RenalDB: A Knowledge Database for Kidney RNA Expression
Institute of Cardiovascular Regeneration, Goethe University Frankfurt

RenalDB is a tool designed to assist researchers in hypothesis-driven research of lncRNAs by allowing in silico screening of enriched/specific transcripts of humans, mice, and zebrafish with respect to nephrotic tissues and cells, developmental stages, and other metadata. For example, RenalDB could help researchers with questions such as, “Are there any RNAs (transcripts) that are expressed specifically in patients suffering from kidney diseases but not in healthy individuals?”

RenalDB also serves as an example for using logic programming to infer complex RNA expression patterns from RNA-seq data. For example, when searching for RNAs expressed in kideny, RNAs expressed in child tissues, such as the kidney cortex, but not detected in whole kidney will be returned with RNAs expressed in whole kidney samples. In RenalDB logic programming is used in two ways:

  1. To extend the functionality of the SQL query system, allowing records to be returned by logic and/or string matching.
  2. To draw heatmaps with hierarchical tree structures based on the relationships described via logic programming.