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SPH 247 Statistical Analysis of Laboratory Data 1May 14, 2013SPH 247 Statistical Analysis of Laboratory Data
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Annotation Given that one has found one of more genes that are differentially expressed, there are a number useful things to know What is the putative function? What pathways are know to contain this gene? What other proteins interact with the given protein? etc. May 14, 2013SPH 247 Statistical Analysis of Laboratory Data2
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Two-color array example May 14, 2013SPH 247 Statistical Analysis of Laboratory Data3 > alldata[1,] [1] 473 888 170 1137 86 290 109 226 370 659 359 484 102 293 174 [16] 324 196 638 102 293 > geneID[1,] Name ID 1 NM_006182 discoidin domain receptor family, member http://www.ncbi.nlm.nih.gov/genome/guide/human/resources.shtml
![Two-color array example May 14, 2013SPH 247 Statistical Analysis of Laboratory Data3 > alldata[1,] [1] [16] > geneID[1,] Name ID 1 NM_ discoidin domain receptor family, member](http://images.slideplayer.com/25/7590018/slides/slide_3.jpg "Two-color array example May 14, 2013SPH 247 Statistical Analysis of Laboratory Data3 > alldata[1,] [1] [16] > geneID[1,] Name ID 1 NM_ discoidin domain receptor family, member")
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May 14, 2013SPH 247 Statistical Analysis of Laboratory Data4 Official SymbolDDR2 provided by HGNCHGNC Official Full Name discoidin domain receptor tyrosine kinase 2 provided by HGNCHGNC Primary sourceHGNC:2731HGNC:2731 Locus tagRP11-572K18.1 See relatedEnsembl:ENSG00000162733; HPRD:01868; MIM:191311; Vega:OTTHUMG00000034423Ensembl:ENSG00000162733;HPRD:01868;MIM:191311;Vega:OTTHUMG00000034423 Gene typeprotein coding RefSeq statusREVIEWED OrganismHomo sapiensHomo sapiens LineageEukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo Also known asTKT; MIG20a; NTRKR3; TYRO10 SummaryReceptor tyrosine kinases (RTKs) play a key role in the communication of cells with their microenvironment. These molecules are involved in the regulation of cell growth, differentiation, and metabolism. In several cases the biochemical mechanism by which RTKs transduce signals across the membrane has been shown to be ligand induced receptor oligomerization and subsequent intracellular phosphorylation. This autophosphorylation leads to phosphorylation of cytosolic targets as well as association with other molecules, which are involved in pleiotropic effects of signal transduction. RTKs have a tripartite structure with extracellular, transmembrane, and cytoplasmic regions. This gene encodes a member of a novel subclass of RTKs and contains a distinct extracellular region encompassing a factor VIII-like domain. Alternative splicing in the 5' UTR results in multiple transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]
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Affy Example May 14, 2013SPH 247 Statistical Analysis of Laboratory Data5 > source("http://bioconductor.org/biocLite.R") > biocLite("annaffy") > biocLite("hgu95av2.db") > library(annaffy) > library(affy) Loading required package: Biobase Loading required package: tools … Loading required package: GO Loading required package: KEGG
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May 14, 2013SPH 247 Statistical Analysis of Laboratory Data6 > probeids <- featureNames(eset)[pv2$Posterior.FDR <.05] > probeids[1:5] [1] "1005_at" "1009_at" "1034_at" "1035_g_at" "1045_s_at" > symbols <- aafSymbol(probeids,"hgu95av2.db") Loading required package: hgu95av2 > symbols[1] An object of class "aafList" [[1]] An object of class “aafSymbol” [1] "DUSP1" > getText(symbols[1]) [1] "DUSP1" > descs <- aafDescription(probeids,"hgu95av2.db")[1] > getText(descs)[1] [1] "dual specificity phosphatase 1" > gos <- aafGO(probeids,"hgu95av2.db")
