Abstract
The recently developed technology of genomic tiling microarrays, which can be used for genome annotation, has required the development of new methodologies [Royce et.al] for their design and analysis. Genomic tiling arrays use PCR amplicons or short oligonucleotide probes to tile the non-repetitive DNA sequence of a genome in an unbiased fashion for the purposes of detecting novel genomic features. Specifically, they can be used for the identification of novel transcripts, distinguishing between different splice isoforms and for finding transcription factor binding sites using Chromatin-Immunoprecipitation on chip experiments (ChIP-chip).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Royce, et.al.: Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping, Trends in Genetics (in press)
Rinn, et al.: The transcriptional activity of human Chromosome 22. Genes Dev. 17(4), 529–540 (2003)
Bertone, et al.: Global identification of human transcribed sequences with genome tiling arrays. Science 306(5705), 2242–2246 (2004); (Epub. November 11, 2004)
Cheng, et al.: Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution. Science (March 29, 2005)
Yamada, et al.: Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302(5646), 842–846 (2003)
Stolc, et al.: Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc. Natl. Acad. Sci. USA 102(12), 4453–4458 (2005); Epub. (March 8, 2005)
Stolc, et al.: A gene expression map for the euchromatic genome of Drosophila melanogaster. Science 306(5696), 655–660 (2004)
Martone, et al.: Distribution of NF-kappaB-binding sites across human chromosome 22. Proc. Natl. Acad. Sci. USA 100(21), 12247–12252 (2003); Epub. (October 3, 2003)
Cawley, et al.: Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNA. Cell. 116(4), 499–509 (2004)
Euskirchen, et al.: CREB binds to multiple loci on human chromosome 22. Mol. Cell. Biol. 24(9), 3804–3814 (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Rozowsky, J., Bertone, P., Royce, T., Weissman, S., Snyder, M., Gerstein, M. (2005). Analysis of Genomic Tiling Microarrays for Transcript Mapping and the Identification of Transcription Factor Binding Sites. In: Setubal, J.C., Verjovski-Almeida, S. (eds) Advances in Bioinformatics and Computational Biology. BSB 2005. Lecture Notes in Computer Science(), vol 3594. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11532323_4
Download citation
DOI: https://doi.org/10.1007/11532323_4
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-28008-8
Online ISBN: 978-3-540-31861-3
eBook Packages: Computer ScienceComputer Science (R0)