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MCL coexpression mm9:639: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.413854914439209,0.881787943371597,0.835792834727366,0.180026585552633,0.273578499709972,0.342107724764957,0.230286214243433,0,0,0,0.119078361648301,0.0558041721483835,0,0,0.0411126530948397,0,0.0644551523736777,0,0,0,0,0,0,0.0839793170280262,0,0,0,0,0,0,0.86455965894399,0.615459892883158,0.490533640609026,1.19605970885837,0.762026887945864,0.643311751835009,0.0514985917256918,0.0419359757688424,0.073185417993707,0,0,0,0,0,0,0.22705576246071,0.389294454188438,0.125836948423969,0,0.033995335178371,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0317017435824471,0,0.68815506582299,0,0,0,0,0,0.0397519380874063,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.427715163864743,0.300173318036138,0.423559264412865,0,0,0,0,0,0,0,0.00508484160320079,0.0509235292940968,0,0,0,0,0,0,0.0285860945550467,0,0,0,0,0,0,0,0,0,0,0,0.231013950740173,0.307365864513145,0.383962049647022,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0774164737207147,0,0,0,0,0.0691813633419548,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.120939615821127,0,0,0,0.0564111250741226,0,0,0,0,0,0,0,0,0.0254340553719351,0,0,0,0,0,0,0,0,0,0,0.431329067459534,0.428040377850264,0.424620276916781,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0417740847988257,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0008538;proteasome activator activity;0.00542317164695645;19188!GO:0008537;proteasome activator complex;0.00542317164695645;19188!GO:0019884;antigen processing and presentation of exogenous antigen;0.0276880692576502;19188!
|ontology_enrichment_celltype=CL:0000838!3.62e-19!12;CL:0000988!4.32e-19!32;CL:0002032!4.32e-19!32;CL:0000037!4.32e-19!32;CL:0000566!4.32e-19!32;CL:0000837!4.32e-19!32;CL:0000791!4.65e-18!9;CL:0000789!4.65e-18!9;CL:0002420!4.65e-18!9;CL:0002419!4.65e-18!9;CL:0000790!4.65e-18!9;CL:0000542!1.71e-17!13;CL:0000051!1.71e-17!13;CL:0000084!1.82e-17!11;CL:0000827!1.82e-17!11;CL:0000624!2.09e-16!8;CL:0002242!9.82e-14!16;CL:0002320!1.97e-13!46;CL:0000134!1.97e-13!46;CL:0000738!8.89e-13!17;CL:0002087!8.89e-13!17;CL:0000893!1.07e-12!6;CL:0002489!1.07e-12!6;CL:0000898!1.07e-12!6;CL:0000809!1.07e-12!6;CL:0000810!1.07e-12!6;CL:0000895!1.07e-12!6;CL:0000808!1.07e-12!6;CL:0000894!1.07e-12!6;CL:0000806!1.07e-12!6;CL:0000807!1.07e-12!