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MCL coexpression mm9:1887: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.68202810436645,0.281903928295643,0.0913378685245542,0.034318863244337,0.0642873521037868,0.53857485942528,0.30513346809278,0,0,0,0,0.0558041721483835,0.0768144049304335,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0628325491627715,0.783727468163968,0.634358518057588,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0447367441903353,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.322240672823314,0.143249948501144,0.416760201697675,0.386932595602202,0.384822022485365,0.356401799953527,0.250482537201495,0.303684733146551,0.368522193920824,0.314134485446744,0.260830528714251,0.223873329656042,0.344816909922768,0.425450238474868,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000791!2.31e-29!9;CL:0000789!2.31e-29!9;CL:0002420!2.31e-29!9;CL:0002419!2.31e-29!9;CL:0000790!2.31e-29!9;CL:0000838!1.83e-26!12;CL:0000624!6.09e-26!8;CL:0000542!2.70e-24!13;CL:0000051!2.70e-24!13;CL:0000084!9.24e-24!11;CL:0000827!9.24e-24!11;CL:0002242!2.05e-19!16;CL:0000893!4.74e-19!6;CL:0002489!4.74e-19!6;CL:0000898!4.74e-19!6;CL:0000809!4.74e-19!6;CL:0000810!4.74e-19!6;CL:0000895!4.74e-19!6;CL:0000808!4.74e-19!6;CL:0000894!4.74e-19!6;CL:0000806!4.74e-19!6;CL:0000807!4.74e-19!6;CL:0000805!4.74e-19!6;CL:0002425!4.74e-19!6;CL:0002436!4.74e-19!6;CL:0002427!4.74e-19!6;CL:0002428!4.74e-19!6;CL:0002429!4.74e-19!6;CL:0002433!4.74e-19!6;CL:0002431!4.74e-19!6;CL:0002432!4.74e-19!6;CL:0000738!3.61e-18!17;CL:0002087!3.61e-18!17;CL:0002031!6.58e-17!25;CL:0000988!1.03e-12!32;CL:0002032!1.03e-12!32;CL:0000037!1.03e-12!32;CL:0000566!1.03e-12!32;CL:0000837!1.03e-12!32;CL:0002320!3.65e-08!46;CL:0000134!3.65e-08!46
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!7.65e-55!23;UBERON:0000974!7.65e-55!23;UBERON:0004807!7.65e-55!23;UBERON:0005058!7.65e-55!23;UBERON:0003351!7.65e-55!23;UBERON:0009113!7.65e-55!23;UBERON:0003295!7.65e-55!23;UBERON:0009722!7.65e-55!23;UBERON:0005562!7.65e-55!23;UBERON:0007690!7.65e-55!23;UBERON:0006562!2.11e-52!24;UBERON:0003408!2.11e-52!24;UBERON:0001557!2.11e-52!24;UBERON:0001042!2.11e-52!24;UBERON:0008814!2.11e-52!24;UBERON:0009145!2.11e-52!24;UBERON:0004177!4.55e-47!29;UBERON:0005057!4.55e-47!29;UBERON:0000072!3.65e-46!27;UBERON:0000077!2.47e-38!35;UBERON:0002390!5.36e-35!45;UBERON:0003061!5.36e-35!45;UBERON:0000063!9.51e-35!35;UBERON:0007811!1.12e-33!36;UBERON:0002193!1.49e-32!48;UBERON:0002405!1.49e-32!48;UBERON:0000065!4.19e-29!41;UBERON:0001004!2.55e-28!42;UBERON:0000153!1.43e-27!43;UBERON:0003929!1.03e-20!55;UBERON:0002368!1.16e-18!60;UBERON:0002530!6.31e-17!65;UBERON:0000490!1.30e-16!66;UBERON:0003081!4.56e-16!87;UBERON:0005911!1.02e-15!69;UBERON:0000949!6.71e-15!72;UBERON:0001041!1.61e-14!80;UBERON:0000064!6.00e-11!99;UBERON:0000926!1.87e-10!120;UBERON:0004120!1.87e-10!120;UBERON:0006603!1.87e-10!120;UBERON:0004921!5.75e-09!114;UBERON:0001007!9.67e-09!116;UBERON:0001555!9.67e-09!116;UBERON:0007026!9.67e-09!116;UBERON:0004119!1.60e-08!118;UBERON:0000925!1.60e-08!118;UBERON:0006595!1.60e-08!118;UBERON:0002384!3.65e-08!46;UBERON:0001048!5.17e-07!134
}}

Latest revision as of 17:39, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:19317974..19317989,-p@chr10:19317974..19317989
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Mm9::chr7:75409731..75409742,+p@chr7:75409731..75409742
+
Mm9::chr7:75422633..75422641,+p@chr7:75422633..75422641
+
Mm9::chr9:44782428..44782442,-p@chr9:44782428..44782442
-


