Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.
Traditional microarrays use probes complementary to known genes to quantitate the differential gene expression between two or more conditions. Genomic tiling microarray experiments differ in that probes that span a genomic region at regular intervals are used to detect the presence or absence of transcription. This difference means the same sets of biases and the methods for addressing them are unlikely to be relevant to both types of experiment. We introduce the informatics challenges arising in the analysis of tiling microarray experiments as open problems to the scientific community and present initial approaches for the analysis of this nascent technology.
Royce
Thomas E
TE
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.
Rozowsky
Joel S
JS
Bertone
Paul
P
Samanta
Manoj
M
Stolc
Viktor
V
Weissman
Sherman
S
Snyder
Michael
M
Gerstein
Mark
M
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D004247:DNA / Q000235:genetics; D006801:Humans; D015335:Molecular Probes; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D014158:Transcription, Genetic
D015335:Molecular Probes; D004247:DNA