ArticleNucleic acids research2016
iGEMS: an integrated model for identification of alternative exon usage events.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Molecular Transducers of Human Skeletal Muscle Remodeling under Different Loading States.Cell reports · 2020Trial
- Network-based modelling reveals cell-type enriched patterns of non-coding RNA regulation during human skeletal muscle remodelling.bioRxiv : the preprint server for biology · 2024Article
- Network-based modelling reveals cell-type enriched patterns of non-coding RNA regulation during human skeletal muscle remodelling.NAR molecular medicine · 2024Article
- Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq.Advanced genetics (Hoboken, N.J.) · 2023Review
- Urgent need for consistent standards in functional enrichment analysis.PLoS computational biology · 2022Article
- A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease.eLife · 2022Article
- Human and mouse muscle transcriptomic analyses identify insulin receptor mRNA downregulation in hyperinsulinemia-associated insulin resistance.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2022Article
- Article
- Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm.BMC genomics · 2018Article
- A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease.Nucleic acids research · 2018Article
- A Systems-Level Analysis Reveals Circadian Regulation of Splicing in Colorectal Cancer.EBioMedicine · 2018Article
- The Usage of Exon-Exon Splice Junctions for the Detection of Alternative Splicing using the REIDS model.Scientific reports · 2018Article
- A random effects model for the identification of differential splicing (REIDS) using exon and HTA arrays.BMC bioinformatics · 2017Article
- Article
- Biomarkers of browning of white adipose tissue and their regulation during exercise- and diet-induced weight loss.The American journal of clinical nutrition · 2016Article
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Authors and funding
13 authors.
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Abstract
DNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with (n = 9) or without (n = 8) the anti-diabetes drug, rosiglitazone. iGEMS identified 555 genes with AEU, and robust verification by RT-qPCR (∼90%). Second, in a three-way human tissue comparison (muscle, adipose and blood, n = 41) iGEMS identified 4421 genes with at least one AEU event, with excellent RT-qPCR verification (95%, n = 22). Importantly, iGEMS identified a variety of AEU events, including 3'UTR extension, as well as exon inclusion/exclusion impacting on protein kinase and extracellular matrix domains. In conclusion, iGEMS is a robust method for identification of AEU while the variety of exon usage between human tissues is 5-10 times more prevalent than reported by the Genotype-Tissue Expression consortium using RNA sequencing.
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