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MCL coexpression mm9:3171: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.833182157289936,0.627175361273284,0.231008947931991,0.127893569522672,0.0333321253665857,0.972611742268638,0.661267014639728,0,0,0.0106897513843695,0.119078361648301,0.149632666139897,0.153628809860867,0.0354470656487682,0.0786677159214676,0.100783889465809,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.689643313234248,1.23285584551451,0.920610194705098,0.337751283747623,0.226095853111613,0.592516742194489,0,0,0,0,0,0,0,0,0,0,0.953227176495255,0.988489338339128,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0317017435824471,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.487350953621439,0,0,0,0,0,0.0482820047261801,0,0,0.0586534975690397,0,0,0,0,0,0,0,0,0.13336176105449,0.204093579732844,0.276344963129511,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.180325425270187,0.108620321524749,0,0.0117148390951421,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.079479943783859,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0849828766602549,0,0,0,0,0,0,0.0294389011296462,0,0,0,0,0,0,0,0,0,0.016771990203214,0,0,0,0,0,0.0219694433443352,0,0,0.0152721857219308,0,0.191523550257637,0,0,0,0,0,0,0,0,0.086880916817156,0,0.0659019793256198,0.128841727545421,0.198271062479628,0,0,0,0.10582914506561,0,0,0,0.0977676536600382,0,0,0,0,0,0,0,0,0,0,0.0576433181427177,0,0,0,0,0.0179824310150462,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0662835200988411,0,0,0,0,0,0,0.226208870161549,0,0,0.138850957170371,0.055643654597214,0.0894734883806707,0.1834399662015,0.185095168672227,0.105986777695408,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0508196513012492,0,0.0801664161057822,0.0811390825906054,0.0530480122014902,0.0715236385554987,0.145309149361067,0.235824448272561,0.112396870443577,0.0417740847988257,0.163531334068437,0.114770581611834,0.111388092060353,0.0764305931706906,0.230771051730937,0,0.0870662137566218,0,0.0673999378519914,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0351544734889112,0.0684580848992459,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0709519923534245,0,0,0,0,0,0,0,0,0,0.0408018333703219,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000084!2.27e-14!11;CL:0000827!2.27e-14!11;CL:0000838!6.67e-13!12;CL:0000791!1.21e-12!9;CL:0000789!1.21e-12!9;CL:0002420!1.21e-12!9;CL:0002419!1.21e-12!9;CL:0000790!1.21e-12!9;CL:0000988!1.42e-12!32;CL:0002032!1.42e-12!32;CL:0000037!1.42e-12!32;CL:0000566!1.42e-12!32;CL:0000837!1.42e-12!32;CL:0000542!1.16e-11!13;CL:0000051!1.16e-11!13;CL:0000624!3.25e-11!8;CL:0002031!4.43e-09!25;CL:0002242!6.78e-09!16;CL:0000893!1.86e-08!6;CL:0002489!1.86e-08!6;CL:0000898!1.86e-08!6;CL:0000809!1.86e-08!6;CL:0000810!1.86e-08!6;CL:0000895!1.86e-08!6;CL:0000808!1.86e-08!6;CL:0000894!1.86e-08!6;CL:0000806!1.86e-08!6;CL:0000807!1.86e-08!6;CL:0000805!1.86e-08!6;CL:0002425!1.86e-08!6;CL:0002436!1.86e-08!6;CL:0002427!1.86e-08!6;CL:0002428!1.86e-08!6;CL:0002429!1.86e-08!6;CL:0002433!1.86e-08!6;CL:0002431!1.86e-08!6;CL:0002432!1.86e-08!6;CL:0000738!3.40e-08!17;CL:0002087!3.40e-08!17;CL:0002320!5.33e-07!46;CL:0000134!5.33e-07!46
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!2.34e-18!29;UBERON:0005057!2.34e-18!29;UBERON:0002390!5.86e-17!45;UBERON:0003061!5.86e-17!45;UBERON:0002193!6.42e-17!48;UBERON:0002405!6.42e-17!48;UBERON:0002370!2.85e-16!23;UBERON:0000974!2.85e-16!23;UBERON:0004807!2.85e-16!23;UBERON:0005058!2.85e-16!23;UBERON:0003351!2.85e-16!23;UBERON:0009113!2.85e-16!23;UBERON:0003295!2.85e-16!23;UBERON:0009722!2.85e-16!23;UBERON:0005562!2.85e-16!23;UBERON:0007690!2.85e-16!23;UBERON:0006562!2.36e-15!24;UBERON:0003408!2.36e-15!24;UBERON:0001557!2.36e-15!24;UBERON:0001042!2.36e-15!24;UBERON:0008814!2.36e-15!24;UBERON:0009145!2.36e-15!24;UBERON:0000077!5.22e-14!35;UBERON:0000072!5.15e-13!27;UBERON:0000065!2.77e-12!41;UBERON:0001004!7.95e-12!42;UBERON:0000063!8.35e-09!35;UBERON:0007811!2.04e-08!36;UBERON:0001041!4.41e-07!80;UBERON:0002384!5.33e-07!46
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.275782,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,1.40911,0.411696,0.608816,0.872889,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.724277,0.610669,0.474221,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.971403,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,0.494668,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.928366,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,1.63982,0.876299,1.63327,0.580657,0.212464,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.38417,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.135528
}}

