DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions
نویسندگان
چکیده
Detection of differential expression in RNA-Seq data is currently limited to studies in which two or more sample conditions are known a priori. However, these biological conditions are typically unknown in cohort, cross-sectional and nonrandomized controlled studies such as the HapMap, the ENCODE or the 1000 Genomes project. We present DEXUS for detecting differential expression in RNA-Seq data for which the sample conditions are unknown. DEXUS models read counts as a finite mixture of negative binomial distributions in which each mixture component corresponds to a condition. A transcript is considered differentially expressed if modeling of its read counts requires more than one condition. DEXUS decomposes read count variation into variation due to noise and variation due to differential expression. Evidence of differential expression is measured by the informative/noninformative (I/NI) value, which allows differentially expressed transcripts to be extracted at a desired specificity (significance level) or sensitivity (power). DEXUS performed excellently in identifying differentially expressed transcripts in data with unknown conditions. On 2400 simulated data sets, I/NI value thresholds of 0.025, 0.05 and 0.1 yielded average specificities of 92, 97 and 99% at sensitivities of 76, 61 and 38%, respectively. On real-world data sets, DEXUS was able to detect differentially expressed transcripts related to sex, species, tissue, structural variants or quantitative trait loci. The DEXUS R package is publicly available from Bioconductor and the scripts for all experiments are available at http://www.bioinf.jku.at/software/dexus/.
منابع مشابه
Regulatory effects of cis- and trans-LncRNAs on differential expression of genes following infection with viral hemorrhagic septicemia virus in rainbow trout (Oncorhynchus mykiss)
In this study the cis and trans regulatory effect of long non-coding genes (lncRNA) on the expression of genes in fish infected by Viral hemorrhagic septicemia virus (VHS) was investigated using RNA-seq technology. At the end of experimental period (the thirty fifth day), total RNA was extracted from spleen tissue (group treated with virus) and physiological serum (control group) was used to pr...
متن کاملInvestigating the Function of Predicted Proteins from RNA-Seq Data in Holstein and Cholistani Cattle Breeds
This study was performed to determine the digital expression profile of different genes expressed in Holstein and Cholistani breeds as well as to evaluate the performance of predicted proteins derived from differentially expressed genes between these two breeds using RNA-Seq data. For this purpose, the whole mRNA sequence for a blood sample of American Holstein and Pakistani Cholistani cattle p...
متن کاملUsing RNA-seq Data to Detect Differentially Expressed Genes
RNA-sequencing (RNA-seq) technology has become a major choice in detecting differentially expressed genes across different biological conditions. Although microarray technology is used for the same purpose, statistical methods available for identifying differential expression for microarray data are generally not readily applicable to the analysis of RNA-seq data, as RNA-seq data comprise discr...
متن کاملEnhanced Probability Plots for Identifying Differential Gene Expression and Methylation Patterns in Breast Cancer Cell Lines via RNA-Seq and MethylC-Seq
Next generation DNA sequencing (NGS) is poised to replace microarray as the primary technology for research in genomics, epigenomics and transcriptomics in the near future. Two NGSbased methods RNA-Seq and MethylC-Seq provide researchers with unprecedented power to map and quantify genome-wide gene expression levels and DNA methylation patterns. In this study, we adopt a simple model-based grap...
متن کاملSequence analysis EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments
Motivation: With improvements in next-generation sequencing technologies and reductions in price, ordered RNA-seq experiments are becoming common. Of primary interest in these experiments is identifying genes that are changing over time or space, for example, and then characterizing the specific expression changes. A number of robust statistical methods are available to identify genes showing d...
متن کامل