Pushing the annotation of cellular activities to a higher resolution Predicting functions at the isoform level》.pdf

Methods xxx (2015) xxx–xxx Contents lists available at ScienceDirect Methods journal homepage: www.else /locate/ymeth Pushing the annotation of cellular activities to a higher resolution: Predicting functions at the isoform level Wenyuan Li a,1, Chun-Chi Liu b,c,d,1, Shuli Kang a,1, Jian-Rong Li b, Yu-Ting Tseng b, Xianghong Jasmine Zhou a,⇑ a Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA b Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan c Institute of Biomedical Sciences, National Chung Hsing University, Taiwan d Agricultural Biotechnology Center, National Chung Hsing University, Taiwan a r t i c l e i n f o a b s t r a c t Article history: In past decades, the experimental determination of protein functions was expensive and Received 1 June 2015 time-consuming, so numerous computational methods were developed to speed up and guide the pro- Received in revised form 20 July 2015 cess. However, most of these methods predict protein functions at the gene level and do not consider Accepted 29 July 2015 the fact that protein isoforms (translated from alternatively spliced transcripts), not genes, are the actual Available online xxxx function carriers. Now, high-throughput RNA-seq technology is providing unprecedented opportunities to unravel protein