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MCL coexpression mm9:476: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=
|ontology_enrichment_celltype=CL:0000838!1.59e-13!12;CL:0002031!4.72e-13!25;CL:0000791!1.16e-12!9;CL:0000789!1.16e-12!9;CL:0002420!1.16e-12!9;CL:0002419!1.16e-12!9;CL:0000790!1.16e-12!9;CL:0000084!2.61e-12!11;CL:0000827!2.61e-12!11;CL:0000542!2.65e-12!13;CL:0000051!2.65e-12!13;CL:0000624!7.08e-11!8;CL:0000988!1.22e-10!32;CL:0002032!1.22e-10!32;CL:0000037!1.22e-10!32;CL:0000566!1.22e-10!32;CL:0000837!1.22e-10!32;CL:0002242!1.46e-09!16;CL:0000738!7.24e-09!17;CL:0002087!7.24e-09!17;CL:0000893!8.66e-08!6;CL:0002489!8.66e-08!6;CL:0000898!8.66e-08!6;CL:0000809!8.66e-08!6;CL:0000810!8.66e-08!6;CL:0000895!8.66e-08!6;CL:0000808!8.66e-08!6;CL:0000894!8.66e-08!6;CL:0000806!8.66e-08!6;CL:0000807!8.66e-08!6;CL:0000805!8.66e-08!6;CL:0002425!8.66e-08!6;CL:0002436!8.66e-08!6;CL:0002427!8.66e-08!6;CL:0002428!8.66e-08!6;CL:0002429!8.66e-08!6;CL:0002433!8.66e-08!6;CL:0002431!8.66e-08!6;CL:0002432!8.66e-08!6;CL:0000553!1.46e-07!6;CL:0000556!1.46e-07!6
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004177!4.44e-26!29;UBERON:0005057!4.44e-26!29;UBERON:0002193!6.89e-24!48;UBERON:0002405!6.89e-24!48;UBERON:0002390!1.09e-23!45;UBERON:0003061!1.09e-23!45;UBERON:0002370!1.95e-22!23;UBERON:0000974!1.95e-22!23;UBERON:0004807!1.95e-22!23;UBERON:0005058!1.95e-22!23;UBERON:0003351!1.95e-22!23;UBERON:0009113!1.95e-22!23;UBERON:0003295!1.95e-22!23;UBERON:0009722!1.95e-22!23;UBERON:0005562!1.95e-22!23;UBERON:0007690!1.95e-22!23;UBERON:0006562!2.76e-21!24;UBERON:0003408!2.76e-21!24;UBERON:0001557!2.76e-21!24;UBERON:0001042!2.76e-21!24;UBERON:0008814!2.76e-21!24;UBERON:0009145!2.76e-21!24;UBERON:0000077!1.61e-20!35;UBERON:0000065!1.63e-19!41;UBERON:0001004!6.84e-19!42;UBERON:0000072!2.38e-18!27;UBERON:0000063!5.23e-13!35;UBERON:0007811!1.64e-12!36;UBERON:0003081!2.39e-11!87;UBERON:0001041!1.23e-10!80;UBERON:0000153!1.08e-09!43;UBERON:0005911!5.39e-09!69;UBERON:0000926!8.03e-09!120;UBERON:0004120!8.03e-09!120;UBERON:0006603!8.03e-09!120
|tfbs_overrepresentation_for_novel_motifs=0.206403,0.236794,0.548514,0.238864,0.110365,0.250289,0.324772,0.210111,0.485477,0.0916344,0.288187,0.314655,0.0577792,0.335151,0.769215,0,0.505674,0.34341,0.0508204,0.409021,0.483972,0.28295,0.334384,0.353775,0.561942,0.35869,0.709203,0.267095,0.851419,0.297581,0.255771,0.598971,0.339783,0.352983,0.121176,0.972588,0.0985485,0.311629,0.0859217,0.902111,0.710516,0.720345,0.121081,0.774932,0.2594,0.230148,0.433813,0.279902,0.0916876,0.141659,0.48979,0.381972,0.281801,0.732469,1.77173,0.341233,0.147717,0.303999,0.166653,0.339495,0.580338,0.390204,0.240695,0.479581,0.350748,0.516415,0.880067,1.22155,0.576002,1.07689,0.173229,0.0605055,0.0555827,0.781142,0.158223,1.36095,0.153229,0.423705,0.564426,0.163487,1.25584,0.521544,0.388944,0.0546645,0.671442,0.106224,1.13444,0.868336,0.438181,1.38183,0.947651,0.676142,0.610915,0.738618,1.00206,0.0741053,0.45422,0.613539,0.43404,0.757772,0.325002,0.59871,0.715894,0.490329,0.489372,0.259558,0.543989,1.38865,0.965679,0.161774,0.201092,0.717588,0.954801,0.292444,0.954503,0.346836,0.0221978,0.678491,0.506861,0.096357,0.786314,1.16518,0.360259,0.422901,1.00724,0.567849,0.331666,0.60459,0.8786,0.115924,0.699779,0.233152,0.850049,0.352905,0.975524,0.0491355,1.14834,0.261043,0.927716,1.74768,1.35029,0.884624,0.969317,0.608735,0.483498,0.260275,0.436593,1.7082,0.214583,0.111457,0.128142,0.0423434,0.733963,0.266555,0.352111,0.81211,0.382849,0.403733,0.204546,0.212571,0.93695,0.670634,0.568261,0.199399,0.480505,0.345769,1.10301,0.313326,0.191888
}}

Latest revision as of 15:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:126758963..126758968,+p9@Arhgap9
Mm9::chr11:113034292..113034355,-p2@2610035D17Rik
Mm9::chr11:52113309..52113321,+p@chr11:52113309..52113321
+
Mm9::chr16:58523871..58523923,-p7@St3gal6
Mm9::chr18:56591573..56591588,-p@chr18:56591573..56591588
-
Mm9::chr18:89375492..89375498,+p@chr18:89375492..89375498
+
Mm9::chr6:136412190..136412214,+p@chr6:136412190..136412214
+
Mm9::chr6:99326015..99326030,-p@chr6:99326015..99326030
-
Mm9::chr6:99326038..99326059,-p@chr6:99326038..99326059
-
Mm9::chr7:31940697..31940708,+p@chr7:31940697..31940708
+
Mm9::chr8:89210633..89210646,-p@chr8:89210633..89210646
-
Mm9::chr8:89210648..89210662,-p@chr8:89210648..89210662
-
Mm9::chr9:22459548..22459572,+p@chr9:22459548..22459572
+
Mm9::chr9:22459577..22459586,+p@chr9:22459577..22459586
+
Mm9::chrX:56842460..56842471,+p@chrX:56842460..56842471
+


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
lymphoid lineage restricted progenitor cell1.59e-1312
hematopoietic lineage restricted progenitor cell4.72e-1325
mature alpha-beta T cell1.16e-129
alpha-beta T cell1.16e-129
immature T cell1.16e-129
mature T cell1.16e-129
immature alpha-beta T cell1.16e-129
T cell2.61e-1211
pro-T cell2.61e-1211
lymphocyte2.65e-1213
common lymphoid progenitor2.65e-1213
CD4-positive, alpha-beta T cell7.08e-118
hematopoietic cell1.22e-1032
hematopoietic oligopotent progenitor cell1.22e-1032
hematopoietic stem cell1.22e-1032
angioblastic mesenchymal cell1.22e-1032
hematopoietic multipotent progenitor cell1.22e-1032
nucleate cell1.46e-0916
leukocyte7.24e-0917
nongranular leukocyte7.24e-0917
thymocyte8.66e-086
double negative thymocyte8.66e-086
naive T cell8.66e-086
double-positive, alpha-beta thymocyte8.66e-086
CD4-positive, alpha-beta thymocyte8.66e-086
naive thymus-derived CD4-positive, alpha-beta T cell8.66e-086
DN4 thymocyte8.66e-086
DN1 thymic pro-T cell8.66e-086
DN2 thymocyte8.66e-086
DN3 thymocyte8.66e-086
immature single positive thymocyte8.66e-086
early T lineage precursor8.66e-086
mature CD4 single-positive thymocyte8.66e-086
resting double-positive thymocyte8.66e-086
double-positive blast8.66e-086
CD69-positive double-positive thymocyte8.66e-086
CD69-positive, CD4-positive single-positive thymocyte8.66e-086
CD4-positive, CD8-intermediate double-positive thymocyte8.66e-086
CD24-positive, CD4 single-positive thymocyte8.66e-086
megakaryocyte progenitor cell1.46e-076
megakaryocyte1.46e-076

Uber Anatomy
Ontology termp-valuen
hemopoietic organ4.44e-2629
immune organ4.44e-2629
