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MCL coexpression mm9:292: Difference between revisions

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{{MCL_coexpression_mm9
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kinase phosphatase activity;0.039921137030804;19252!GO:0017017;MAP kinase tyrosine/serine/threonine phosphatase 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|coexpression_dpi_cluster_scores_median=0,0,0,0.0573828993656285,0.062908599447199,0,0.0911788108631387,0.864861282589211,0.380892504618774,0.357877580566854,0.136894152503244,0.0787347879396902,0.729564525854225,0.676862313506086,0,0,0,0.190346765729239,0.149632666139897,0.153628809860867,0,0.0411126530948397,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0415192773019274,0.157045365050363,0,0,0,0.200913802025349,0,0,0.0514985917256918,0.0419359757688424,0.0113260474263052,0,0,0,0,0,0,0.22301034595168,0.501892311714437,0.479512370320439,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.91796371343602,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.100004302423367,0,0,0,0,0,0,0,0,0.00183184857363957,0,0,0,0,0,0,0,0,0.120046814898098,0.190778633576452,0.140259928189304,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.180325425270187,0.108620321524749,0,0,0,0,0,0,0,0,0,0,0,0.0075698410043086,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0156529493032097,0,0,0,0,0,0,0,0,0,0,0.0442950572662417,0,0.033405693853525,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0383569641205167,0,0,0,0,0,0,0,0,0,0,0.0138800150590559,0,0,0,0,0,0,0,0,0,0,0,0,0.201993230613794,0.230386905221361,0.15063362961962,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0463148334396615,0,0,0,0.0715236385554987,0.0787037500278776,0.0215126239715145,0.0598244186619439,0.0798802230592418,0.0467520571956962,0.0797788474440915,0.0642863497013468,0.108916251331407,0.117221673010779,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0033549;MAP kinase phosphatase activity;0.039921137030804;19252!GO:0017017;MAP kinase tyrosine/serine/threonine phosphatase activity;0.039921137030804;19252!
|ontology_enrichment_celltype=CL:0000838!6.60e-19!12;CL:0000988!2.73e-18!32;CL:0002032!2.73e-18!32;CL:0000037!2.73e-18!32;CL:0000566!2.73e-18!32;CL:0000837!2.73e-18!32;CL:0000791!7.15e-18!9;CL:0000789!7.15e-18!9;CL:0002420!7.15e-18!9;CL:0002419!7.15e-18!9;CL:0000790!7.15e-18!9;CL:0000542!3.12e-17!13;CL:0000051!3.12e-17!13;CL:0000084!4.21e-17!11;CL:0000827!4.21e-17!11;CL:0000624!5.52e-16!8;CL:0002242!1.79e-13!16;CL:0002031!6.93e-13!25;CL:0002320!1.05e-12!46;CL:0000134!1.05e-12!46;CL:0000738!1.62e-12!17;CL:0002087!1.62e-12!17;CL:0000893!3.94e-12!6;CL:0002489!3.94e-12!6;CL:0000898!3.94e-12!6;CL:0000809!3.94e-12!6;CL:0000810!3.94e-12!6;CL:0000895!3.94e-12!6;CL:0000808!3.94e-12!6;CL:0000894!3.94e-12!6;CL:0000806!3.94e-12!6;CL:0000807!3.94e-12!6;CL:0000805!3.94e-12!6;CL:0002425!3.94e-12!6;CL:0002436!3.94e-12!6;CL:0002427!3.94e-12!6;CL:0002428!3.94e-12!6;CL:0002429!3.94e-12!6;CL:0002433!3.94e-12!6;CL:0002431!3.94e-12!6;CL:0002432!3.94e-12!6;CL:0000219!5.00e-10!54;CL:0000034!7.04e-09!97;CL:0000723!3.85e-07!91;CL:0000048!3.85e-07!91
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002370!2.78e-19!23;UBERON:0000974!2.78e-19!23;UBERON:0004807!2.78e-19!23;UBERON:0005058!2.78e-19!23;UBERON:0003351!2.78e-19!23;UBERON:0009113!2.78e-19!23;UBERON:0003295!2.78e-19!23;UBERON:0009722!2.78e-19!23;UBERON:0005562!2.78e-19!23;UBERON:0007690!2.78e-19!23;UBERON:0006562!2.73e-18!24;UBERON:0003408!2.73e-18!24;UBERON:0001557!2.73e-18!24;UBERON:0001042!2.73e-18!24;UBERON:0008814!2.73e-18!24;UBERON:0009145!2.73e-18!24;UBERON:0000072!9.22e-16!27;UBERON:0002193!6.09e-15!48;UBERON:0002405!6.09e-15!48;UBERON:0002390!1.01e-14!45;UBERON:0003061!1.01e-14!45;UBERON:0004177!2.27e-14!29;UBERON:0005057!2.27e-14!29;UBERON:0000077!6.06e-13!35;UBERON:0002384!1.05e-12!46;UBERON:0000065!1.17e-12!41;UBERON:0001004!3.08e-12!42;UBERON:0000490!4.18e-12!66;UBERON:0003929!5.25e-12!55;UBERON:0005911!2.89e-11!69;UBERON:0000063!3.65e-11!35;UBERON:0007811!9.79e-11!36;UBERON:0003081!1.68e-09!87;UBERON:0000153!2.60e-08!43;UBERON:0000055!2.82e-08!5;UBERON:0007500!2.82e-08!5;UBERON:0001981!2.82e-08!5;UBERON:0002049!2.82e-08!5;UBERON:0007798!2.82e-08!5;UBERON:0004537!2.82e-08!5;UBERON:0006965!2.82e-08!5
}}

