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MCL coexpression mm9:363: Difference between revisions

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{{MCL_coexpression_mm9
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alpha-subunit 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|coexpression_dpi_cluster_scores_median=0.0511331705127143,0.100348428349114,0.118661214911273,0.0742329500129511,0.176350522035494,0.0673979504369913,0.0911788108631387,0.338305066013194,0.409188761557951,0.336524299153945,0.127893569522672,0.0875881631095468,0.401494605878021,0.371474778712675,0,0,0,0.119078361648301,0.105247439647798,0.153628809860867,0.506657285314008,0.0786677159214676,0.100783889465809,0,0,0.197068726315728,0,0.07631378064262,0,0,0,0.0463916334559523,0,0,0.19802531727213,0.133332486121186,0.160277301906003,0.545454304287177,0.523653174287599,0.44998590032864,1.04645810331042,0.815087915332415,0.468648781556237,0,0,0,0,0,0,0,0,0,0.427782363794443,0.389294454188438,0.330966376408921,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.434082051378957,0,0,0,0,0,0.0570741246689917,0,0,0,0.107781924973909,0,0,0,0.0861225251447526,0,0,0.139859774185417,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.156644408065653,0.315890049924411,0.140259928189304,0,0,0,0,0,0,0,0,0.0509235292940968,0.0978549673988937,0,0,0,0,0,0,0,0.00701898430796533,0,0,0,0.0642854890366857,0,0,0,0,0,0,0.165577644050908,0.200157522212723,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00347721145778292,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00621629886618591,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0659019793256198,0,0.0586723554240733,0,0,0,0,0.0174394821335513,0,0,0,0,0,0,0,0,0,0,0,0,0.00174888217737934,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0137711540544081,0,0,0.0668789380564715,0,0.115432414129512,0,0,0,0,0.00227692943214108,0,0,0,0,0,0.00840937817146895,0,0,0,0,0,0.197290472420318,0.195033573140198,0.191115493074292,0,0,0,0,0,0,0,0,0,0,0,1.00082814860724,0,0,0,0,0,0,0,0,0.396645726271941,0.910056981743651,0,0,0,0,0,0,0,0,0,0,0,0,0.0292059986091096,0.0032360472139612,0,0,0,0,0,0,0,0,0,0,0,0,0.0688732037536692,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0001965;G-protein alpha-subunit binding;0.0226799604204372;101489!
|ontology_enrichment_celltype=CL:0000838!4.82e-16!12;CL:0000988!6.17e-15!32;CL:0002032!6.17e-15!32;CL:0000037!6.17e-15!32;CL:0000566!6.17e-15!32;CL:0000837!6.17e-15!32;CL:0000084!1.21e-14!11;CL:0000827!1.21e-14!11;CL:0000542!1.52e-14!13;CL:0000051!1.52e-14!13;CL:0002242!6.08e-13!16;CL:0000791!9.08e-13!9;CL:0000789!9.08e-13!9;CL:0002420!9.08e-13!9;CL:0002419!9.08e-13!9;CL:0000790!9.08e-13!9;CL:0000624!1.73e-11!8;CL:0002031!3.99e-11!25;CL:0002563!8.04e-11!9;CL:0002251!8.04e-11!9;CL:0000738!2.46e-10!17;CL:0002087!2.46e-10!17;CL:0002320!9.28e-10!46;CL:0000134!9.28e-10!46;CL:0000893!7.42e-09!6;CL:0002489!7.42e-09!6;CL:0000898!7.42e-09!6;CL:0000809!7.42e-09!6;CL:0000810!7.42e-09!6;CL:0000895!7.42e-09!6;CL:0000808!7.42e-09!6;CL:0000894!7.42e-09!6;CL:0000806!7.42e-09!6;CL:0000807!7.42e-09!6;CL:0000805!7.42e-09!6;CL:0002425!7.42e-09!6;CL:0002436!7.42e-09!6;CL:0002427!7.42e-09!6;CL:0002428!7.42e-09!6;CL:0002429!7.42e-09!6;CL:0002433!7.42e-09!6;CL:0002431!7.42e-09!6;CL:0002432!7.42e-09!6;CL:0000066!1.20e-08!25;CL:0000075!2.13e-08!7;CL:0002371!2.23e-08!118;CL:0000219!1.97e-07!54;CL:0000239!2.17e-07!6;CL:0000677!2.17e-07!6;CL:0000212!2.17e-07!6;CL:0000584!2.17e-07!6;CL:0000034!3.63e-07!97;CL:0002076!4.55e-07!15
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000485!1.27e-12!11;UBERON:0003350!8.04e-11!9;UBERON:0004808!8.04e-11!9;UBERON:0001277!8.04e-11!9;UBERON:0002384!9.28e-10!46;UBERON:0001242!6.86e-07!13;UBERON:0000060!6.86e-07!13;UBERON:0001262!6.86e-07!13;UBERON:0004786!6.86e-07!13
}}

