AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States.

ABSTRACT: As an economically important crop, apple is one of the most cultivated fruit trees in temperate regions worldwide. Recently, a large number of high-quality transcriptomic and epigenomic datasets for apple were made available to the public, which could be helpful in inferring gene regulatory relationships and thus predicting gene function at the genome level. Through integration of the available apple genomic, transcriptomic, and epigenomic datasets, we constructed co-expression networks, identified functional modules, and predicted chromatin states. A total of 112 RNA-seq datasets were integrated to construct a global network and a conditional network (tissue-preferential network). Furthermore, a total of 1,076 functional modules with closely related gene sets were identified to assess the

SUBMITTER: Da L 

PROVIDER: S-EPMC6817610 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature