Cross-species analysis of gene expression in non-model mammals: reproducibility of hybridization on high density oligonucleotide microarrays

Nieto-Díaz, Manuel; Pita-Thomas, Wolfgang; Nieto-Sampedro, Manuel
January 2007
BMC Genomics;2007, Vol. 8, p89
Academic Journal
Background: Gene expression profiles of non-model mammals may provide valuable data for biomedical and evolutionary studies. However, due to lack of sequence information of other species, DNA microarrays are currently restricted to humans and a few model species. This limitation may be overcome by using arrays developed for a given species to analyse gene expression in a related one, an approach known as "cross-species analysis". In spite of its potential usefulness, the accuracy and reproducibility of the gene expression measures obtained in this way are still open to doubt. The present study examines whether or not hybridization values from cross-species analyses are as reproducible as those from same-species analyses when using Affymetrix oligonucleotide microarrays. Results: The reproducibility of the probe data obtained hybridizing deer, Old-World primates, and human RNA samples to Affymetrix human GeneChip® U133 Plus 2.0 was compared. The results show that cross-species hybridization affected neither the distribution of the hybridization reproducibility among different categories, nor the reproducibility values of the individual probes. Our analyses also show that a 0.5% of the probes analysed in the U133 plus 2.0 GeneChip are significantly associated to unreproducible hybridizations. Such probes-called in the text un-reproducible probe sequences- do not increase in number in cross-species analyses. Conclusion: Our study demonstrates that cross-species analyses do not significantly affect hybridization reproducibility of GeneChips, at least within the range of the mammal species analysed here. The differences in reproducibility between same-species and cross-species analyses observed in previous studies were probably caused by the analytical methods used to calculate the gene expression measures. Together with previous observations on the accuracy of GeneChips for cross-species analysis, our analyses demonstrate that cross-species hybridizations may provide useful gene expression data. However, the reproducibility and accuracy of these measures largely depends on the use of appropriated algorithms to derive the gene expression data from the probe data. Also, the identification of probes associated to un-reproducible hybridizations-useless for gene expression analyses- in the studied GeneChip, stress the need of a re-evaluation of the probes' performance.


Related Articles

  • Three microarray platforms: an analysis of their concordance in profiling gene expression. Petersen, David; Chandramouli, GVR; Geoghegan, Joel; Hilburn, Joanne; Paarlberg, Jonathon; Chang Hee Kim; Munroe, David; Gangi, Lisa; Han, Jing; Puri, Raj; Staudt, Lou; Weinstein, John; Barrett, J Carl; Green, Jeffrey; Kawasaki, Ernest S // BMC Genomics;2005, Vol. 6, p63 

    Background: Microarrays for the analysis of gene expression are of three different types: short oligonucleotide (25-30 base), long oligonucleotide (50-80 base), and cDNA (highly variable in length). The short oligonucleotide and cDNA arrays have been the mainstay of expression analysis to date,...

  • Therapeutic Applications of Antisense Oligonucleotides in Asthma and Allergy. Isidoro-Garc�a, Mar�a; D�vila, Ignacio // Recent Patents on Inflammation & Allergy Drug Discovery;Nov2007, Vol. 1 Issue 3, p171 

    Antisense oligonucleotides represent a novel therapeutic approach for manipulation of gene expression in the treatment of respiratory diseases. This methodology is based on the use of synthetic oligonucleotides to inhibit the expression of a specific target gene by inhibiting the function of the...

  • Direct Quantification of Gene Expression Using Fluorescence Correlation Spectroscopy. Nomura, Yasutomo; Nakamura, Takao; Feng, Zhonggang; Kinjo, Masataka // Current Pharmaceutical Biotechnology;Oct2007, Vol. 8 Issue 5, p286 

    Among the methods for single molecule detection in the field of medicinal chemistry, the importance of fluorescence correlation spectroscopy (FCS) is growing. FCS has the advantage of permitting us to determine the number of fluorescent molecules and the diffusion constant dependent on the...

  • Effective inhibition of HCMV UL49 gene expression and viral replication by oligonucleotide external guide sequences and RNase P. Wen Jun Zhang; Hong Jian Li; Yue Qin Li; Zhi Feng Zeng; Shi Qian Li; Xin Zhang; Yi Zou; Tian Hong Zhou // Virology Journal;2010, Vol. 7, p100 

    Background: Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus that typically causes asymptomatic infections in healthy individuals but may lead to serious complications in newborns and immunodeficient individuals. The emergence of drug-resistant strains of HCMV has posed a need for the...

  • SOAP: short oligonucleotide alignment program. Ruiqiang Li; Yingrui Li; Karsten Kristiansen; Jun Wang // Bioinformatics;Mar2008, Vol. 24 Issue 5, p713 

    Summary: We have developed a program SOAP for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The program is designed to handle the huge amounts of short reads generated by parallel sequencing using the new generation Illumina-Solexa sequencing...

  • Gene expression analysis by transcript profiling coupled to a gene database query. Shimkets, Richard A.; Lowe, David G.; Tai, Julie Tsu-Ning; Sehl, Patricia; Jin, Hongkui; Yang, Renhui; Predki, Paul F.; Rothberg, Bonnie E. G.; Murtha, Michael T.; Roth, Matthew E.; Shenoy, Suresh G.; Windemuth, Andreas; Simpson, John W.; Simons, Jan F.; Daley, Michael P.; Gold, Steven A.; McKenna, Michael P.; Hillan, Kenneth; Went, Gregory T. // Nature Biotechnology;Aug99, Vol. 17 Issue 8, p798 

    We describe an mRNA profiling technique for determining differential gene expression that utilizes, but does not require, prior knowledge of gene sequences. This method permits high-throughput reproducible detection of most expressed sequences with a sensitivity of greater than 1 part in...

  • The Utility of cDNA Microarrays. Clark, Charles T. // Genomics & Proteomics;Jan/Feb2003, Vol. 3 Issue 1, p35 

    Focuses on the increasing use of complementary DNA microarrays in gene expression analysis. Amount of RNA expressed by a gene; Components of complementary DNA microarrays; Advantages of oligonucleotide arrays over complementary DNA arrays.

  • CDNA Blotting Offers an Alternative Method for Gene Expression Studies. Jaakola, Laura // Plant Molecular Biology Reporter;Jun2001, Vol. 19 Issue 2, p125 

    Abstract. Northern analysis of bilberry fruit RNA using a non-radioactive detection system proved to be extremely difficult. To overcome this problem, we used cDNA instead of RNA for the blotting step. The RNA was translated to cDNA directly after isolation. The cDNA was then separated by...

  • Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays. Auer, Herbert; Newsom, David L; Nowak, Norma J; McHugh, Kirk M; Singh, Sunita; Chack-Yung Yu; Yan Yang; Wenger, Gail D; Gastier-Foster, Julie M; Kornacker, Karl // BMC Genomics;2007, Vol. 8, p111 

    Background: Array-based comparative genomic hybridization (aCGH) is a high-throughput method for measuring genome-wide DNA copy number changes. Current aCGH methods have limited resolution, sensitivity and reproducibility. Microarrays for aCGH are available only for a few organisms and...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics