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MCL coexpression mm9:1157: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0.901603214580908,0.153011413271348,0,0,0,0.268578825882798,0.207349631308431,0,0.0800761525331175,0,0.634714277490948,0.540086578053177,0.753451767972442,0,0.0411126530948397,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.200913802025349,0,0,0,0,0,0,0,0,0,0,0,0.454175174874543,0,0.125836948423969,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0681778550615498,0.056886356216389,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0002031!1.14e-29!25;CL:0000838!2.73e-25!12;CL:0000542!2.59e-23!13;CL:0000051!2.59e-23!13;CL:0000988!6.05e-23!32;CL:0002032!6.05e-23!32;CL:0000037!6.05e-23!32;CL:0000566!6.05e-23!32;CL:0000837!6.05e-23!32;CL:0000084!2.42e-20!11;CL:0000827!2.42e-20!11;CL:0002242!7.34e-19!16;CL:0000738!1.01e-17!17;CL:0002087!1.01e-17!17;CL:0000791!1.02e-17!9;CL:0000789!1.02e-17!9;CL:0002420!1.02e-17!9;CL:0002419!1.02e-17!9;CL:0000790!1.02e-17!9;CL:0000553!1.41e-17!6;CL:0000556!1.41e-17!6;CL:0002320!1.30e-15!46;CL:0000134!1.30e-15!46;CL:0000624!3.67e-13!8;CL:0000219!4.04e-13!54;CL:0000050!8.23e-12!9;CL:0000893!4.12e-10!6;CL:0002489!4.12e-10!6;CL:0000898!4.12e-10!6;CL:0000809!4.12e-10!6;CL:0000810!4.12e-10!6;CL:0000895!4.12e-10!6;CL:0000808!4.12e-10!6;CL:0000894!4.12e-10!6;CL:0000806!4.12e-10!6;CL:0000807!4.12e-10!6;CL:0000805!4.12e-10!6;CL:0002425!4.12e-10!6;CL:0002436!4.12e-10!6;CL:0002427!4.12e-10!6;CL:0002428!4.12e-10!6;CL:0002429!4.12e-10!6;CL:0002433!4.12e-10!6;CL:0002431!4.12e-10!6;CL:0002432!4.12e-10!6;CL:0000034!1.16e-09!97;CL:0000839!3.06e-08!13;CL:0000815!4.65e-08!1;CL:0000792!4.65e-08!1;CL:0000945!8.50e-08!1;CL:0000236!8.50e-08!1;CL:0000826!8.50e-08!1;CL:0000625!1.78e-07!1;CL:0000723!2.98e-07!91;CL:0000048!2.98e-07!91
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002384!1.30e-15!46
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,0.480627,0.810002,0.495263,0.587291,1.12275,0.616096,0.478312,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.291368,0.19222,0.361892,0.374752,0.27937,0.598814,0.29769,0.419327,0.62766,1.0368,0.516511,0.344372,0.446946,0.50223,0.897561,0.289148,0.166577,0.848378,0.248902,0.279977,0.57142,0.717242,0.230656,0.295233,0.507468,0.932136,0.317766,0.515031,0.469348,0.714592,0.532496,0.478447,0.917701,0.777641,0.654933,0.851157,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.0869413,1.09164,0.17012,0.159969,0.498755,0.703064,0.859987,0.378988,1.79723,0.812889,0.663039,0.580284,0.975495,0.0369809,0.164297,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.589174,0.913319,0.71485,0.127063,0.7665,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,0.187586,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,1.45183,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.813943,0.147909,0.0736236,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.0907999
}}

Latest revision as of 16:29, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:29574198..29574200,-p@chr17:29574198..29574200
-
Mm9::chr17:35164579..35164592,-p4@Ng23
Mm9::chr2:3632851..3632870,-p@chr2:3632851..3632870
-
Mm9::chr2:3644059..3644080,-p@chr2:3644059..3644080
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Mm9::chr9:32423528..32423533,-p@chr9:32423528..32423533
-
Mm9::chr9:7868276..7868285,+p@chr9:7868276..7868285
+
Mm9::chr9:7870721..7870735,+p@chr9:7870721..7870735
+