Latest revision as of 19:41, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:11593078..11593101,+p2@Ms4a6b
Mm9::chr2:33764191..33764206,+p@chr2:33764191..33764206
+
Mm9::chr8:35279878..35279900,+p@chr8:35279878..35279900
+


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 cell2.27e-1411
pro-T cell2.27e-1411
lymphoid lineage restricted progenitor cell6.67e-1312
mature alpha-beta T cell1.21e-129
alpha-beta T cell1.21e-129
immature T cell1.21e-129
mature T cell1.21e-129
immature alpha-beta T cell1.21e-129
hematopoietic cell1.42e-1232
hematopoietic oligopotent progenitor cell1.42e-1232
hematopoietic stem cell1.42e-1232
angioblastic mesenchymal cell1.42e-1232
hematopoietic multipotent progenitor cell1.42e-1232
lymphocyte1.16e-1113
common lymphoid progenitor1.16e-1113
CD4-positive, alpha-beta T cell3.25e-118
hematopoietic lineage restricted progenitor cell4.43e-0925
nucleate cell6.78e-0916
thymocyte1.86e-086
double negative thymocyte1.86e-086
naive T cell1.86e-086
double-positive, alpha-beta thymocyte1.86e-086
CD4-positive, alpha-beta thymocyte1.86e-086
naive thymus-derived CD4-positive, alpha-beta T cell1.86e-086
DN4 thymocyte1.86e-086
DN1 thymic pro-T cell1.86e-086
DN2 thymocyte1.86e-086
DN3 thymocyte1.86e-086
immature single positive thymocyte1.86e-086
early T lineage precursor1.86e-086
mature CD4 single-positive thymocyte1.86e-086
resting double-positive thymocyte1.86e-086
double-positive blast1.86e-086
CD69-positive double-positive thymocyte1.86e-086
CD69-positive, CD4-positive single-positive thymocyte1.86e-086
CD4-positive, CD8-intermediate double-positive thymocyte1.86e-086
CD24-positive, CD4 single-positive thymocyte1.86e-086
leukocyte3.40e-0817
nongranular leukocyte3.40e-0817
connective tissue cell5.33e-0746
mesenchymal cell5.33e-0746

Uber Anatomy
Ontology termp-valuen
hemopoietic organ2.34e-1829
immune organ2.34e-1829
hematopoietic system5.86e-1745
blood island5.86e-1745
hemolymphoid system6.42e-1748
immune system6.42e-1748
thymus2.85e-1623
neck2.85e-1623
respiratory system epithelium2.85e-1623
hemolymphoid system gland2.85e-1623
pharyngeal epithelium2.85e-1623
thymic region2.85e-1623
pharyngeal gland2.85e-1623
entire pharyngeal arch endoderm2.85e-1623
thymus primordium2.85e-1623
early pharyngeal endoderm2.85e-1623
pharynx2.36e-1524
gland of gut2.36e-1524
upper respiratory tract2.36e-1524
chordate pharynx2.36e-1524
pharyngeal arch system2.36e-1524
pharyngeal region of foregut2.36e-1524
mixed endoderm/mesoderm-derived structure5.22e-1435
segment of respiratory tract5.15e-1327
respiratory tract2.77e-1241
respiratory system7.95e-1242
organ segment8.35e-0935
craniocervical region2.04e-0836
foregut4.41e-0780
connective tissue5.33e-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)
MA0003.10.0699972
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.133574
MA0017.10.635031
MA0019.14.00152
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
MA0057.10.896032
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
MA0081.11.73701
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.766354
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
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
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
MA0144.10.541532
MA0145.11.44606
MA0146.10.151124
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.20.40695
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.11.58027
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.157796
MA0164.10.933981
MA0080.21.54848
MA0018.20.944669
MA0099.21.06348
MA0079.20.00937321
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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