title: Logic programming to infer complex RNA expression patterns from RNA-seq data.
abstract: To meet the increasing demand in the field, numerous long noncoding RNA (lncRNA) databases are available. Given many lncRNAs are specifically expressed in certain cell types and/or time-dependent manners, most lncRNA databases fall short of providing such profiles. We developed a strategy using logic programming to handle the complex organization of organs, their tissues and cell types as well as gender and developmental time points. To showcase this strategy, we introduce 'RenalDB' (http://renaldb.uni-frankfurt.de), a database providing expression profiles of RNAs in major organs focusing on kidney tissues and cells. RenalDB uses logic programming to describe complex anatomy, sample metadata and logical relationships defining expression, enrichment or specificity. We validated the content of RenalDB with biological experiments and functionally characterized two long intergenic noncoding RNAs: LOC440173 is important for cell growth or cell survival, whereas PAXIP1-AS1 is a regulator of cell death. We anticipate RenalDB will be used as a first step toward functional studies of lncRNAs in the kidney.
authors.affiliation: Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.|German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt am Main, Germany.|Cardiovascular Innovation Institute, University of Louisville, 302 E Muhammad Ali Blvd, Louisville, KY, U.S.A.
authors.forename: Tyler
authors.initials: T
authors.lastname: Weirick
authors.affiliation: Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.|German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt am Main, Germany.|Cardiovascular Innovation Institute, University of Louisville, 302 E Muhammad Ali Blvd, Louisville, KY, U.S.A.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Militello
authors.affiliation: Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.|German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt am Main, Germany.
authors.forename: Yuliya
authors.initials: Y
authors.lastname: Ponomareva
authors.affiliation: Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.|German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt am Main, Germany.
authors.forename: David
authors.initials: D
authors.lastname: John
authors.affiliation: Dr. Senckenberg Institute of Pathology, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.
authors.forename: Claudia
authors.initials: C
authors.lastname: Döring
authors.affiliation: Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.|German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt am Main, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Dimmeler
authors.affiliation: Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt am Main, Germany.|German Center for Cardiovascular Research, Partner side Rhein-Main, Frankfurt am Main, Germany.|Cardiovascular Innovation Institute, University of Louisville, 302 E Muhammad Ali Blvd, Louisville, KY, U.S.A.
authors.forename: Shizuka
authors.initials: S
authors.lastname: Uchida
mesh_terms: D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D057809:HEK293 Cells; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D062085:RNA, Long Noncoding; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D062085:RNA, Long Noncoding