Latest revision as of 15:10, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:116661302..116661324,+p@chr10:116661302..116661324
+
Mm9::chr11:109512773..109512784,+p@chr11:109512773..109512784
+
Mm9::chr11:23206302..23206316,-p@chr11:23206302..23206316
-
Mm9::chr11:68912249..68912254,-p@chr11:68912249..68912254
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Mm9::chr12:112680511..112680520,-p@chr12:112680511..112680520
-
Mm9::chr13:81024809..81024820,-p3@ENSMUST00000161006
Mm9::chr14:122504223..122504252,+p@chr14:122504223..122504252
+
Mm9::chr15:79518396..79518423,+p@chr15:79518396..79518423
+
Mm9::chr17:48548802..48548850,-p@chr17:48548802..48548850
-
Mm9::chr17:48548913..48548924,-p@chr17:48548913..48548924
-
Mm9::chr18:3337339..3337397,-p5@Crem
Mm9::chr1:31006709..31006727,+p@chr1:31006709..31006727
+
Mm9::chr1:31007100..31007109,+p@chr1:31007100..31007109
+
Mm9::chr2:121275931..121275949,-p@chr2:121275931..121275949
-
Mm9::chr4:109157479..109157491,+p@chr4:109157479..109157491
+
Mm9::chr4:132909391..132909420,-p9@Wdtc1
Mm9::chr7:148042635..148042666,+p8@Ric8
Mm9::chr7:52494411..52494436,-p5@Cd37
Mm9::chr8:4678338..4678356,-p1@Gm7461
Mm9::chr8:4678528..4678538,+p6@ENSMUST00000105524
Mm9::chr9:108552145..108552149,+p@chr9:108552145..108552149
+


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

GO IDGO nameFDR corrected p-value
GO:0001965G-protein alpha-subunit binding0.0226799604204372



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
lymphoid lineage restricted progenitor cell4.82e-1612
hematopoietic cell6.17e-1532
hematopoietic oligopotent progenitor cell6.17e-1532
hematopoietic stem cell6.17e-1532
angioblastic mesenchymal cell6.17e-1532
hematopoietic multipotent progenitor cell6.17e-1532
T cell1.21e-1411
pro-T cell1.21e-1411
lymphocyte1.52e-1413
common lymphoid progenitor1.52e-1413
nucleate cell6.08e-1316
mature alpha-beta T cell9.08e-139
alpha-beta T cell9.08e-139
immature T cell9.08e-139
mature T cell9.08e-139
immature alpha-beta T cell9.08e-139
CD4-positive, alpha-beta T cell1.73e-118
hematopoietic lineage restricted progenitor cell3.99e-1125
intestinal epithelial cell8.04e-119
epithelial cell of alimentary canal8.04e-119
leukocyte2.46e-1017
nongranular leukocyte2.46e-1017
connective tissue cell9.28e-1046
mesenchymal cell9.28e-1046
thymocyte7.42e-096
double negative thymocyte7.42e-096
naive T cell7.42e-096
double-positive, alpha-beta thymocyte7.42e-096
CD4-positive, alpha-beta thymocyte7.42e-096
naive thymus-derived CD4-positive, alpha-beta T cell7.42e-096
DN4 thymocyte7.42e-096
DN1 thymic pro-T cell7.42e-096
DN2 thymocyte7.42e-096
DN3 thymocyte7.42e-096
immature single positive thymocyte7.42e-096
early T lineage precursor7.42e-096
mature CD4 single-positive thymocyte7.42e-096
resting double-positive thymocyte7.42e-096
double-positive blast7.42e-096
CD69-positive double-positive thymocyte7.42e-096
CD69-positive, CD4-positive single-positive thymocyte7.42e-096
CD4-positive, CD8-intermediate double-positive thymocyte7.42e-096
CD24-positive, CD4 single-positive thymocyte7.42e-096
epithelial cell1.20e-0825
columnar/cuboidal epithelial cell2.13e-087
somatic cell2.23e-08118
motile cell1.97e-0754
brush border epithelial cell2.17e-076
gut absorptive cell2.17e-076
absorptive cell2.17e-076
enterocyte2.17e-076
stem cell3.63e-0797
endo-epithelial cell4.55e-0715