6;CL:0000805!1.07e-12!6;CL:0002425!1.07e-12!6;CL:0002436!1.07e-12!6;CL:0002427!1.07e-12!6;CL:0002428!1.07e-12!6;CL:0002429!1.07e-12!6;CL:0002433!1.07e-12!6;CL:0002431!1.07e-12!6;CL:0002432!1.07e-12!6;CL:0000034!2.34e-12!97;CL:0000219!7.03e-12!54;CL:0002031!4.08e-11!25;CL:0000355!3.65e-10!9;CL:0000723!3.83e-10!91;CL:0000048!3.83e-10!91;CL:0002371!5.18e-07!118
|ontology_enrichment_disease=DOID:0060100!1.06e-07!3;DOID:4045!1.06e-07!3
|ontology_enrichment_uberon=UBERON:0002384!1.97e-13!46;UBERON:0001134!3.65e-10!9;UBERON:0002036!3.65e-10!9;UBERON:0002385!3.65e-10!9;UBERON:0000486!3.65e-10!9;UBERON:0007503!3.65e-10!9;UBERON:0001015!3.65e-10!9;UBERON:0002329!3.65e-10!9;UBERON:0003082!3.65e-10!9;UBERON:0003059!3.65e-10!9;UBERON:0007282!3.65e-10!9;UBERON:0004290!3.65e-10!9;UBERON:0009618!3.65e-10!9;UBERON:0000383!4.90e-09!10;UBERON:0007524!4.10e-08!11;UBERON:0003077!4.10e-08!11;UBERON:0007285!4.10e-08!11
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.0513547,0.269904,0.329881,0.176699,0.342839,0.425757,0.106126,0.112618,0.660314,0.385334,1.06556,0.106288,0.437133,0.555819,0,0.619876,0.170475,0.318616,0.0448402,0.670854,0.281622,0.436294,0.520732,0.276437,0.4628,0.0908349,0.361771,0.611503,0.0650265,0.349031,0.717576,0.168723,0.570676,0.19035,0.075793,0.161521,0.411296,0.873942,0.391645,0.992655,0.353696,0.255102,0.191571,0.812209,0.319944,0.543674,0.376103,0.660525,0.215702,0.603113,0.488021,0.0612063,0.855661,0.87275,0.443782,0.223087,0.40287,0.60268,0.441884,0.698157,1.24284,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.706068,1.18624,0.0307733,0.905636,0.0810502,0.54852,0.570456,0.532872,0.681539,0.242107,0.357936,0.636582,0.495545,0.101814,0.792744,0.00855221,0.0106044,1.29984,0.548334,1.51408,1.07554,0.797601,0.730003,0.535058,0.141946,0.805383,0.694736,0.732731,0.543917,0.197581,0.486605,0.717305,0.838603,0.603683,1.46677,0.353298,0.660145,0.372438,0.688705,0.240055,0.286453,0.840348,0.243062,0.390066,1.0825,0.512539,0.170188,0.333247,0.621127,0.158673,0.910937,0.572279,0.464505,0.532013,1.13603,1.63906,0.433317,0.723425,1.00525,0.183744,0.821997,0.323373,0.976125,0.456508,1.10385,9.76511,0.300001,1.66879,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,0.527071,0.0664621,0.0240729,1.99431,0.415832,0.455644,0.93735,0.488969,0.199652,0.790184,0.299755,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.939822,1.06237,0.148813
}}

