1 Annotation EPP 245/298 Statistical Analysis of Laboratory Data.

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1 Annotation EPP 245/298 Statistical Analysis of Laboratory Data

November 10, 2004EPP 245 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.

November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 3 Two-color array example > alldata[1,] [1] [16] > geneID[1,] Name ID 1 NM_ discoidin domain receptor family, member

November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 4 Affy Example > library(annaffy) Loading required package: GO Loading required package: KEGG Loading required package: annotate > probeids <- geneNames(eset.rma)[allp1adj <.05] > symbols <- aafSymbol(probeids,"hgu95av2") Loading required package: hgu95av2 > symbols[[1]] An object of class "aafSymbol" [1] "DDR1" > getText(symbols[[1]]) [1] "DDR1" > gos <- aafGO(probeids,"hgu95av2")

November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 5 > gos[[1]] An object of class "aafGO" [[1]] An object of class "ATP "Molecular "IEA" [[2]] An object of class "cell "Biological "IEA" [[3]] An object of class "cell "Biological "TAS"

November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 6 [[4]] An object of class "integral to plasma "Cellular "TAS" [[5]] An object of class "Cellular "IEA" [[6]] An object of class "protein amino acid "Biological "IEA"

November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 7 [[7]] An object of class "protein serine/threonine kinase "Molecular "IEA" [[8]] An object of class "receptor "Molecular "IEA" [[9]] An object of class "transferase "Molecular "IEA"

November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 8 [[10]] An object of class "transmembrane receptor protein tyrosine kinase "Molecular "IEA" [[11]] An object of class "transmembrane receptor protein tyrosine kinase "Molecular "TAS" [[12]] An object of class "transmembrane receptor protein tyrosine kinase signaling "Biological "IEA"

November 10, 2004EPP 245 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).

November 10, 2004EPP 245 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

November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 11 Online Access > gbs <- aafGenBank(probeids,"hgu95av2") > getURL(gbs[[1]]) [1] " fcgi?cmd=search&db=nucleotide&term=U48705% 5BACCN%5D&doptcmdl=GenBank" > lls <- aafLocusLink(probeids,"hgu95av2") > getURL(lls[[1]]) [1] " fcgi?db=gene&cmd=Retrieve&dopt=Graphics&li st_uids=780"

November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 12 Abstracts > pmids <- aafPubMed(probeids,"hgu95av2") > pmids[[1]] An object of class "aafPubMed" [1] [13] > getURL(pmids[[1]]) [1] " oconductor&cmd=Retrieve&db=PubMed&list_uids= %2c %2c %2c %2c %2c %2c %2c %2c %2c %2c %2c %2c %2c %2c %2c “ > browseURL(getURL(lls[[1]]))