Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data

• Published in: PLoS computational biology 2013-11, Vol.9 (11), p.e1003314-e1003314
• Main Authors: Eksi, Ridvan, Li, Hong-Dong, Menon, Rajasree, Wen, Yuchen, Omenn, Gilbert S, Kretzler, Matthias, Guan, Yuanfang
• Format: Article
• Language: English
• Subjects: Algorithms; Alternative Splicing - physiology; Animals; Cluster Analysis; Computational Biology - methods; Data processing; Databases, Protein; Gene expression; Humans; Mice; Models, Molecular; Neural networks; Protein Isoforms - chemistry; Protein Isoforms - genetics; Protein Isoforms - physiology; Proteins; Reproducibility of Results; RNA - chemistry; RNA - genetics; RNA - physiology; RNA sequencing; Sequence Analysis, RNA
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1003314

Integrating large-scale functional genomic data has significantly accelerated our understanding of gene functions. However, no algorithm has been developed to differentiate functions for isoforms of the same gene using high-throughput genomic data. This is because standard supervised learning requires 'ground-truth' functional annotations, which are lacking at the isoform level. To address this challenge, we developed a generic framework that interrogates public RNA-seq data at the transcript level to differentiate functions for alternatively spliced isoforms. For a specific function, our algorithm identifies the 'responsible' isoform(s) of a gene and generates classifying models at the isoform level instead of at the gene level. Through cross-validation, we demonstrated that our algorithm is effective in assigning functions to genes, especially the ones with multiple isoforms, and robust to gene expression levels and removal of homologous gene pairs. We identified genes in the mouse whose isoforms are predicted to have disparate functionalities and experimentally validated the 'responsible' isoforms using data from mammary tissue. With protein structure modeling and experimental evidence, we further validated the predicted isoform functional differences for the genes Cdkn2a and Anxa6. Our generic framework is the first to predict and differentiate functions for alternatively spliced isoforms, instead of genes, using genomic data. It is extendable to any base machine learner and other species with alternatively spliced isoforms, and shifts the current gene-centered function prediction to isoform-level predictions.