Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
Nucleic Acids Res. 2007;35(15):e99. Epub 2007 Aug 7.

Toward a universal microarray: prediction of gene expression through nearest-neighbor probe sequence identification.

Author information

  • 1Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, USA.

Abstract

A generic DNA microarray design applicable to any species would greatly benefit comparative genomics. We have addressed the feasibility of such a design by leveraging the great feature densities and relatively unbiased nature of genomic tiling microarrays. Specifically, we first divided each Homo sapiens Refseq-derived gene's spliced nucleotide sequence into all of its possible contiguous 25 nt subsequences. For each of these 25 nt subsequences, we searched a recent human transcript mapping experiment's probe design for the 25 nt probe sequence having the fewest mismatches with the subsequence, but that did not match the subsequence exactly. Signal intensities measured with each gene's nearest-neighbor features were subsequently averaged to predict their gene expression levels in each of the experiment's thirty-three hybridizations. We examined the fidelity of this approach in terms of both sensitivity and specificity for detecting actively transcribed genes, for transcriptional consistency between exons of the same gene, and for reproducibility between tiling array designs. Taken together, our results provide proof-of-principle for probing nucleic acid targets with off-target, nearest-neighbor features.

PMID:
17686789
[PubMed - indexed for MEDLINE]
PMCID:
PMC1976448
Free PMC Article

Images from this publication.See all images (8)Free text

Figure 1.
Figure 2.
Figure 3.
Figure 4.
Figure 5.
Figure 6.
Figure 7.
Figure 8.
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for HighWire Icon for PubMed Central
    Loading ...
    Write to the Help Desk