title: RNA-seq analysis for detecting quantitative trait-associated genes.
abstract: Many recent RNA-seq studies were focused mainly on detecting the differentially expressed genes (DEGs) between two or more conditions. In contrast, only a few attempts have been made to detect genes associated with quantitative traits, such as obesity index and milk yield, on RNA-seq experiment with large number of biological replicates. This study illustrates the linear model application on trait associated genes (TAGs) detection in two real RNA-seq datasets: 89 replicated human obesity related data and 21 replicated Holsteins' milk production related RNA-seq data. Based on these two datasets, the performance between suggesting methods, such as ordinary regression and robust regression, and existing methods: DESeq2 and Voom, were compared. The results indicate that suggesting methods have much lower false discoveries compared to the precedent two group comparisons based approaches in our simulation study and qRT-PCR experiment. In particular, the robust regression outperforms existing DEG finding method as well as ordinary regression in terms of precision. Given the current trend in RNA-seq pricing, we expect our methods to be successfully applied in various RNA-seq studies with numerous biological replicates that handle continuous response traits.
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea 151-741, Republic of Korea.|CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul 151-919, Republic of Korea.
authors.forename: Minseok
authors.initials: M
authors.lastname: Seo
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea 151-741, Republic of Korea.|CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul 151-919, Republic of Korea.
authors.forename: Kwondo
authors.initials: K
authors.lastname: Kim
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea 151-741, Republic of Korea.|CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul 151-919, Republic of Korea.
authors.forename: Joon
authors.initials: J
authors.lastname: Yoon
authors.affiliation: Division of Animal Products R&D, National Institute of Animal Science, #1500 Kongjwipatjwi-ro, Wansan-gu, Jeonju-si, Jeollabuk-do, 55365, Republic of Korea.
authors.forename: Jin Young
authors.initials: JY
authors.lastname: Jeong
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea 151-741, Republic of Korea.|Animal Nutritional physiology Team, National Institute of Animal science, #1500 Kongjwipatjwi-ro, Wansan-gu, Jeonju-si, Jeollabuk-do, 55365, Republic of Korea.
authors.forename: Hyun-Jeong
authors.initials: HJ
authors.lastname: Lee
authors.affiliation: CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul 151-919, Republic of Korea.
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.affiliation: Interdisciplinary Program in Bioinformatics, Seoul National University, Kwan-ak St. 599, Kwan-ak Gu, Seoul, South Korea 151-741, Republic of Korea.|CHO&KIM genomics, Main Bldg. #514, SNU Research Park, Seoul National University Mt.4-2, NakSeoungDae, Gwanakgu, Seoul 151-919, Republic of Korea.|Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea.
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
mesh_terms: D000818:Animals; D002417:Cattle; D005260:Female; D006801:Humans; D016014:Linear Models; D008297:Male; D008892:Milk; D009765:Obesity / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods*; D014280:Triglycerides / Q000378:metabolism
chemical_list: D014280:Triglycerides