Latest revision as of 15:02, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:18735503..18735513,+p@chr10:18735503..18735513
+
Mm9::chr11:106077832..106077846,+p7@Ddx42
Mm9::chr11:106640128..106640133,-p@chr11:106640128..106640133
-
Mm9::chr11:48741726..48741731,-p@chr11:48741726..48741731
-
Mm9::chr11:48807684..48807688,-p1@Tgtp1
p1@Tgtp2
Mm9::chr11:48877704..48877708,-p2@Tgtp1
p2@Tgtp2
Mm9::chr11:48900808..48900825,-p@chr11:48900808..48900825
-
Mm9::chr11:53577462..53577476,-p@chr11:53577462..53577476
-
Mm9::chr11:54769726..54769742,+p@chr11:54769726..54769742
+
Mm9::chr11:86297814..86297852,-p@chr11:86297814..86297852
-
Mm9::chr13:113230195..113230209,-p@chr13:113230195..113230209
-
Mm9::chr13:42148379..42148391,+p@chr13:42148379..42148391
+
Mm9::chr15:27715131..27715143,-p@chr15:27715131..27715143
-
Mm9::chr17:26645134..26645152,-p5@Dusp1
Mm9::chr17:26645159..26645192,-p3@Dusp1
Mm9::chr17:64681746..64681757,+p@chr17:64681746..64681757
+
Mm9::chr18:35900045..35900092,-p3@Tmem173
Mm9::chr3:148989729..148989732,-p@chr3:148989729..148989732
-
Mm9::chr4:132071343..132071349,-p@chr4:132071343..132071349
-
Mm9::chr5:114442415..114442421,-p@chr5:114442415..114442421
-
Mm9::chr5:135484708..135484730,-p@chr5:135484708..135484730
-
Mm9::chr5:139858874..139858903,-p@chr5:139858874..139858903
-
Mm9::chr6:128374733..128374747,+p@chr6:128374733..128374747
+
Mm9::chr6:48658357..48658367,+p@chr6:48658357..48658367
+
Mm9::chr7:132634885..132634897,-p@chr7:132634885..132634897
-
Mm9::chr7:135111618..135111623,+p@chr7:135111618..135111623
+
Mm9::chr9:119891850..119891862,+p@chr9:119891850..119891862
+
Mm9::chr9:7873196..7873213,+p@chr9:7873196..7873213
+


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:0033549MAP kinase phosphatase activity0.039921137030804
GO:0017017MAP kinase tyrosine/serine/threonine phosphatase activity0.039921137030804



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 cell6.60e-1912
hematopoietic cell2.73e-1832
hematopoietic oligopotent progenitor cell2.73e-1832
hematopoietic stem cell2.73e-1832
angioblastic mesenchymal cell2.73e-1832
hematopoietic multipotent progenitor cell2.73e-1832
mature alpha-beta T cell7.15e-189
alpha-beta T cell7.15e-189
immature T cell7.15e-189
mature T cell7.15e-189
immature alpha-beta T cell7.15e-189
lymphocyte3.12e-1713
common lymphoid progenitor3.12e-1713
T cell4.21e-1711
pro-T cell4.21e-1711
CD4-positive, alpha-beta T cell5.52e-168
nucleate cell1.79e-1316
hematopoietic lineage restricted progenitor cell6.93e-1325
connective tissue cell1.05e-1246
mesenchymal cell1.05e-1246
leukocyte1.62e-1217
nongranular leukocyte1.62e-1217
thymocyte3.94e-126
double negative thymocyte3.94e-126
naive T cell3.94e-126
double-positive, alpha-beta thymocyte3.94e-126
CD4-positive, alpha-beta thymocyte3.94e-126
naive thymus-derived CD4-positive, alpha-beta T cell3.94e-126
DN4 thymocyte3.94e-126
DN1 thymic pro-T cell3.94e-126
DN2 thymocyte3.94e-126
DN3 thymocyte3.94e-126
immature single positive thymocyte3.94e-126
early T lineage precursor3.94e-126
mature CD4 single-positive thymocyte3.94e-126
resting double-positive thymocyte3.94e-126
double-positive blast3.94e-126
CD69-positive double-positive thymocyte3.94e-126
CD69-positive, CD4-positive single-positive thymocyte3.94e-126
CD4-positive, CD8-intermediate double-positive thymocyte3.94e-126
CD24-positive, CD4 single-positive thymocyte3.94e-126
motile cell5.00e-1054
stem cell7.04e-0997
somatic stem cell3.85e-0791
multi fate stem cell3.85e-0791

