Document information
Affymetrix probes containing runs of contiguous guanines are not gene-specific
Correspondence: (Login to view email address)
- Departments of Mathematical and Biological Sciences, University of Essex
PDF (225.9 KB)
- Document Type:
- Manuscript
- Date:
- Received 22 April 2008 10:54 UTC; Posted 22 April 2008
- Subjects:
- Biotechnology, Bioinformatics
- Abstract:
High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe set will provide a consistent message signifying the gene’s presence. However, we demonstrate by data mining thousands of CEL files from NCBI’s GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that 4G-probes should be ignored when calculating gene expression levels. Furthermore, future microarray designs should make no use of 4G-probes.
Discussion
- Votes:
-
4 votes
- Comments:
-
0 comments
- (Login to share with a colleague)
Additional information
- License:
- This document is licensed to the public under the Creative Commons Attribution 3.0 License
- How to cite this document:
-
Upton, Graham, Langdon, William, and Harrison, Andrew. Affymetrix probes containing runs of contiguous guanines are not gene-specific. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2008.1825.1> (2008)
- Version info:
-
Other versions of this document in Nature Precedings
None.
Other versions of this document elsewhere on the web
None known.