![May 14, 2013SPH 247 Statistical Analysis of Laboratory Data6 > probeids <- featureNames(eset)[pv2$Posterior.FDR <.05] > probeids[1:5] [1] 1005_at 1009_at 1034_at 1035_g_at 1045_s_at > symbols <- aafSymbol(probeids, hgu95av2.db ) Loading required package: hgu95av2 > symbols[1] An object of class aafList [[1]] An object of class aafSymbol [1] DUSP1 > getText(symbols[1]) [1] DUSP1 > descs <- aafDescription(probeids, hgu95av2.db )[1] > getText(descs)[1] [1] dual specificity phosphatase 1 > gos <- aafGO(probeids, hgu95av2.db )](http://images.slideplayer.com/25/7590018/slides/slide_6.jpg "May 14, 2013SPH 247 Statistical Analysis of Laboratory Data6 > probeids <- featureNames(eset)[pv2$Posterior.FDR <.05] > probeids[1:5] [1] 1005_at 1009_at 1034_at 1035_g_at 1045_s_at > symbols <- aafSymbol(probeids, hgu95av2.db ) Loading required package: hgu95av2 > symbols[1] An object of class aafList [[1]] An object of class aafSymbol [1] DUSP1 > getText(symbols[1]) [1] DUSP1 > descs <- aafDescription(probeids, hgu95av2.db )[1] > getText(descs)[1] [1] dual specificity phosphatase 1 > gos <- aafGO(probeids, hgu95av2.db )")
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May 14, 2013SPH 247 Statistical Analysis of Laboratory Data7 > gos[1] An object of class "aafList" [[1]] An object of class "aafGO" [[1]][[1]] An object of class "aafGOItem" @id "GO:0006470" @name "protein amino acid dephosphorylation" @type "Biological Process" @evid "IEA" [[1]][[2]] An object of class "aafGOItem" @id "GO:0006979" @name "response to oxidative stress" @type "Biological Process" @evid "TAS" [[1]][[3]] An object of class "aafGOItem" @id "GO:0007049" @name "cell cycle" @type "Biological Process" @evid "IEA”
![May 14, 2013SPH 247 Statistical Analysis of Laboratory Data7 > gos[1] An object of class aafList [[1]] An object of class aafGO [[1]][[1]] An object of class protein amino acid Biological IEA [[1]][[2]] An object of class response to oxidative Biological TAS [[1]][[3]] An object of class cell Biological IEA](http://images.slideplayer.com/25/7590018/slides/slide_7.jpg "May 14, 2013SPH 247 Statistical Analysis of Laboratory Data7 > gos[1] An object of class aafList [[1]] An object of class aafGO [[1]][[1]] An object of class protein amino acid Biological IEA [[1]][[2]] An object of class response to oxidative Biological TAS [[1]][[3]] An object of class cell Biological IEA")
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May 14, 2013SPH 247 Statistical Analysis of Laboratory Data8 [[1]][[4]] An object of class "aafGOItem" @id "GO:0004726" @name "non-membrane spanning protein tyrosine phosphatase activity" @type "Molecular Function" @evid "TAS" [[1]][[5]] An object of class "aafGOItem" @id "GO:0005515" @name "protein binding" @type "Molecular Function" @evid "IPI" [[1]][[6]] An object of class "aafGOItem" @id "GO:0016787" @name "hydrolase activity" @type "Molecular Function" @evid "IEA"
![May 14, 2013SPH 247 Statistical Analysis of Laboratory Data8 [[1]][[4]] An object of class non-membrane spanning protein tyrosine phosphatase Molecular TAS [[1]][[5]] An object of class protein Molecular IPI [[1]][[6]] An object of class hydrolase Molecular IEA](http://images.slideplayer.com/25/7590018/slides/slide_8.jpg "May 14, 2013SPH 247 Statistical Analysis of Laboratory Data8 [[1]][[4]] An object of class non-membrane spanning protein tyrosine phosphatase Molecular TAS [[1]][[5]] An object of class protein Molecular IPI [[1]][[6]] An object of class hydrolase Molecular IEA")
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May 14, 2013SPH 247 Statistical Analysis of Laboratory Data9 [[1]][[7]] An object of class "aafGOItem" @id "GO:0017017" @name "MAP kinase tyrosine/serine/threonine phosphatase activity" @type "Molecular Function" @evid "IEA"
![May 14, 2013SPH 247 Statistical Analysis of Laboratory Data9 [[1]][[7]] An object of class MAP kinase tyrosine/serine/threonine phosphatase Molecular IEA](http://images.slideplayer.com/25/7590018/slides/slide_9.jpg "May 14, 2013SPH 247 Statistical Analysis of Laboratory Data9 [[1]][[7]] An object of class MAP kinase tyrosine/serine/threonine phosphatase Molecular IEA")
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GO Evidence Codes IEA = inferred from electronic annotation (e.g., BLAST). Uncurated TAS = traceable author statement (i.e., someone said so). May 14, 2013SPH 247 Statistical Analysis of Laboratory Data10
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IDA = inferred from direct assay IEP = inferred from expression pattern IGI = inferred from genetic interaction IMP = inferred from mutant phenotype IPI = inferred from physical interaction ISS = inferred from sequence similarity NAS = non-traceable author statement ND = no biological data available NR = not recorded May 14, 2013SPH 247 Statistical Analysis of Laboratory Data11
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Online Access > gbs <- aafGenBank(probeids,"hgu95av2.db") > getURL(gbs[[1]]) [1] "http://www.ncbi.nlm.nih.gov/entrez/query. fcgi?cmd=search&db=nucleotide&term=X68277% 5BACCN%5D&doptcmdl=GenBank" > lls <- aafLocusLink(probeids,"hgu95av2.db") > getURL(lls[[1]]) [1] "http://www.ncbi.nlm.nih.gov/sites/entrez? Db=gene&Cmd=DetailsSearch&Term=1843" May 14, 2013SPH 247 Statistical Analysis of Laboratory Data12
![Online Access > gbs <- aafGenBank(probeids, hgu95av2.db ) > getURL(gbs[[1]]) [1]](http://images.slideplayer.com/25/7590018/slides/slide_12.jpg "fcgi cmd=search&db=nucleotide&term=X68277% 5BACCN%5D&doptcmdl=GenBank > lls <- aafLocusLink(probeids, hgu95av2.db ) > getURL(lls[[1]]) [1] Db=gene&Cmd=DetailsSearch&Term=1843 May 14, 2013SPH 247 Statistical Analysis of Laboratory Data12.")
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Abstracts > pmids <- aafPubMed(probeids,"hgu95av2.db") > pmids[[1]] An object of class "aafPubMed" [1] 15111304 14764702 14500648 12935821 12477932 9659899 8977099 8796349 8682498 8622863 8390675 8302582 [13] 8226977 7848919 7789998 7774938 > pmids[1] An object of class “aafPubMed” [1] 1406996 7535770 7806236 8106404 8168826 8221888 8389479 8390041 [9] 9571625 9599409 10617468 11062068 11278799 12080474 12356755 12391149 [17] 12432554 12477932 12506119 12765304 12890671 12947325 12960255 14551204 [25] 14680833 14702039 14724291 15059515 15173070 15247770 15339908 15448190 [33] 15489334 15569826 15590693 15614136 15677475 16044158 16081065 16224818 [41] 16286470 16289033 16293973 16387640 17073741 17131384 17489738 > browseURL(getURL(lls[[1]])) May 14, 2013SPH 247 Statistical Analysis of Laboratory Data13
![Abstracts > pmids <- aafPubMed(probeids, hgu95av2.db ) > pmids[[1]] An object of class aafPubMed [1] [13] > pmids[1] An object of class aafPubMed [1] [9] [17] [25] [33] [41] > browseURL(getURL(lls[[1]])) May 14, 2013SPH 247 Statistical Analysis of Laboratory Data13](http://images.slideplayer.com/25/7590018/slides/slide_13.jpg "Abstracts > pmids <- aafPubMed(probeids, hgu95av2.db ) > pmids[[1]] An object of class aafPubMed [1] [13] > pmids[1] An object of class aafPubMed [1] [9] [17] [25] [33] [41] > browseURL(getURL(lls[[1]])) May 14, 2013SPH 247 Statistical Analysis of Laboratory Data13")
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Direct Browsing > browseURL(getURL(lls[[1]])) > browseURL(getURL(gbs[[1]])) > browseURL(getURL(pmids[1])) May 14, 2013SPH 247 Statistical Analysis of Laboratory Data14
![Direct Browsing > browseURL(getURL(lls[[1]])) > browseURL(getURL(gbs[[1]])) > browseURL(getURL(pmids[1])) May 14, 2013SPH 247 Statistical Analysis of Laboratory Data14](http://images.slideplayer.com/25/7590018/slides/slide_14.jpg "Direct Browsing > browseURL(getURL(lls[[1]])) > browseURL(getURL(gbs[[1]])) > browseURL(getURL(pmids[1])) May 14, 2013SPH 247 Statistical Analysis of Laboratory Data14")