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 cell2.31e-299
alpha-beta T cell2.31e-299
immature T cell2.31e-299
mature T cell2.31e-299
immature alpha-beta T cell2.31e-299
lymphoid lineage restricted progenitor cell1.83e-2612
CD4-positive, alpha-beta T cell6.09e-268
lymphocyte2.70e-2413
common lymphoid progenitor2.70e-2413
T cell9.24e-2411
pro-T cell9.24e-2411
nucleate cell2.05e-1916
thymocyte4.74e-196
double negative thymocyte4.74e-196
naive T cell4.74e-196
double-positive, alpha-beta thymocyte4.74e-196
CD4-positive, alpha-beta thymocyte4.74e-196
naive thymus-derived CD4-positive, alpha-beta T cell4.74e-196
DN4 thymocyte4.74e-196
DN1 thymic pro-T cell4.74e-196
DN2 thymocyte4.74e-196
DN3 thymocyte4.74e-196
immature single positive thymocyte4.74e-196
early T lineage precursor4.74e-196
mature CD4 single-positive thymocyte4.74e-196
resting double-positive thymocyte4.74e-196
double-positive blast4.74e-196
CD69-positive double-positive thymocyte4.74e-196
CD69-positive, CD4-positive single-positive thymocyte4.74e-196
CD4-positive, CD8-intermediate double-positive thymocyte4.74e-196
CD24-positive, CD4 single-positive thymocyte4.74e-196
leukocyte3.61e-1817
nongranular leukocyte3.61e-1817
hematopoietic lineage restricted progenitor cell6.58e-1725
hematopoietic cell1.03e-1232
hematopoietic oligopotent progenitor cell1.03e-1232
hematopoietic stem cell1.03e-1232
angioblastic mesenchymal cell1.03e-1232
hematopoietic multipotent progenitor cell1.03e-1232
connective tissue cell3.65e-0846
mesenchymal cell3.65e-0846

Uber Anatomy
Ontology termp-valuen
thymus7.65e-5523
neck7.65e-5523
respiratory system epithelium7.65e-5523
hemolymphoid system gland7.65e-5523
pharyngeal epithelium7.65e-5523
thymic region7.65e-5523
pharyngeal gland7.65e-5523
entire pharyngeal arch endoderm7.65e-5523
thymus primordium7.65e-5523
early pharyngeal endoderm7.65e-5523
pharynx2.11e-5224
gland of gut2.11e-5224
upper respiratory tract2.11e-5224
chordate pharynx2.11e-5224
pharyngeal arch system2.11e-5224
pharyngeal region of foregut2.11e-5224
hemopoietic organ4.55e-4729
immune organ4.55e-4729
segment of respiratory tract3.65e-4627
mixed endoderm/mesoderm-derived structure2.47e-3835
hematopoietic system5.36e-3545
blood island5.36e-3545
organ segment9.51e-3535
craniocervical region1.12e-3336
hemolymphoid system1.49e-3248
immune system1.49e-3248
respiratory tract4.19e-2941
respiratory system2.55e-2842
anterior region of body1.43e-2743
gut epithelium1.03e-2055
endocrine gland1.16e-1860
gland6.31e-1765
unilaminar epithelium1.30e-1666
lateral plate mesoderm4.56e-1687
endo-epithelium1.02e-1569
endocrine system6.71e-1572
foregut1.61e-1480
organ part6.00e-1199
mesoderm1.87e-10120
mesoderm-derived structure1.87e-10120
presumptive mesoderm1.87e-10120
subdivision of digestive tract5.75e-09114
digestive system9.67e-09116
digestive tract9.67e-09116
primitive gut9.67e-09116
endoderm-derived structure1.60e-08118
endoderm1.60e-08118
presumptive endoderm1.60e-08118
connective tissue3.65e-0846
primordium5.17e-07134


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)
MA0003.10.0356887
MA0004.10.6888
MA0006.10.497533
MA0007.10.672186
MA0009.11.15569
MA0014.10.0809287
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.10.509589
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.11.35097
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.11.28762
MA0056.10
MA0057.10.251896
MA0058.10.581673
MA0059.10.59559
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.713436
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0140887
MA0074.10.795862
MA0076.10.550092
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.201215
MA0089.10
MA0090.10.650768
MA0091.12.81846
MA0092.10.651119
MA0093.10.519148
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.841866
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.10.43587
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.10.439506
MA0145.10.21199
MA0146.10.0944145
MA0147.10.453952
MA0148.10.706718
MA0149.10.611881
MA0062.20.319836
MA0035.20.788288
MA0039.20.0959929
MA0138.20.951653
MA0002.20.965577
MA0137.20.559766
MA0104.20.386166
MA0047.20.845655
MA0112.20.608441
MA0065.20.212467
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.230016
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.346529
MA0163.10.0996272
MA0164.10.817786
MA0080.20.534538
MA0018.20.828253
MA0099.20.944966
MA0079.20.300141
MA0102.21.8929
MA0258.11.07695
MA0259.10.441366
MA0442.10
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