Uber Anatomy
Ontology termp-valuen
thymus2.78e-1923
neck2.78e-1923
respiratory system epithelium2.78e-1923
hemolymphoid system gland2.78e-1923
pharyngeal epithelium2.78e-1923
thymic region2.78e-1923
pharyngeal gland2.78e-1923
entire pharyngeal arch endoderm2.78e-1923
thymus primordium2.78e-1923
early pharyngeal endoderm2.78e-1923
pharynx2.73e-1824
gland of gut2.73e-1824
upper respiratory tract2.73e-1824
chordate pharynx2.73e-1824
pharyngeal arch system2.73e-1824
pharyngeal region of foregut2.73e-1824
segment of respiratory tract9.22e-1627
hemolymphoid system6.09e-1548
immune system6.09e-1548
hematopoietic system1.01e-1445
blood island1.01e-1445
hemopoietic organ2.27e-1429
immune organ2.27e-1429
mixed endoderm/mesoderm-derived structure6.06e-1335
connective tissue1.05e-1246
respiratory tract1.17e-1241
respiratory system3.08e-1242
unilaminar epithelium4.18e-1266
gut epithelium5.25e-1255
endo-epithelium2.89e-1169
organ segment3.65e-1135
craniocervical region9.79e-1136
lateral plate mesoderm1.68e-0987
anterior region of body2.60e-0843
vessel2.82e-085
epithelial tube open at both ends2.82e-085
blood vessel2.82e-085
vasculature2.82e-085
vascular system2.82e-085
blood vasculature2.82e-085
vascular cord2.82e-085


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)
MA0003.10.0727645
MA0004.10.322185
MA0006.10.872768
MA0007.10.627108
MA0009.10.400415
MA0014.10.0606528
MA0017.10.350698
MA0019.10.257924
MA0024.10.956106
MA0025.14.89101
MA0027.11.97512
MA0028.10.581784
MA0029.10.347243
MA0030.10.352483
MA0031.10.32434
MA0038.10.181232
MA0040.11.05719
MA0041.10.0630027
MA0042.10.210366
MA0043.13.11095
MA0046.10.430358
MA0048.10.100397
MA0050.11.23694
MA0051.11.04714
MA0052.10.417501
MA0055.10.0160469
MA0056.10
MA0057.10.290249
MA0058.10.20257
MA0059.10.216766
MA0060.10.165546
MA0061.13.33641
MA0063.10
MA0066.10.174169
MA0067.10.70379
MA0068.10.08935
MA0069.10.417784
MA0070.10.409709
MA0071.10.117424
MA0072.10.402681
MA0073.10.0041288
MA0074.10.903107
MA0076.10.38889
MA0077.10.384853
MA0078.10.209135
MA0081.10.523649
MA0083.10.481435
MA0084.11.01381
MA0087.10.444612
MA0088.10.266004
MA0089.10
MA0090.10.58254
MA0091.10.104243
MA0092.10.983972
MA0093.10.335373
MA0095.10
MA0098.10
MA0100.10.445082
MA0101.12.34994
MA0103.10.0422686
MA0105.12.07095
MA0106.10.214456
MA0107.13.66104
MA0108.20.75446
MA0109.10
MA0111.10.0876986
MA0113.10.56883
MA0114.10.979011
MA0115.10.484531
MA0116.10.87191
MA0117.10.45687
MA0119.10.228018
MA0122.10.473843
MA0124.10.654966
MA0125.10.587987
MA0130.10
MA0131.11.30728
MA0132.10
MA0133.10
MA0135.10.513709
MA0136.10.492774
MA0139.10.684466
MA0140.10.44491
MA0141.10.184267
MA0142.10.313054
MA0143.10.206363
MA0144.14.5587
MA0145.10.184626
MA0146.10.585165
MA0147.10.233511
MA0148.10.105845
MA0149.10.0658075
MA0062.21.03745
MA0035.20.45195
MA0039.22.98779
MA0138.21.28575
MA0002.20.452601
MA0137.23.90774
MA0104.20.295049
MA0047.20.180736
MA0112.20.184613
MA0065.20.645507
MA0150.10.626845
MA0151.10
MA0152.10.180805
MA0153.10.528268
MA0154.10.324998
MA0155.10.0235582
MA0156.12.00668
MA0157.10.288518
MA0158.10
MA0159.10.10218
MA0160.10.348502
MA0161.10
MA0162.10.205773
MA0163.10.0337879
MA0164.10.954895
MA0080.20.647846
MA0018.20.1704
MA0099.20.244313
MA0079.20.671266
MA0102.21.06444
MA0258.10.186786
MA0259.11.00321
MA0442.10
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