The impact of choice of reference gene annotation

OPPELT, Jan and Marek MRÁZ. The impact of choice of reference gene annotation. In CEITEC PhD Retreat II. 2017. ISBN 978-80-210-8550-3.

Basic information

• Original name: The impact of choice of reference gene annotation
• Name in Czech: Dopad výběru referenční genové anotace
• Authors: OPPELT, Jan and Marek MRÁZ.
• Edition: CEITEC PhD Retreat II, 2017.

Other information

• Original language: English
• Type of outcome: Requested lectures
• Field of Study: Genetics and molecular biology
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Organization unit: Central European Institute of Technology
• ISBN: 978-80-210-8550-3
• Keywords (in Czech): RNA-Seq, genová anotace, exprese, dopad
• Keywords in English: RNA-Seq, gene annotation, expression, impact

Abstract

Analysis of various sequencing data often relies on so called reference gene annotation. Reference gene annotation describes where the genes are located in a genome, how many there are and how they look like. It sounds simple, but as always there is a catch. Thanks to a progress in massive-parallel sequencing methods we are able to analyze not only genes themselves but also their isoforms. We can also explore differences in expression between samples in different conditions. But before we are able to examine the changes we have to determine the level of expression of each gene. Unfortunately, most of the common model organisms have multiple reference gene annotations curated by different consortia. The main difference lies in required gene evidence – some consortia strictly require experimental evidence whereas some include gene predictions. This results in difference in number of genes and associated isoforms. We analyzed human gene expression data using  different reference gene annotations and explored the impact on the expression of genes and isoforms. We have observed that choice of the annotation has a considerable impact on the expression levels as well as on the evaluation of differential expression.