TY  - JOUR
A1  - Müller, Sören
A1  - Rycak, Lukas
A1  - Afonso-Grunz, Fabian
A1  - Winter, Peter
A1  - Zawada, Adam M.
A1  - Damrath, Ewa
A1  - Scheider, Jessica
A1  - Schmäh, Juliane
A1  - Koch, Ina
A1  - Kahl, Günter
A1  - Rotter, Björn
T1  - APADB : a database for alternative polyadenylation and microRNA regulation events
T2  - Database
N2  - Alternative polyadenylation (APA) is a widespread mechanism that contributes to the sophisticated dynamics of gene regulation. Approximately 50% of all protein-coding human genes harbor multiple polyadenylation (PA) sites; their selective and combinatorial use gives rise to transcript variants with differing length of their 3' untranslated region (3'UTR). Shortened variants escape UTR-mediated regulation by microRNAs (miRNAs), especially in cancer, where global 3'UTR shortening accelerates disease progression, dedifferentiation and proliferation. Here we present APADB, a database of vertebrate PA sites determined by 3' end sequencing, using massive analysis of complementary DNA ends. APADB provides (A)PA sites for coding and non-coding transcripts of human, mouse and chicken genes. For human and mouse, several tissue types, including different cancer specimens, are available. APADB records the loss of predicted miRNA binding sites and visualizes next-generation sequencing reads that support each PA site in a genome browser. The database tables can either be browsed according to organism and tissue or alternatively searched for a gene of interest. APADB is the largest database of APA in human, chicken and mouse. The stored information provides experimental evidence for thousands of PA sites and APA events. APADB combines 3' end sequencing data with prediction algorithms of miRNA binding sites, allowing to further improve prediction algorithms. Current databases lack correct information about 3'UTR lengths, especially for chicken, and APADB provides necessary information to close this gap. Database URL: http://tools.genxpro.net/apadb/
Y1  - 2014
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/34688
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-346887
SN  - 1758-0463
N1  - This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
VL  - 2014
IS  - bau076
SP  - 1
EP  - 11
PB  - Oxford University Press
CY  - Oxford
ER  -