TY  - JOUR
AU  - Tichy, Diana
AU  - Pickl, Julia Maria Anna
AU  - Benner, Axel
AU  - Sültmann, Holger
TI  - Experimental design and data analysis of Ago-RIP-Seq experiments for the identification of microRNA targets.
JO  - Briefings in bioinformatics
VL  - 19
IS  - 5
SN  - 1477-4054
CY  - Oxford [u.a.]
PB  - Oxford University Press
M1  - DKFZ-2018-02374
SP  - 918 - 929
PY  - 2018
AB  - The identification of microRNA (miRNA) target genes is crucial for understanding miRNA function. Many methods for the genome-wide miRNA target identification have been developed in recent years; however, they have several limitations including the dependence on low-confident prediction programs and artificial miRNA manipulations. Ago-RNA immunoprecipitation combined with high-throughput sequencing (Ago-RIP-Seq) is a promising alternative. However, appropriate statistical data analysis algorithms taking into account the experimental design and the inherent noise of such experiments are largely lacking.Here, we investigate the experimental design for Ago-RIP-Seq and examine biostatistical methods to identify de novo miRNA target genes. Statistical approaches considered are either based on a negative binomial model fit to the read count data or applied to transformed data using a normal distribution-based generalized linear model. We compare them by a real data simulation study using plasmode data sets and evaluate the suitability of the approaches to detect true miRNA targets by sensitivity and false discovery rates. Our results suggest that simple approaches like linear regression models on (appropriately) transformed read count data are preferable.
LB  - PUB:(DE-HGF)16
C6  - pmid:28379479
DO  - DOI:10.1093/bib/bbx032
UR  - https://inrepo02.dkfz.de/record/142144
ER  -