ArticleBMC genomics2012
RNA-seq and microarray complement each other in transcriptome profiling.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 1 of them a synthesis that pooled it.
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Who cites it
83 citing papers in PubMed, 1 synthesis or guideline pooled it, 162 citations in OpenAlex.
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- Mechanisms of flavonoids in quinoa's response to flooding stress in grain filling stage.Frontiers in plant science · 2025Article
- Comparative transcriptomics reveals a highly polymorphic Xanthomonas HrpG virulence regulon.BMC genomics · 2024Article
- Molecular and Systems Biology Approaches for Harnessing the Symbiotic Interaction in Mycorrhizal Symbiosis for Grain and Oil Crop Cultivation.International journal of molecular sciences · 2024Review
- Comparison of RNA-Seq and microarray in the prediction of protein expression and survival prediction.Frontiers in genetics · 2024Article
- Gene Expression Profile Analysis of the Molecular Mechanism of HOXD10 Regulation of Epithelial Ovarian Cancer Cells.Journal of Cancer · 2024Article
- Data Mining of Microarray Datasets in Translational Neuroscience.Brain sciences · 2023Review
- Transcriptome and Metabolome Analyses Reveal Mechanisms Underlying the Response of Quinoa Seedlings to Nitrogen Fertilizers.International journal of molecular sciences · 2023Article
- Genes critical for development and differentiation of dopaminergic neurons are downregulated in Parkinson's disease.Journal of neural transmission (Vienna, Austria : 1996) · 2023Article
- TiSA: TimeSeriesAnalysis-a pipeline for the analysis of longitudinal transcriptomics data.NAR genomics and bioinformatics · 2023Article
- Comparative transcriptome analysis provides novel insights into molecular response of salt-tolerant and sensitive polyembryonic mango genotypes to salinity stress at seedling stage.Frontiers in plant science · 2023Article
- Meta-analysis of fungal plant pathogenFrontiers in microbiology · 2022Article
- rePROBE: Workflow for Revised Probe Assignment and Updated Probe-set Annotation in Microarrays.Genomics, proteomics & bioinformatics · 2021Article
- Comparison of transcriptional profiles of Treponema pallidum during experimental infection of rabbits and in vitro culture: Highly similar, yet different.PLoS pathogens · 2021Article
- Pathomechanisms and biomarkers in facioscapulohumeral muscular dystrophy: roles of DUX4 and PAX7.EMBO molecular medicine · 2021Review
23 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.