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MCL coexpression mm9:316: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0048002;antigen processing and presentation of peptide antigen;0.0208037826654645;54445,14964!GO:0019882;antigen processing and presentation;0.0294189354332319;54445,14964!
|ontology_enrichment_celltype=CL:0000988!3.14e-11!32;CL:0002032!3.14e-11!32;CL:0000037!3.14e-11!32;CL:0000566!3.14e-11!32;CL:0000837!3.14e-11!32;CL:0002031!3.27e-09!25;CL:0002320!1.90e-08!46;CL:0000134!1.90e-08!46;CL:0000738!5.13e-08!17;CL:0002087!5.13e-08!17;CL:0000838!6.49e-07!12;CL:0000049!7.52e-07!19
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002193!1.38e-21!48;UBERON:0002405!1.38e-21!48;UBERON:0002390!4.84e-20!45;UBERON:0003061!4.84e-20!45;UBERON:0003081!1.47e-13!87;UBERON:0000077!8.77e-11!35;UBERON:0004177!1.01e-10!29;UBERON:0005057!1.01e-10!29;UBERON:0002371!2.32e-10!16;UBERON:0002204!1.33e-09!32;UBERON:0000926!1.94e-09!120;UBERON:0004120!1.94e-09!120;UBERON:0006603!1.94e-09!120;UBERON:0001474!5.67e-09!22;UBERON:0004765!5.67e-09!22;UBERON:0001434!5.67e-09!22;UBERON:0003408!1.51e-08!24;UBERON:0002384!1.90e-08!46;UBERON:0002370!2.21e-08!23;UBERON:0000974!2.21e-08!23;UBERON:0004807!2.21e-08!23;UBERON:0005058!2.21e-08!23;UBERON:0003351!2.21e-08!23;UBERON:0009113!2.21e-08!23;UBERON:0003295!2.21e-08!23;UBERON:0009722!2.21e-08!23;UBERON:0005562!2.21e-08!23;UBERON:0007690!2.21e-08!23;UBERON:0006562!4.10e-08!24;UBERON:0001557!4.10e-08!24;UBERON:0001042!4.10e-08!24;UBERON:0008814!4.10e-08!24;UBERON:0009145!4.10e-08!24;UBERON:0001004!4.99e-08!42;UBERON:0000065!7.74e-08!41;UBERON:0001041!9.78e-08!80
|tfbs_overrepresentation_for_novel_motifs=0.653885,2.16662,0.591347,0.118279,0.343185,0.398187,0.538273,0.339268,0.364548,0.135725,0.914267,0.174808,0.339897,0.19087,0.377417,0,0.88698,0.140166,0.300991,0.553915,0.506129,0.527386,0.556548,0.146692,0.0864761,0.209658,0.13702,0.429523,0.438605,0.332722,0.13045,0.416414,0.587062,1.24884,1.48141,0.586878,0.558216,0.172462,1.15054,0.212494,0.144141,0.416106,1.74366,0.678914,0.689276,0.729854,0.747448,0.888045,0.705568,0.776322,0.85605,0.647534,0.310742,1.33224,0.554419,0.569593,0.0584059,0.498914,1.33106,0.194311,0.39965,0.66335,0.396933,0.836197,0.20328,0.90792,0.678037,1.00855,0.395762,0.867464,0.547195,0.180319,0.244404,0.584436,0.116124,0.606254,0.111084,0.263199,0.38541,0.515733,0.894329,0.917924,0.234292,0.161313,0.48244,2.64181,1.57517,0.778474,0.755897,1.16606,0.74267,0.486763,0.427209,0.355202,0.255947,0.0896384,0.559504,0.429584,0.271907,1.20965,0.0315985,0.416179,0.523506,0.320141,0.31931,0.823515,0.367229,0.447363,0.526859,0.0668927,0.0921762,0.525078,0.241499,0.157745,0.749248,0.331504,0.0480311,0.382478,0.334542,0.867284,0.589296,0.294572,0.210922,0.262524,0.800032,0.388466,0.551377,0.421488,0.67664,1.43396,0.508573,0.366432,0.649498,0.591864,0.769462,0.96091,0.100083,0.134301,0.723554,1.52843,1.13499,0.682379,0.219341,1.0886,0.31422,0.416785,0.274066,1.4892,0.101315,0.150113,0.793002,0.45923,0.540306,0.0945798,0.590347,0.613593,0.229288,1.0962,2.17887,0.673649,0.732404,0.481698,0.388835,0.304588,0.311631,0.199302,0.878448,0.99364,1.26067
}}

Latest revision as of 15:05, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127962917..127962936,-p1@Esyt1
Mm9::chr11:68245614..68245672,+p1@Pik3r5
Mm9::chr12:87027598..87027652,+p1@Batf
Mm9::chr15:6530936..6530950,+p@chr15:6530936..6530950
+
Mm9::chr15:6530960..6530979,+p@chr15:6530960..6530979
+
Mm9::chr15:78391895..78391920,-p@chr15:78391895..78391920
-
Mm9::chr15:78396374..78396387,-p@chr15:78396374..78396387
-
Mm9::chr15:78427542..78427551,+p2@Cyth4
Mm9::chr15:78427563..78427582,+p1@Cyth4
Mm9::chr15:79572948..79572992,-p2@Sun2
Mm9::chr16:91485540..91485554,+p3@Ifnar1
Mm9::chr17:35400991..35401003,+p7@H2-D1
Mm9::chr17:36004124..36004178,+p@chr17:36004124..36004178
+
Mm9::chr19:3907087..3907117,-p2@Tcirg1
Mm9::chr19:3935252..3935261,+p2@Unc93b1
Mm9::chr1:34529559..34529602,+p1@Ptpn18
Mm9::chr2:167328914..167328961,+p1@Rnf114
Mm9::chr3:90070429..90070488,+p1@Dennd4b
Mm9::chr4:130469179..130469263,+p1@Laptm5
Mm9::chr4:149072707..149072726,-p1@Pik3cd
Mm9::chr5:138070397..138070430,+p1@Lrch4-sap25
p1@Lrch4
Mm9::chr5:139848167..139848196,-p@chr5:139848167..139848196
-
Mm9::chr6:124678463..124678472,-p@chr6:124678463..124678472
-
Mm9::chr7:108510511..108510558,+p4@Arap1
Mm9::chr7:31827125..31827193,-p1@Fxyd5


