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MCL coexpression mm9:3302: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0006562!4.44e-27!24;UBERON:0001557!4.44e-27!24;UBERON:0001042!4.44e-27!24;UBERON:0008814!4.44e-27!24;UBERON:0009145!4.44e-27!24;UBERON:0002370!9.65e-26!23;UBERON:0000974!9.65e-26!23;UBERON:0004807!9.65e-26!23;UBERON:0005058!9.65e-26!23;UBERON:0003351!9.65e-26!23;UBERON:0009113!9.65e-26!23;UBERON:0003295!9.65e-26!23;UBERON:0009722!9.65e-26!23;UBERON:0005562!9.65e-26!23;UBERON:0007690!9.65e-26!23;UBERON:0003408!1.98e-24!24;UBERON:0000072!2.13e-23!27;UBERON:0004177!3.48e-21!29;UBERON:0005057!3.48e-21!29;UBERON:0000065!5.42e-18!41;UBERON:0007811!6.28e-18!36;UBERON:0001004!2.09e-17!42;UBERON:0000063!1.08e-16!35;UBERON:0000077!1.53e-16!35;UBERON:0002193!6.06e-16!48;UBERON:0002405!6.06e-16!48;UBERON:0002390!1.00e-15!45;UBERON:0003061!1.00e-15!45;UBERON:0000153!5.11e-14!43;UBERON:0003081!1.33e-09!87;UBERON:0001041!2.24e-09!80;UBERON:0003929!1.30e-08!55;UBERON:0002368!2.59e-08!60;UBERON:0005911!3.80e-08!69;UBERON:0000926!2.45e-07!120;UBERON:0004120!2.45e-07!120;UBERON:0006603!2.45e-07!120;UBERON:0002530!2.95e-07!65
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.564138,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.235304,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,0.156582,0.788421,1.05665,0.859154,0.663409,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,1.05896,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,0.99201,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.928366,0.563856,1.24872,3.05198,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,4.01769,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,2.72046,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
}}

Latest revision as of 19:53, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:11564469..11564490,+p1@Il2ra
Mm9::chr2:11611489..11611507,+p@chr2:11611489..11611507
+
Mm9::chr2:11611628..11611650,+p@chr2:11611628..11611650
+


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
T cell2.09e-1211
pro-T cell2.09e-1211
lymphoid lineage restricted progenitor cell3.39e-1112
lymphocyte3.58e-1013
common lymphoid progenitor3.58e-1013
mature alpha-beta T cell1.68e-099
alpha-beta T cell1.68e-099
immature T cell1.68e-099
mature T cell1.68e-099
immature alpha-beta T cell1.68e-099
CD4-positive, alpha-beta T cell3.44e-088
nucleate cell7.02e-0816
thymocyte7.96e-086
double negative thymocyte7.96e-086
naive T cell7.96e-086
double-positive, alpha-beta thymocyte7.96e-086
CD4-positive, alpha-beta thymocyte7.96e-086
naive thymus-derived CD4-positive, alpha-beta T cell7.96e-086
DN4 thymocyte7.96e-086
DN1 thymic pro-T cell7.96e-086
DN2 thymocyte7.96e-086
DN3 thymocyte7.96e-086
immature single positive thymocyte7.96e-086
early T lineage precursor7.96e-086
mature CD4 single-positive thymocyte7.96e-086
resting double-positive thymocyte7.96e-086
double-positive blast7.96e-086
CD69-positive double-positive thymocyte7.96e-086
CD69-positive, CD4-positive single-positive thymocyte7.96e-086
CD4-positive, CD8-intermediate double-positive thymocyte7.96e-086
CD24-positive, CD4 single-positive thymocyte7.96e-086
hematopoietic lineage restricted progenitor cell1.17e-0725
leukocyte2.68e-0717
nongranular leukocyte2.68e-0717

Uber Anatomy
Ontology termp-valuen
pharynx4.44e-2724
upper respiratory tract4.44e-2724
chordate pharynx4.44e-2724
pharyngeal arch system4.44e-2724
pharyngeal region of foregut4.44e-2724
thymus9.65e-2623
neck9.65e-2623
respiratory system epithelium9.65e-2623
hemolymphoid system gland9.65e-2623
pharyngeal epithelium9.65e-2623
thymic region9.65e-2623
pharyngeal gland9.65e-2623
entire pharyngeal arch endoderm9.65e-2623
thymus primordium9.65e-2623
early pharyngeal endoderm9.65e-2623
gland of gut1.98e-2424
segment of respiratory tract2.13e-2327
hemopoietic organ3.48e-2129
immune organ3.48e-2129
respiratory tract5.42e-1841
craniocervical region6.28e-1836
respiratory system2.09e-1742
organ segment1.08e-1635
mixed endoderm/mesoderm-derived structure1.53e-1635
hemolymphoid system6.06e-1648
immune system6.06e-1648
hematopoietic system1.00e-1545
blood island1.00e-1545
anterior region of body5.11e-1443
lateral plate mesoderm1.33e-0987
foregut2.24e-0980
gut epithelium1.30e-0855
endocrine gland2.59e-0860
endo-epithelium3.80e-0869
mesoderm2.45e-07120
mesoderm-derived structure2.45e-07120
presumptive mesoderm2.45e-07120
gland2.95e-0765


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)
MA0003.10.0699972
MA0004.10.801718
MA0006.10.60285
MA0007.11.84502
MA0009.11.27673
MA0014.10.133574
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.10.61552
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.10.353763
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.10.190475
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.11.33581
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.10.657929
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.11.04599
MA0106.11.01755
MA0107.11.54626
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.11.3296
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.12.29766
MA0145.10.292366
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.0481552
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.79573
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.477233
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.00137444
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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