TITLE:
Isoform Inference From RNA-Seq Samples Based on Gene Structures on Chromosomes
AUTHORS:
Yan Ji, Jia Wei
KEYWORDS:
RNA-Seq; isoform inference; cancer genes; Cufflinks; RSEM
JOURNAL NAME:
Journal of Biosciences and Medicines,
Vol.1 No.1,
February
6,
2013
ABSTRACT: The emerging RNA-Seq technology makes it possible to infer splicing variants from millions of short sequence reads. Here we present a method to identify isoforms by their specific signatures on chromosomes including both exons and junctions. By applying this method to a RNA-Seq dataset of gastric cancer, we showed that our method is more accurate and sensitive than other isoform inference tools such as RSEM and Cufflinks. By constructing a network from gene list identified by our method but missed by other tools, we found that some cancer-related genes enriched in network modules have significant implications for cancer drug discovery.