English   español  
Por favor, use este identificador para citar o enlazar a este item: http://hdl.handle.net/10261/3421
logo share SHARE logo core CORE   Add this article to your Mendeley library MendeleyBASE

Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL
Exportar a otros formatos:

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

AutorNieto-Díaz, Manuel; Pita-Thomas, Daniel W.; Nieto-Sampedro, Manuel
Fecha de publicación3-abr-2007
EditorBioMed Central
CitaciónBMC Genomics. 2007; 8: 89
Resumen[Background] Gene expression profiles of non-model mammals may provide valuable data for biomedical and evolutionary studies. However, due to lack of sequences compared. The results show that crossspecies hybridization affected neither the distribution of the hybridization reproducibility 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 samespecies 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 crossspecies 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 un-reproducible 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.
DescripciónThis article is available from: http://www.biomedcentral.com/1471-2164/8/89
Aparece en las colecciones: (IC) Artículos
Ficheros en este ítem:
Fichero Descripción Tamaño Formato  
picrender.pdfPrincipal464,89 kBAdobe PDFVista previa
1471-2164-8-89-S1.xlsArchivo adicional 14,31 MBMicrosoft ExcelVisualizar/Abrir
1471-2164-8-89-S2.xlsArchivo adicional 274,5 kBMicrosoft ExcelVisualizar/Abrir
1471-2164-8-89-S3.txtArchivo adicional 34,9 MBTextVisualizar/Abrir
1471-2164-8-89-S4.xlsArchivo adicional 4341 kBMicrosoft ExcelVisualizar/Abrir
1471-2164-8-89-S5.xlsArchivo adicional 529,5 kBMicrosoft ExcelVisualizar/Abrir
1471-2164-8-89-S6.xlsArchivo adicional 642,5 kBMicrosoft ExcelVisualizar/Abrir
1471-2164-8-89-S7.xlsArchivo adicional 783 kBMicrosoft ExcelVisualizar/Abrir
1471-2164-8-89-S8.xlsArchivo adicional 840 kBMicrosoft ExcelVisualizar/Abrir
1471-2164-8-89-S9.xlsArchivo adicional 93,49 MBMicrosoft ExcelVisualizar/Abrir
Mostrar el registro completo

Artículos relacionados:

NOTA: Los ítems de Digital.CSIC están protegidos por copyright, con todos los derechos reservados, a menos que se indique lo contrario.