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Top Genes > probeids.ord <- featureNames(eset)[order(pv1$Posterior)] > getText(aafSymbol(probeids.ord[1:10],"hgu95av2.db")) [1] "" "PSPHP1" "" "COPA" "" "GM2A" "S100A2" "RPLP1" "" "" > getText(aafDescription(probeids.ord[1:10],"hgu95av2.db")) [1] "" "phosphoserine phosphatase pseudogene 1" [3] "" "coatomer protein complex, subunit alpha" [5] "" "GM2 ganglioside activator" [7] "S100 calcium binding protein A2" "ribosomal protein, large, P1" [9] "" "" > aafGO(probeids.ord[7],"hgu95av2.db") An object of class "aafList" [[1]] An object of class "aafGO" [[1]][[1]] An object of class "aafGOItem" @id "GO:0005509" @name "calcium ion binding" @type "Molecular Function" @evid "NAS" [[1]][[2]] An object of class "aafGOItem" @id "GO:0005575" @name "cellular_component" @type "Cellular Component" @evid "ND" [[1]][[3]] An object of class "aafGOItem" @id "GO:0043542" @name "endothelial cell migration" @type "Biological Process" @evid "IMP" May 14, 2013SPH 247 Statistical Analysis of Laboratory Data15
![Top Genes > probeids.ord <- featureNames(eset)[order(pv1$Posterior)] > getText(aafSymbol(probeids.ord[1:10], hgu95av2.db )) [1] PSPHP1 COPA GM2A S100A2 RPLP1 > getText(aafDescription(probeids.ord[1:10], hgu95av2.db )) [1] phosphoserine phosphatase pseudogene 1 [3] coatomer protein complex, subunit alpha [5] GM2 ganglioside activator [7] S100 calcium binding protein A2 ribosomal protein, large, P1 [9] > aafGO(probeids.ord[7], hgu95av2.db ) An object of class aafList [[1]] An object of class aafGO [[1]][[1]] An object of class calcium ion Molecular NAS [[1]][[2]] An object of class Cellular ND [[1]][[3]] An object of class endothelial cell Biological IMP May 14, 2013SPH 247 Statistical Analysis of Laboratory Data15](http://images.slideplayer.com/25/7590018/slides/slide_15.jpg "Top Genes > probeids.ord <- featureNames(eset)[order(pv1$Posterior)] > getText(aafSymbol(probeids.ord[1:10], hgu95av2.db )) [1] PSPHP1 COPA GM2A S100A2 RPLP1 > getText(aafDescription(probeids.ord[1:10], hgu95av2.db )) [1] phosphoserine phosphatase pseudogene 1 [3] coatomer protein complex, subunit alpha [5] GM2 ganglioside activator [7] S100 calcium binding protein A2 ribosomal protein, large, P1 [9] > aafGO(probeids.ord[7], hgu95av2.db ) An object of class aafList [[1]] An object of class aafGO [[1]][[1]] An object of class calcium ion Molecular NAS [[1]][[2]] An object of class Cellular ND [[1]][[3]] An object of class endothelial cell Biological IMP May 14, 2013SPH 247 Statistical Analysis of Laboratory Data15")
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> aafGO(probeids.ord[7],"hgu95av2.db") An object of class "aafList" [[1]] An object of class "aafGO" [[1]][[1]] An object of class "aafGOItem" @id "GO:0005509" @name "calcium ion binding" @type "Molecular Function" @evid "NAS" [[1]][[2]] An object of class "aafGOItem" @id "GO:0005575" @name "cellular_component" @type "Cellular Component" @evid "ND" [[1]][[3]] An object of class "aafGOItem" @id "GO:0043542" @name "endothelial cell migration" @type "Biological Process" @evid "IMP" May 14, 2013SPH 247 Statistical Analysis of Laboratory Data16
![> aafGO(probeids.ord[7], hgu95av2.db ) An object of class aafList [[1]] An object of class aafGO [[1]][[1]] An object of class calcium ion Molecular NAS [[1]][[2]] An object of class Cellular ND [[1]][[3]] An object of class endothelial cell Biological IMP May 14, 2013SPH 247 Statistical Analysis of Laboratory Data16](http://images.slideplayer.com/25/7590018/slides/slide_16.jpg "> aafGO(probeids.ord[7], hgu95av2.db ) An object of class aafList [[1]] An object of class aafGO [[1]][[1]] An object of class calcium ion Molecular NAS [[1]][[2]] An object of class Cellular ND [[1]][[3]] An object of class endothelial cell Biological IMP May 14, 2013SPH 247 Statistical Analysis of Laboratory Data16")
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