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 tra...

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Bibliographic Details
Published in:Trends in genetics 2005-08, Vol.21 (8), p.466-475
Main Authors: Royce, Thomas E., Rozowsky, Joel S., Bertone, Paul, Samanta, Manoj, Stolc, Viktor, Weissman, Sherman, Snyder, Michael, Gerstein, Mark
Format: Article
Language:English
Subjects:
Algorithms
Base Sequence
Biological and medical sciences
Computational Biology
DNA - genetics
Fundamental and applied biological sciences. Psychology
Genetics of eukaryotes. Biological and molecular evolution
Humans
Life Sciences (General)
Molecular and cellular biology
Molecular Probes
Oligonucleotide Array Sequence Analysis - methods
Oligonucleotide Array Sequence Analysis - statistics & numerical data
Space life sciences
Transcription, Genetic
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Summary: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.
ISSN:0168-9525
DOI:10.1016/j.tig.2005.06.007