Dataset Information

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.

ABSTRACT: Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles that can be further analyzed using correlation analysis, co-expression analysis, clustering, differential gene expression (DGE), among many other studies. While these analyses can provide invaluable information related to gene expression, integration and interpretation of the results can prove challenging. Here we present a tool called IRIS-EDA, which is a Shiny web server for expression data analysis. It provides a straightforward and user-friendly platform for performing numerous computational analyses on user-provided RNA-Seq or Single-cell RNA-Seq (scRNA-Seq) data. Specifically, three commonly used R packages (edgeR, DESeq2, and limma) are implemented in the DGE analysis with seven unique experimental design functionalities, including a user-specified design matrix option. Seven discovery-driven methods and tools (correlation analysis, heatmap, clustering, biclustering, Principal Component Analysis (PCA), Multidimensional Scaling (MDS), and t-distributed Stochastic Neighbor Embedding (t-SNE)) are provided for gene expression exploration which is useful for designing experimental hypotheses and determining key factors for comprehensive DGE analysis. Furthermore, this platform integrates seven visualization tools in a highly interactive manner, for improved interpretation of the analyses. It is noteworthy that, for the first time, IRIS-EDA provides a framework to expedite submission of data and results to NCBI's Gene Expression Omnibus following the FAIR (Findable, Accessible, Interoperable and Reusable) Data Principles. IRIS-EDA is freely available at http://bmbl.sdstate.edu/IRIS/.

SUBMITTER: Monier B

PROVIDER: S-EPMC6392338 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

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IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.

Monier Brandon B McDermaid Adam A Wang Cankun C Zhao Jing J Miller Allison A Fennell Anne A Ma Qin Q

PLoS computational biology 20190214 2

Next-Generation Sequencing has made available substantial amounts of large-scale Omics data, providing unprecedented opportunities to understand complex biological systems. Specifically, the value of RNA-Sequencing (RNA-Seq) data has been confirmed in inferring how gene regulatory systems will respond under various conditions (bulk data) or cell types (single-cell data). RNA-Seq can generate genome-scale gene expression profiles that can be further analyzed using correlation analysis, co-express ...[more]

PMID: 30763315

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Project description:BackgroundUse of next-generation sequencing technologies to transcriptomics (RNA-seq) for gene expression profiling has found widespread application in studying different biological conditions including cancers. However, RNA-seq experiments are still small sample size experiments due to the cost. Recently, an increased focus has been on meta-analysis methods for integrated differential expression analysis for exploration of potential biomarkers. In this study, we propose a p-value combination method for meta-analysis of multiple independent but related RNA-seq studies that accounts for sample size of a study and direction of expression of genes in individual studies.ResultsThe proposed method generalizes the inverse-normal method without an increase in statistical or computational complexity and does not pre- or post-hoc filter genes that have conflicting direction of expression in different studies. Thus, the proposed method, as compared to the inverse-normal, has better potential for the discovery of differentially expressed genes (DEGs) with potentially conflicting differential signals from multiple studies related to disease. We demonstrated the use of the proposed method in detection of biologically relevant DEGs in glioblastoma (GBM), the most aggressive brain cancer. Our approach notably enabled the identification of over-expressed tumour suppressor gene RAD51 in GBM compared to healthy controls, which has recently been shown to be a target for inhibition to enhance radiosensitivity of GBM cells during treatment. Pathway analysis identified multiple aberrant GBM related pathways as well as novel regulators such as TCF7L2 and MAPT as important upstream regulators in GBM.ConclusionsThe proposed meta-analysis method generalizes the existing inverse-normal method by providing a way to establish differential expression status for genes with conflicting direction of expression in individual RNA-seq studies. Hence, leading to further exploration of them as potential biomarkers for the disease.

Dataset Information

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.

Publications

IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis.

Similar Datasets

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