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)
MA0003.10.890085
MA0004.11.46848
MA0006.10.486909
MA0007.10.145624
MA0009.10.499857
MA0014.10.344511
MA0017.10.935226
MA0019.10.344318
MA0024.10.461433
MA0025.10.712532
MA0027.12.09948
MA0028.10.511618
MA0029.10.442582
MA0030.10.448261
MA0031.10.417663
MA0038.11.31548
MA0040.10.510947
MA0041.10.109446
MA0042.10.102161
MA0043.11.43301
MA0046.10.531807
MA0048.10.409427
MA0050.10.180744
MA0051.10.263603
MA0052.10.518112
MA0055.10.231647
MA0056.10
MA0057.10.0321706
MA0058.10.324689
MA0059.10.105184
MA0060.14.66952
MA0061.11.03103
MA0063.10
MA0066.10.694084
MA0067.10.817149
MA0068.10.100153
MA0069.10.518414
MA0070.10.509795
MA0071.10.180178
MA0072.10.502282
MA0073.10.0360649
MA0074.10.632353
MA0076.10.0840393
MA0077.10.48317
MA0078.10.289095
MA0081.10.37696
MA0083.10.585897
MA0084.11.1333
MA0087.10.546952
MA0088.10.225275
MA0089.10
MA0090.10.416778
MA0091.10.163657
MA0092.10.417266
MA0093.11.88694
MA0095.10
MA0098.10
MA0100.10.612698
MA0101.11.18628
MA0103.10.57683
MA0105.11.18816
MA0106.10.800883
MA0107.11.4231
MA0108.20.363107
MA0109.10
MA0111.10.14244
MA0113.10.273246
MA0114.10.656298
MA0115.11.43837
MA0116.10.0624169
MA0117.10.559943
MA0119.10.356648
MA0122.10.577888
MA0124.10.766819
MA0125.10.697415
MA0130.10
MA0131.10.340612
MA0132.10
MA0133.10
MA0135.10.619844
MA0136.10.666439
MA0139.10.245643
MA0140.10.2137
MA0141.10.625596
MA0142.10.40532
MA0143.10.285913
MA0144.10.373777
MA0145.10.625223
MA0146.12.84612
MA0147.10.708858
MA0148.10.165681
MA0149.10.113293
MA0062.21.22637
MA0035.20.217072
MA0039.21.71403
MA0138.20.334152
MA0002.20.251244
MA0137.20.0883456
MA0104.20.279424
MA0047.20.256234
MA0112.21.86652
MA0065.20.418537
MA0150.10.87649
MA0151.10
MA0152.10.256315
MA0153.10.635107
MA0154.10.400841
MA0155.10.301849
MA0156.11.00164
MA0157.10.378326
MA0158.10
MA0159.10.190402
MA0160.10.167661
MA0161.10
MA0162.13.18529
MA0163.10.489707
MA0164.10.23692
MA0080.20.563938
MA0018.22.74968
MA0099.20.329046
MA0079.20.267699
MA0102.21.18455
MA0258.10.610753
MA0259.11.47814
MA0442.10
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