Microarrays, deep sequencing and the true measure of the transcriptome

Malone, John H.; Oliver, Brian

doi:10.1186/1741-7007-9-34

Cited by 461 publications

(373 citation statements)

References 51 publications

Supporting

Mentioning

353

Contrasting

Unclassified

Order By: Relevance

“…Although high-throughput RNA sequencing has recently become popular as an alternative to microarray analysis, the microarray platform, with its robust sample process and data analysis pipelines, is still the preferred choice for transcriptomic profiling involving a large number of samples in model plants with well-annotated genomes [14,15]. Many microarray-based studies have been carried out to identify abiotic stress responsive genes in specific rice varieties and transgenic rice [9,10,16,17], and comparative transcriptional profiling of two contrasting rice genotypes under salinity and drought stress have revealed novel genetic regulatory mechanisms involved in stress tolerance [18,19].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background

Zhang¹,

Huang²,

Wang³

et al. 2012

BMC Genomics

View full text Add to dashboard Cite

BackgroundRice in tropical and sub-tropical areas is often subjected to cold stress at the seedling stage, resulting in poor growth and yield loss. Although japonica rice is generally more cold tolerant (CT) than indica rice, there are several favorable alleles for CT exist in indica that can be used to enhance CT in rice with a japonica background. Genome-wide gene expression profiling is an efficient way to decipher the molecular genetic mechanisms of CT enhancement and to provide valuable information for CT improvement in rice molecular breeding. In this study, the transcriptome of the CT introgression line (IL) K354 and its recurrent parent C418 under cold stress were comparatively analyzed to explore the possible CT enhancement mechanisms of K354.ResultsA total of 3184 differentially expressed genes (DEGs), including 195 transcription factors, were identified in both lines under cold stress. About half of these DEGs were commonly regulated and involved in major cold responsive pathways associated with OsDREB1 and OsMyb4 regulons. K354-specific cold-induced genes were functionally related to stimulus response, cellular cell wall organization, and microtubule-based movement processes that may contribute to increase CT. A set of genes encoding membrane fluidity and defensive proteins were highly enriched only in K354, suggesting that they contribute to the inherent CT of K354. Candidate gene prediction based on introgressed regions in K354 revealed genotype-dependent CT enhancement mechanisms, associated with Sir2, OsFAD7, OsWAK112d, and programmed cell death (PCD) related genes, present in CT IL K354 but absent in its recurrent parent C418. In K354, a number of DEGs were co-localized onto introgressed segments associated with CT QTLs, providing a basis for gene cloning and elucidation of molecular mechanisms responsible for CT in rice.ConclusionsGenome-wide gene expression analysis revealed that genotype-specific cold induced genes and genes with higher basal expression in the CT genotype contribute jointly to CT improvement. The molecular genetic pathways of cold stress tolerance uncovered in this study, as well as the DEGs co-localized with CT-related QTLs, will serve as useful resources for further functional dissection of the molecular mechanisms of cold stress response in rice.

show abstract

Section: Introductionmentioning

confidence: 99%

Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background

Zhang¹,

Huang²,

Wang³

et al. 2012

BMC Genomics

View full text Add to dashboard Cite

show abstract

“…The most common analysis is differential expression, which is defined by molecular features that experience large changes in expression or abundance between groups (Malone and Oliver, 2011;Oshlack et al, 2010). In addition to differential variance (i.e.…”

Section: Introductionmentioning

confidence: 99%

The discordant method: a novel approach for differential correlation

2015

View full text Add to dashboard Cite

Motivation: Current differential correlation methods are designed to determine molecular feature pairs that have the largest magnitude of difference between correlation coefficients. These methods do not easily capture molecular feature pairs that experience no correlation in one group but correlation in another, which may reflect certain types of biological interactions. We have developed a tool, the Discordant method, which categorizes the correlation types for each group to make this possible. Results: We compare the Discordant method to existing approaches using simulations and two biological datasets with different types of -omics data. In contrast to other methods, Discordant identifies phenotype-related features at a similar or higher rate while maintaining reasonable computational tractability and usability. Availability and implementation: R code and sample data are available at https://github.com/siskac/

show abstract

“…The information generated by RNA-seq and microarrays is thus complementary, highly congruent and in most cases allows for an integrative analysis of cellular pathways. A high correlation for mRNA abundance (0.7-0.9) between microarray-and RNA-seq-based gene expression analyses has been demonstrated (Malone and Oliver 2011;Marioni et al 2008), and matches differentially expressed genes ranges between 62 and 81 % (Brunskill et al 2011;Malone and Oliver 2011;Marioni et al 2008). Small discrepancies usually have been associated with sequencing depth and the number of reads to satisfactorily cover the genome in RNA-seq, and therefore a higher correlation between microarray and RNA-seq data is found at higher sequencing depth (genes mapped by more than 32 reads) (Marioni et al 2008).…”

Section: Rna-seq and Microarraysmentioning

confidence: 94%

“…As a consequence, arrays may have an advantage in measuring differential gene expression for low-abundance transcripts when RNA-seq is not deep enough (Bloom et al 2009). Moreover, due to their intrinsic methodological properties, microarrays and RNA-seq approaches usually identify different sets of differentially expressed genes (Bradford et al 2010;Brunskill et al 2011;Malone and Oliver 2011;Marioni et al 2008), which suggests that a combination of RNA-seq and custom microarrays represents a powerful strategy to uncover wider transcriptome responses.…”

Section: Rna-seq and Microarraysmentioning

confidence: 99%

Advances in genomics for flatfish aquaculture

Cerdà

Manchado

2012

Genes Nutr

View full text Add to dashboard Cite

Fish aquaculture is considered to be one of the most sustainable sources of protein for humans. Many different species are cultured worldwide, but among them, marine flatfishes comprise a group of teleosts of high commercial interest because of their highly prized white flesh. However, the aquaculture of these fishes is seriously hampered by the scarce knowledge on their biology. In recent years, various experimental 'omics' approaches have been applied to farmed flatfishes to increment the genomic resources available. These tools are beginning to identify genetic markers associated with traits of commercial interest, and to unravel the molecular basis of different physiological processes. This article summarizes recent advances in flatfish genomics research in Europe. We focus on the new generation sequencing technologies, which can produce a massive amount of DNA sequencing data, and discuss their potentials and applications for de novo genome sequencing and transcriptome analysis. The relevance of these methods in nutrigenomics and foodomics approaches for the production of healthy animals, as well as high quality and safety products for the consumer, is also briefly discussed.

show abstract

Microarrays, deep sequencing and the true measure of the transcriptome

Cited by 461 publications

References 51 publications

Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background

Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background

The discordant method: a novel approach for differential correlation

Advances in genomics for flatfish aquaculture

Contact Info

Product

Resources

About