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
hematopoietic lineage restricted progenitor cell1.14e-2925
lymphoid lineage restricted progenitor cell2.73e-2512
lymphocyte2.59e-2313
common lymphoid progenitor2.59e-2313
hematopoietic cell6.05e-2332
hematopoietic oligopotent progenitor cell6.05e-2332
hematopoietic stem cell6.05e-2332
angioblastic mesenchymal cell6.05e-2332
hematopoietic multipotent progenitor cell6.05e-2332
T cell2.42e-2011
pro-T cell2.42e-2011
nucleate cell7.34e-1916
leukocyte1.01e-1717
nongranular leukocyte1.01e-1717
mature alpha-beta T cell1.02e-179
alpha-beta T cell1.02e-179
immature T cell1.02e-179
mature T cell1.02e-179
immature alpha-beta T cell1.02e-179
megakaryocyte progenitor cell1.41e-176
megakaryocyte1.41e-176
connective tissue cell1.30e-1546
mesenchymal cell1.30e-1546
CD4-positive, alpha-beta T cell3.67e-138
motile cell4.04e-1354
megakaryocyte-erythroid progenitor cell8.23e-129
thymocyte4.12e-106
double negative thymocyte4.12e-106
naive T cell4.12e-106
double-positive, alpha-beta thymocyte4.12e-106
CD4-positive, alpha-beta thymocyte4.12e-106
naive thymus-derived CD4-positive, alpha-beta T cell4.12e-106
DN4 thymocyte4.12e-106
DN1 thymic pro-T cell4.12e-106
DN2 thymocyte4.12e-106
DN3 thymocyte4.12e-106
immature single positive thymocyte4.12e-106
early T lineage precursor4.12e-106
mature CD4 single-positive thymocyte4.12e-106
resting double-positive thymocyte4.12e-106
double-positive blast4.12e-106
CD69-positive double-positive thymocyte4.12e-106
CD69-positive, CD4-positive single-positive thymocyte4.12e-106
CD4-positive, CD8-intermediate double-positive thymocyte4.12e-106
CD24-positive, CD4 single-positive thymocyte4.12e-106
stem cell1.16e-0997
myeloid lineage restricted progenitor cell3.06e-0813
regulatory T cell4.65e-081
CD4-positive, CD25-positive, alpha-beta regulatory T cell4.65e-081
lymphocyte of B lineage8.50e-081
B cell8.50e-081
pro-B cell8.50e-081
CD8-positive, alpha-beta T cell1.78e-071
somatic stem cell2.98e-0791
multi fate stem cell2.98e-0791

Uber Anatomy
Ontology termp-valuen
connective tissue1.30e-1546


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)
MA0003.10.0861444
MA0004.11.20906
MA0006.10.311391
MA0007.12.04776
MA0009.10.92425
MA0014.10.222567
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.10.117936
MA0058.11.00014
MA0059.11.02718
MA0060.10.232592
MA0061.11.33382
MA0063.10
MA0066.12.54082
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.00223012
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.11.07783
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.11.1347
MA0091.10.494398
MA0092.10.446857
MA0093.10.879104
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.488671
MA0106.10.677988
MA0107.10.906859
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.12.64666
MA0114.10.259463
MA0115.11.0246
MA0116.10.836994
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.11.46167
MA0139.10.585936
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.11.59922
MA0144.10.262477
MA0145.10.0910975
MA0146.10.792204
MA0147.10.753844
MA0148.11.24416
MA0149.10.411562
MA0062.20.500692
MA0035.20.573016
MA0039.20.113749
MA0138.20.727395
MA0002.20.592533
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.20.304722
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.687925
MA0156.10.936991
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.0312493
MA0163.10.0280055
MA0164.10.600609
MA0080.21.62792
MA0018.20.610433
MA0099.20.721008
MA0079.20.000323799
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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