title: Assessing differential expression measurements by highly parallel pyrosequencing and DNA microarrays: a comparative study.
abstract: To explore the feasibility of pyrosequencing for quantitative differential gene expression analysis we have performed a comparative study of the results of the sequencing experiments to those obtained by a conventional DNA microarray platform. A conclusion from our analysis is that, over a threshold of 35 normalized reads per gene, the measurements of gene expression display a good correlation with the references. The observed concordance between pyrosequencing and DNA microarray platforms beyond the threshold was of 0.8, measured as a Pearson's correlation coefficient. In differential gene expression the initial aim is the quantification the differences among transcripts when comparing experimental conditions. Thus, even in a scenario of low coverage the concordance in the measurements is quite acceptable. On the other hand, the comparatively longer read size obtained by pyrosequencing allows detecting unconventional splicing forms.
authors.affiliation: Departament de Bioquímica y Biología Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Ariño
authors.forename: Antonio
authors.initials: A
authors.lastname: Casamayor
authors.forename: Julián Perez
authors.initials: JP
authors.lastname: Pérez
authors.forename: Laia
authors.initials: L
authors.lastname: Pedrola
authors.forename: Miguel
authors.initials: M
authors.lastname: Álvarez-Tejado
authors.forename: Martina
authors.initials: M
authors.lastname: Marbà
authors.forename: Javier
authors.initials: J
authors.lastname: Santoyo
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
mesh_terms: D005786:Gene Expression Regulation; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics
chemical_list: D012333:RNA, Messenger