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

2. 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.

3. November 10, 2004EPP 245 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

4. 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")

5. November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 5 > gos[[1]] An object of class "aafGO" [[1]] An object of class "aafGOItem" @id "GO:0005524" @name "ATP binding" @type "Molecular Function" @evid "IEA" [[2]] An object of class "aafGOItem" @id "GO:0007155" @name "cell adhesion" @type "Biological Process" @evid "IEA" [[3]] An object of class "aafGOItem" @id "GO:0007155" @name "cell adhesion" @type "Biological Process" @evid "TAS"

6. November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 6 [[4]] An object of class "aafGOItem" @id "GO:0005887" @name "integral to plasma membrane" @type "Cellular Component" @evid "TAS" [[5]] An object of class "aafGOItem" @id "GO:0016020" @name "membrane" @type "Cellular Component" @evid "IEA" [[6]] An object of class "aafGOItem" @id "GO:0006468" @name "protein amino acid phosphorylation" @type "Biological Process" @evid "IEA"

7. November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 7 [[7]] An object of class "aafGOItem" @id "GO:0004674" @name "protein serine/threonine kinase activity" @type "Molecular Function" @evid "IEA" [[8]] An object of class "aafGOItem" @id "GO:0004872" @name "receptor activity" @type "Molecular Function" @evid "IEA" [[9]] An object of class "aafGOItem" @id "GO:0016740" @name "transferase activity" @type "Molecular Function" @evid "IEA"

8. November 10, 2004EPP 245 Statistical Analysis of Laboratory Data 8 [[10]] An object of class "aafGOItem" @id "GO:0004714" @name "transmembrane receptor protein tyrosine kinase activity" @type "Molecular Function" @evid "IEA" [[11]] An object of class "aafGOItem" @id "GO:0004714" @name "transmembrane receptor protein tyrosine kinase activity" @type "Molecular Function" @evid "TAS" [[12]] An object of class "aafGOItem" @id "GO:0007169" @name "transmembrane receptor protein tyrosine kinase signaling pathway" @type "Biological Process" @evid "IEA"

9. 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).

10. 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

11. November 10, 2004EPP 245 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=U48705% 5BACCN%5D&doptcmdl=GenBank" > lls <- aafLocusLink(probeids,"hgu95av2") > getURL(lls[[1]]) [1] "http://www.ncbi.nlm.nih.gov/entrez/query. fcgi?db=gene&cmd=Retrieve&dopt=Graphics&li st_uids=780"

12. November 10, 2004EPP 245 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 > getURL(pmids[[1]]) [1] "http://www.ncbi.nih.gov/entrez/query.fcgi?tool=bi oconductor&cmd=Retrieve&db=PubMed&list_uids=151113 04%2c14764702%2c14500648%2c12935821%2c12477932%2c9 659899%2c8977099%2c8796349%2c8682498%2c8622863%2c8 390675%2c8302582%2c8226977%2c7848919%2c7789998%2c7 774938“ > browseURL(getURL(lls[[1]]))