title: REMAS: a new regression model to identify alternative splicing events from exon array data.
abstract: BACKGROUND
  Alternative splicing (AS) is an important regulatory mechanism for gene expression and protein diversity in eukaryotes. Previous studies have demonstrated that it can be causative for, or specific to splicing-related diseases. Understanding the regulation of AS will be helpful for diagnostic efforts and drug discoveries on those splicing-related diseases. As a novel exon-centric microarray platform, exon array enables a comprehensive analysis of AS by investigating the expression of known and predicted exons. Identifying of AS events from exon array has raised much attention, however, new and powerful algorithms for exon array data analysis are still absent till now.
  
  
  RESULTS
  Here, we considered identifying of AS events in the framework of variable selection and developed a regression method for AS detection (REMAS). Firstly, features of alternatively spliced exons were scaled by reasonably defined variables. Secondly, we designed a hierarchical model which can represent gene structure and transcriptional influence to exons, and the lasso type penalties were introduced in calculation because of huge variable size. Thirdly, an iterative two-step algorithm was developed to select alternatively spliced genes and exons. To avoid negative effects introduced by small sample size, we ranked genes as parameters indicating their AS capabilities in an iterative manner. After that, both simulation and real data evaluation showed that REMAS could efficiently identify potential AS events, some of which had been validated by RT-PCR or supported by literature evidence.
  
  
  CONCLUSIONS
  As a new lasso regression algorithm based on hierarchical model, REMAS has been demonstrated as a reliable and effective method to identify AS events from exon array data.
authors.affiliation: LMAM, School of Mathematical Sciences and Center for Theoretical Biology, Peking University, Beijing 100871, PR China. porcupine.hao@gmail.com
authors.forename: Hao
authors.initials: H
authors.lastname: Zheng
authors.forename: Xingyi
authors.initials: X
authors.lastname: Hang
authors.forename: Ji
authors.initials: J
authors.lastname: Zhu
authors.forename: Minping
authors.initials: M
authors.lastname: Qian
authors.forename: Wubin
authors.initials: W
authors.lastname: Qu
authors.forename: Chenggang
authors.initials: C
authors.lastname: Zhang
authors.forename: Minghua
authors.initials: M
authors.lastname: Deng
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D005091:Exons / Q000235:genetics*; D016014:Linear Models; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*