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Annotation

Annotation. SPH 247 Statistical Analysis of Laboratory Data. 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?

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Annotation

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  1. Annotation SPH 247 Statistical Analysis of Laboratory Data SPH 247 Statistical Analysis of Laboratory Data

  2. 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. SPH 247 Statistical Analysis of Laboratory Data

  3. Two-color array example > 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 SPH 247 Statistical Analysis of Laboratory Data

  4. Affy Example > library(annaffy) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: GO Loading required package: KEGG SPH 247 Statistical Analysis of Laboratory Data

  5. > 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") Loading required package: hgu95av2 > symbols[1] An object of class "aafList" [[1]] An object of class “aafSymbol” [1] "DUSP1" > getText(symbols[1]) [1] "DUSP1" > gos <- aafGO(probeids,"hgu95av2") SPH 247 Statistical Analysis of Laboratory Data

  6. > 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” SPH 247 Statistical Analysis of Laboratory Data

  7. [[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" SPH 247 Statistical Analysis of Laboratory Data

  8. [[1]][[7]] An object of class "aafGOItem" @id "GO:0017017" @name "MAP kinase tyrosine/serine/threoninephosphatase activity" @type "Molecular Function" @evid "IEA" SPH 247 Statistical Analysis of Laboratory Data

  9. GO Evidence Codes • IEA = inferred from electronic annotation (e.g., BLAST). Uncurated • TAS = traceable author statement (i.e., someone said so). SPH 247 Statistical Analysis of Laboratory Data

  10. 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 SPH 247 Statistical Analysis of Laboratory Data

  11. Online Access > gbs <- aafGenBank(probeids,"hgu95av2") > 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") > getURL(lls[[1]]) [1] "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=DetailsSearch&Term=1843" SPH 247 Statistical Analysis of Laboratory Data

  12. Abstracts > pmids <- aafPubMed(probeids,"hgu95av2") > 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]])) SPH 247 Statistical Analysis of Laboratory Data

  13. Direct Browsing > browseURL(getURL(lls[[1]])) > browseURL(getURL(gbs[[1]])) > browseURL(getURL(pmids[1])) SPH 247 Statistical Analysis of Laboratory Data

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