RNA-seq and microarray complement each other in transcriptome profiling

Abstract

BackgroundRNA-seq and microarray are the two popular methods employed for genome-wide transcriptome profiling. Current comparison studies have shown that transcriptome quantified by these two methods correlated well. However, none of them have addressed if they complement each other, considering the strengths and the limitations inherent with them. The pivotal requirement to address this question is the knowledge of a well known data set. In this regard, HrpX regulome from pathogenic bacteria serves as an ideal choice as the target genes of HrpX transcription factor are well studied due to their central role in pathogenicity.ResultsWe compared the performance of RNA-seq and microarray in their ability to detect known HrpX target genes by profiling the transcriptome from the wild-type and the hrpX mutant strains of γ-Proteobacterium Xanthomonas citri subsp. citri. Our comparative analysis indicated that gene expression levels quantified by RNA-seq and microarray well-correlated both at absolute as well as relative levels (Spearman correlation-coefficient, rs > 0.76). Further, the expression levels quantified by RNA-seq and microarray for the significantly differentially expressed genes (DEGs) also well-correlated with qRT-PCR based quantification (rs = 0.58 to 0.94). Finally, in addition to the 55 newly identified DEGs, 72% of the already known HrpX target genes were detected by both RNA-seq and microarray, while, the remaining 28% could only be detected by either one of the methods.ConclusionsThis study has significantly advanced our understanding of the regulome of the critical transcriptional factor HrpX. RNA-seq and microarray together provide a more comprehensive picture of HrpX regulome by uniquely identifying new DEGs. Our study demonstrated that RNA-seq and microarray complement each other in transcriptome profiling.

Identificação de transcritos diferencialmente expressos por Pasteurella multocida em condições de privação de ferro

“…(Kogenaru et al 2012). O perfil de transcritos superexpressos na condição de Fe -está associado a transoporte celular e proteínas de membrana que são descritos em P. multocida e outras bactérias.…”

“…Até recentemente a análise de transcritos expressos por patógenos de interesse médico eram baseados apenas em técnicas de microarray, o que vem sendo complementado e melhorado pelas técnicas de sequenciamento de nova geração (Paustian et al 2001, Paustian et al 2002, Kogenaru et al 2012.…”

Bioinformatics: Concepts, Methods, and Data

“…RNA-seq, however, can detect SNPs and other genetic variations, fusion genes, and levels of different splice variants. It has also been suggested that the two technologies should be used together where possible to detect the maximum coverage of the transcriptome [59]. All data in GEO and ArrayExpress must adhere to "minimum information about a microarray experiments" (MIAME) [60] or "minimum information about sequencing experiments" (MINSEQE) [61]; these are standards dictating that enough information must be included for a second party to sufficiently analyze and/or recreate the experiment.…”

Detecting Dysregulated Processes and Pathways

“…For more than 10 years, microarrays have been the state-of-the-art for measuring comprehensive expression profiles of genes, although they are now quickly being replaced by NGS technologies, called RNA-Seq [11][12][13]. Both technologies are relatively cost-efficient, require tolerable experimental effort, and allow for measuring the expression of all genes simultaneously.…”