Latest revision as of 15:38, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:61969312..61969341,+p@chr10:61969312..61969341
+
Mm9::chr10:89208517..89208523,-p@chr10:89208517..89208523
-
Mm9::chr10:89208554..89208568,-p@chr10:89208554..89208568
-
Mm9::chr11:103558635..103558654,+p2@ENSMUST00000129780
p2@ENSMUST00000154471
p2@uc007lvp.1
p2@uc011yfx.1
Mm9::chr11:78059245..78059323,+p2@Sdf2
Mm9::chr14:56210316..56210343,-p6@Psme2
Mm9::chr1:58769066..58769089,-p@chr1:58769066..58769089
-
Mm9::chr1:58769240..58769278,+p@chr1:58769240..58769278
+
Mm9::chr1:58783936..58783956,-p@chr1:58783936..58783956
-
Mm9::chr2:160472300..160472306,-p@chr2:160472300..160472306
-
Mm9::chr7:148127785..148127855,+p2@Athl1


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:0008538proteasome activator activity0.00542317164695645
GO:0008537proteasome activator complex0.00542317164695645
GO:0019884antigen processing and presentation of exogenous antigen0.0276880692576502



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>disease_data<br>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell3.62e-1912
hematopoietic cell4.32e-1932
hematopoietic oligopotent progenitor cell4.32e-1932
hematopoietic stem cell4.32e-1932
angioblastic mesenchymal cell4.32e-1932
hematopoietic multipotent progenitor cell4.32e-1932
mature alpha-beta T cell4.65e-189
alpha-beta T cell4.65e-189
immature T cell4.65e-189
mature T cell4.65e-189
immature alpha-beta T cell4.65e-189
lymphocyte1.71e-1713
common lymphoid progenitor1.71e-1713
T cell1.82e-1711
pro-T cell1.82e-1711
CD4-positive, alpha-beta T cell2.09e-168
nucleate cell9.82e-1416
connective tissue cell1.97e-1346
mesenchymal cell1.97e-1346
leukocyte8.89e-1317
nongranular leukocyte8.89e-1317
thymocyte1.07e-126
double negative thymocyte1.07e-126
naive T cell1.07e-126
double-positive, alpha-beta thymocyte1.07e-126
CD4-positive, alpha-beta thymocyte1.07e-126
naive thymus-derived CD4-positive, alpha-beta T cell1.07e-126
DN4 thymocyte1.07e-126
DN1 thymic pro-T cell1.07e-126
DN2 thymocyte1.07e-126
DN3 thymocyte1.07e-126
immature single positive thymocyte1.07e-126
early T lineage precursor1.07e-126
mature CD4 single-positive thymocyte1.07e-126
resting double-positive thymocyte1.07e-126
double-positive blast1.07e-126
CD69-positive double-positive thymocyte1.07e-126
CD69-positive, CD4-positive single-positive thymocyte1.07e-126
CD4-positive, CD8-intermediate double-positive thymocyte1.07e-126
CD24-positive, CD4 single-positive thymocyte1.07e-126
stem cell2.34e-1297
motile cell7.03e-1254
hematopoietic lineage restricted progenitor cell4.08e-1125
multi-potent skeletal muscle stem cell3.65e-109
somatic stem cell3.83e-1091
multi fate stem cell3.83e-1091
somatic cell5.18e-07118

Disease
Ontology termp-valuen
musculoskeletal system cancer1.06e-073
muscle cancer1.06e-073


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)
MA0003.10.156602
MA0004.10.330313
MA0006.10.186435
MA0007.10.316976
MA0009.10.743257
MA0014.10.144697
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.567414
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.11.34187
MA0042.10.703657
MA0043.10.837621
MA0046.10.778239
MA0048.10.199479
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.0098576
MA0056.10
MA0057.10.181039
MA0058.10.246908
MA0059.10.257372
MA0060.10.789184
MA0061.10.451296
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.418079
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.0672071
MA0074.10.419185
MA0076.10.635923
MA0077.10.724865
MA0078.10.502121
MA0081.10.760108
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.0293443
MA0089.10
MA0090.10.299987
MA0091.10.906056
MA0092.10.300264
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.73212
MA0103.10.216742
MA0105.10.26272
MA0106.10.509454
MA0107.10.607721
MA0108.20.589413
MA0109.10
MA0111.10.312463
MA0113.11.21288
MA0114.10.145642
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.10.265536
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.11.95245
MA0139.10.103495
MA0140.10.408417
MA0141.10.658164
MA0142.10.63775
MA0143.10.49828
MA0144.10.147954
MA0145.10.57264
MA0146.10.0833862
MA0147.10.157258
MA0148.10.344843
MA0149.10.269772
MA0062.20.573094
MA0035.20.412747
MA0039.20.499196
MA0138.20.555696
MA0002.20.343346
MA0137.20.230686
MA0104.20.11535
MA0047.20.46201
MA0112.20.313687
MA0065.20.314773
MA0150.10.849777
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.195907
MA0155.10.354827
MA0156.11.851
MA0157.10.606944
MA0158.10
MA0159.10.165031
MA0160.10.347545
MA0161.10
MA0162.10.0355033
MA0163.10.0916052
MA0164.11.95358
MA0080.20.609443
MA0018.20.446948
MA0099.21.35508
MA0079.20.00532751
MA0102.21.45844
MA0258.10.421574
MA0259.10.14914
MA0442.10
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