e-1255
endocrine gland3.88e-1160
gland4.02e-1065
unilaminar epithelium6.15e-1066
lateral plate mesoderm9.39e-1087
endo-epithelium2.04e-0969
foregut2.88e-0980
connective tissue3.52e-0946
endocrine system6.16e-0972
organ part2.63e-0899


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)
MA0003.10.04894
MA0004.11.3269
MA0006.10.359699
MA0007.10.52077
MA0009.10.987341
MA0014.10.0315641
MA0017.10.387481
MA0019.10.800946
MA0024.10.942716
MA0025.11.22395
MA0027.12.64231
MA0028.10.969171
MA0029.10.920529
MA0030.10.927235
MA0031.10.890871
MA0038.10.686534
MA0040.11.00009
MA0041.10.457338
MA0042.10.443591
MA0043.11.08567
MA0046.11.02391
MA0048.10.161427
MA0050.10.57678
MA0051.10.695779
MA0052.11.00829
MA0055.10.0585191
MA0056.10
MA0057.10.457693
MA0058.10.436487
MA0059.10.449345
MA0060.10.757042
MA0061.10.827788
MA0063.10
MA0066.10.675169
MA0067.11.33603
MA0068.10.467569
MA0069.11.00864
MA0070.10.998765
MA0071.11.41046
MA0072.10.990133
MA0073.10.000157319
MA0074.11.54084
MA0076.11.04996
MA0077.10.968053
MA0078.10.729877
MA0081.10.473489
MA0083.11.08487
MA0084.11.66561
MA0087.11.04109
MA0088.10.111145
MA0089.10
MA0090.10.500693
MA0091.10.55008
MA0092.10.501022
MA0093.10.988233
MA0095.10
MA0098.10
MA0100.10.626021
MA0101.10.458688
MA0103.10.398766
MA0105.10.57901
MA0106.10.737893
MA0107.10.392331
MA0108.20.824407
MA0109.10
MA0111.10.515457
MA0113.10.708789
MA0114.10.304661
MA0115.11.08851
MA0116.10.359483
MA0117.11.05576
MA0119.10.459301
MA0122.11.07591
MA0124.11.28237
MA0125.11.20757
MA0130.10
MA0131.10.796279
MA0132.10
MA0133.10
MA0135.11.1226
MA0136.10.658622
MA0139.10.243463
MA0140.10.625902
MA0141.10.419361
MA0142.10.876028
MA0143.10.725672
MA0144.10.307873
MA0145.10.119202
MA0146.10.153598
MA0147.10.320675
MA0148.10.553294
MA0149.10.464445
MA0062.20.204999
MA0035.20.630778
MA0039.20.0823004
MA0138.20.788113
MA0002.20.689262
MA0137.20.416331
MA0104.20.261255
MA0047.20.685741
MA0112.20.119197
MA0065.20.119561
MA0150.10.520653
MA0151.10
MA0152.10.685852
MA0153.11.13945
MA0154.11.49271
MA0155.10.414701
MA0156.10.406559
MA0157.10.843181
MA0158.10
MA0159.10.881902
MA0160.10.556423
MA0161.10
MA0162.10.0465447
MA0163.10.163321
MA0164.10.658997
MA0080.20.393257
MA0018.20.669032
MA0099.20.781628
MA0079.20.00464563
MA0102.21.7182
MA0258.10.290587
MA0259.10.309517
MA0442.10
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