Evidence of systematic expressed sequence tag IMAGE clone cross-hybridization on cDNA microarrays.
We present evidence of a potentially serious source of error intrinsic to all spotted cDNA microarrays that use IMAGE clones of expressed sequence tags (ESTs). We found that a high proportion of these EST sequences contain 5'-end poly(dT) sequences that are remnants from the oligo(dT)-primed reverse transcription of polyadenylated mRNA templates used to generate EST cDNA for sequence clone libraries. Analysis of expression data from two single-dye cDNA microarray experiments showed that ESTs whose sequences contain repeats of consecutive 5'-end dT residues appeared to be strongly coexpressed, while expression data of all other sequences exhibited no such pattern. Our analysis suggests that expression data from sequences containing 5' poly(dT) tracts are more likely to be due to systematic cross-hybridization of these poly(dT) tracts than to true mRNA coexpression. This indicates that existing data generated by cDNA microarrays containing IMAGE clone ESTs should be filtered to remove expression data containing significant 5' poly(dT) tracts.
Handley
Daniel
D
Department of Statistics, Carnegie Mellon University, Pittsburgh, PA 15213, USA. dhandley@andrew.cmu.edu
Serban
Nicoleta
N
Peters
David
D
O'Doherty
Robert
R
Field
Melvin
M
Wasserman
Larry
L
Spirtes
Peter
P
Scheines
Richard
R
Glymour
Clark
C
D017667:Adipocytes / Q000187:drug effects; D000818:Animals; D016477:Artifacts; D002839:Chromans / Q000494:pharmacology; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011071:Poly T / Q000032:analysis; D012333:RNA, Messenger / Q000032:analysis; D045162:Thiazolidinediones / Q000494:pharmacology; D000077288:Troglitazone
D002839:Chromans; D012333:RNA, Messenger; D045162:Thiazolidinediones; D011071:Poly T; D000077288:Troglitazone