GSE108140 Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify

Contributors : Malgorzata A Komor ; Annemieke C Hiemstra ; Anne S Bolijn ; Pien M Delis-van Diemen ; Marianne Tijssen ; Robert P Sebra ; Meredith Ashby ; Gerrit A Meijer ; Connie R Jimenez ; Remond J FijnemanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensProteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, we focus on this rich source of cancer specific biomarkers. To this end, we developed a proteogenomic pipeline, Splicify, which is able to detect differentially expressed protein isoforms. Splicify is based on integrating RNA massive parallel sequencing data and tandem mass spectrometry proteomics data to identify protein isoforms resulting from differential splicing between two conditions. Proof of concept was obtained by applying Splicify to RNA sequencing and mass spectrometry data obtained from colorectal cancer cell line SW480, before and after siRNA-mediated down-modulation of the splicing factors SF3B1 and SRSF1. These analyses revealed 2172 and 149 differentially expressed isoforms, respectively, with peptide confirmation upon knock-down of SF3B1 and SRSF1 compared to their controls. Splice variants identified included RAC1, OSBPL3, MKI67 and SYK. One additional sample was ana...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research