hemolymphoid system6.89e-2448
immune system6.89e-2448
hematopoietic system1.09e-2345
blood island1.09e-2345
thymus1.95e-2223
neck1.95e-2223
respiratory system epithelium1.95e-2223
hemolymphoid system gland1.95e-2223
pharyngeal epithelium1.95e-2223
thymic region1.95e-2223
pharyngeal gland1.95e-2223
entire pharyngeal arch endoderm1.95e-2223
thymus primordium1.95e-2223
early pharyngeal endoderm1.95e-2223
pharynx2.76e-2124
gland of gut2.76e-2124
upper respiratory tract2.76e-2124
chordate pharynx2.76e-2124
pharyngeal arch system2.76e-2124
pharyngeal region of foregut2.76e-2124
mixed endoderm/mesoderm-derived structure1.61e-2035
respiratory tract1.63e-1941
respiratory system6.84e-1942
segment of respiratory tract2.38e-1827
organ segment5.23e-1335
craniocervical region1.64e-1236
lateral plate mesoderm2.39e-1187
foregut1.23e-1080
anterior region of body1.08e-0943
endo-epithelium5.39e-0969
mesoderm8.03e-09120
mesoderm-derived structure8.03e-09120
presumptive mesoderm8.03e-09120


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)
MA0003.10.0017772
MA0004.10.239244
MA0006.10.118059
MA0007.10.227553
MA0009.10.623671
MA0014.10.00434123
MA0017.10.135289
MA0019.10.456268
MA0024.10.582844
MA0025.10.845702
MA0027.12.24512
MA0028.10.12472
MA0029.10.562703
MA0030.10.568779
MA0031.11.32597
MA0038.10.358622
MA0040.10.635404
MA0041.11.62403
MA0042.10.513077
MA0043.10.71494
MA0046.10.657417
MA0048.10.0239691
MA0050.10.743895
MA0051.10.366328
MA0052.10.642973
MA0055.10.0508438
MA0056.10
MA0057.10.431584
MA0058.10.167504
MA0059.10.176308
MA0060.10.533733
MA0061.11.03173
MA0063.10
MA0066.10.349199
MA0067.10.953264
MA0068.10.0216542
MA0069.10.643292
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.10.220215
MA0074.10.318792
MA0076.10.148159
MA0077.10.605975
MA0078.11.02284
MA0081.10.193203
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.10.292366
MA0089.10
MA0090.10.212772
MA0091.11.28859
MA0092.10.213012
MA0093.10.130107
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.538493
MA0103.10.863534
MA0105.10.341877
MA0106.10.401864
MA0107.10.84583
MA0108.20.476838
MA0109.10
MA0111.10.635898
MA0113.10.983782
MA0114.10.291992
MA0115.10.717599
MA0116.10.37608
MA0117.10.686999
MA0119.11.03177
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.10.452196
MA0132.10
MA0133.10
MA0135.10.749615
MA0136.10.891604
MA0139.10.20466
MA0140.10.30902
MA0141.10.155997
MA0142.11.29772
MA0143.11.01504
MA0144.10.296781
MA0145.10.320696
MA0146.10.000953111
MA0147.10.0952713
MA0148.10.252062
MA0149.10.18682
MA0062.20.154316
MA0035.20.312946
MA0039.20.00549298
MA0138.20.445088
MA0002.20.0572064
MA0137.20.153989
MA0104.20.0641853
MA0047.20.357963
MA0112.20.54155
MA0065.20.160972
MA0150.10.227466
MA0151.10
MA0152.10.9415
MA0153.10.765498
MA0154.10.10034
MA0155.10.189024
MA0156.11.42296
MA0157.12.13916
MA0158.10
MA0159.10.101261
MA0160.10.707761
MA0161.10
MA0162.10.00971175
MA0163.10.0289848
MA0164.11.60174
MA0080.20.430071
MA0018.20.344133
MA0099.21.1194
MA0079.20.105321
MA0102.21.32652
MA0258.10.572032
MA0259.10.299239
MA0442.10
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