This article is part of the supplement: The International Conference on Intelligent Biology and Medicine (ICIBM) Genomics
DFI: gene feature discovery in RNA-seq experiments from multiple sources
The Department of Biomedical Informatics and The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210, USA
BMC Genomics 2012, 13(Suppl 8):S11 doi:10.1186/1471-2164-13-S8-S11Published: 17 December 2012
Differential expression detection for RNA-seq experiments is often biased by normalization algorithms due to their sensitivity to parametric assumptions on the gene count distributions, extreme values of gene expression, gene length and total number of sequence reads.
To overcome limitations of current methodologies, we developed Differential Feature Index (DFI), a non-parametric method for characterizing distinctive gene features across any number of diverse RNA-seq experiments without inter-sample normalization. Validated with qRT-PCR datasets, DFI accurately detected differentially expressed genes regardless of expression levels and consistent with tissue selective expression. Accuracy of DFI was very similar to the currently accepted methods: EdgeR, DESeq and Cuffdiff.
In this study, we demonstrated that DFI can efficiently handle multiple groups of data simultaneously, and identify differential gene features for RNA-Seq experiments from different laboratories, tissue types, and cell origins, and is robust to extreme values of gene expression, size of the datasets and gene length.