The impact of choice of reference gene annotation

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

Základní údaje

• Originální název: The impact of choice of reference gene annotation
• Název česky: Dopad výběru referenční genové anotace
• Autoři: OPPELT, Jan a Marek MRÁZ.
• Vydání: CEITEC PhD Retreat II, 2017.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Vyžádané přednášky
• Obor: Genetika a molekulární biologie
• Stát vydavatele: Česká republika
• Utajení: není předmětem státního či obchodního tajemství
• WWW: URL
• Organizační jednotka: Středoevropský technologický institut
• ISBN: 978-80-210-8550-3
• Klíčová slova česky: RNA-Seq, genová anotace, exprese, dopad
• Klíčová slova anglicky: RNA-Seq, gene annotation, expression, impact

Anotace

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.