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:0048002antigen processing and presentation of peptide antigen0.0208037826654645
GO:0019882antigen processing and presentation0.0294189354332319



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>

Uber Anatomy
Ontology termp-valuen
hemolymphoid system1.38e-2148
immune system1.38e-2148
hematopoietic system4.84e-2045
blood island4.84e-2045
lateral plate mesoderm1.47e-1387
mixed endoderm/mesoderm-derived structure8.77e-1135
hemopoietic organ1.01e-1029
immune organ1.01e-1029
bone marrow2.32e-1016
musculoskeletal system1.33e-0932
mesoderm1.94e-09120
mesoderm-derived structure1.94e-09120
presumptive mesoderm1.94e-09120
bone element5.67e-0922
skeletal element5.67e-0922
skeletal system5.67e-0922
gland of gut1.51e-0824
connective tissue1.90e-0846
thymus2.21e-0823
neck2.21e-0823
respiratory system epithelium2.21e-0823
hemolymphoid system gland2.21e-0823
pharyngeal epithelium2.21e-0823
thymic region2.21e-0823
pharyngeal gland2.21e-0823
entire pharyngeal arch endoderm2.21e-0823
thymus primordium2.21e-0823
early pharyngeal endoderm2.21e-0823
pharynx4.10e-0824
upper respiratory tract4.10e-0824
chordate pharynx4.10e-0824
pharyngeal arch system4.10e-0824
pharyngeal region of foregut4.10e-0824
respiratory system4.99e-0842
respiratory tract7.74e-0841
foregut9.78e-0880


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)
MA0003.11.26439
MA0004.10.377695
MA0006.10.658229
MA0007.10.721566
MA0009.10.438777
MA0014.11.01494
MA0017.10.424347
MA0019.10.290797
MA0024.10.401898
MA0025.10.645374
MA0027.12.02409
MA0028.10.0452573
MA0029.10.383872
MA0030.11.01026
MA0031.10.360121
MA0038.10.209603
MA0040.10.449452
MA0041.10.0795363
MA0042.10.255859
MA0043.10.522621
MA0046.10.469568
MA0048.12.78974
MA0050.11.38305
MA0051.10.617538
MA0052.10.456356
MA0055.11.80474
MA0056.10
MA0057.10.390656
MA0058.10.24722
MA0059.10.262933
MA0060.11.00385
MA0061.10.501826
MA0063.10
MA0066.10.20204
MA0067.10.748059
MA0068.10.613449
MA0069.11.1565
MA0070.10.448343
MA0071.10.140522
MA0072.10.44111
MA0073.13.77889
MA0074.10.526923
MA0076.10.213074
MA0077.10.422739
MA0078.10.239324
MA0081.10.611511
MA0083.10.521922
MA0084.11.0607
MA0087.10.484199
MA0088.10.370727
MA0089.10
MA0090.10.100075
MA0091.10.396925
MA0092.10.100239
MA0093.10.407499
MA0095.10
MA0098.10
MA0100.10.508591
MA0101.10.274567
MA0103.10.780527
MA0105.10.61924
MA0106.10.244965
MA0107.10.196036
MA0108.20.308463
MA0109.10
MA0111.10.348856
MA0113.10.638437
MA0114.10.793821
MA0115.10.525089
MA0116.10.657566
MA0117.10.496768
MA0119.10.275337
MA0122.10.514153
MA0124.10.698593
MA0125.10.630583
MA0130.10
MA0131.10.287321
MA0132.10
MA0133.10
MA0135.10.554905
MA0136.10.191208
MA0139.11.98709
MA0140.10.50841
MA0141.10.226841
MA0142.10.34839
MA0143.10.236381
MA0144.10.504053
MA0145.11.39335
MA0146.11.0243
MA0147.11.68084
MA0148.10.127756
MA0149.10.590986
MA0062.20.645231
MA0035.20.515842
MA0039.22.99817
MA0138.20.281269
MA0002.22.0152
MA0137.20.485005
MA0104.20.927697
MA0047.20.209072
MA0112.20.414515
MA0065.21.09952
MA0150.10.721287
MA0151.10
MA0152.10.209147
MA0153.10.569763
MA0154.10.64506
MA0155.10.9573
MA0156.10.464199
MA0157.10.322822
MA0158.10
MA0159.10.313465
MA0160.10.405937
MA0161.10
MA0162.10.78032
MA0163.13.20796
MA0164.10.191451
MA0080.21.63838
MA0018.20.197998
MA0099.20.276491
MA0079.22.95532
MA0102.21.11159
MA0258.10.097198
MA0259.10.273672
MA0442.10
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