ncRDeathDB: A Comprehensive Bioinformatics Resource for Deciphering Network Organization of the ncRNA-mediated Cell Death System

Autophagy. 2015;11(10):1917-26. doi: 10.1080/15548627.2015.1089375.

Abstract

Programmed cell death (PCD) is a critical biological process involved in many important processes, and defects in PCD have been linked with numerous human diseases. In recent years, the protein architecture in different PCD subroutines has been explored, but our understanding of the global network organization of the noncoding RNA (ncRNA)-mediated cell death system is limited and ambiguous. Hence, we developed the comprehensive bioinformatics resource (ncRDeathDB, www.rna-society.org/ncrdeathdb ) to archive ncRNA-associated cell death interactions. The current version of ncRDeathDB documents a total of more than 4600 ncRNA-mediated PCD entries in 12 species. ncRDeathDB provides a user-friendly interface to query, browse and manipulate these ncRNA-associated cell death interactions. Furthermore, this resource will help to visualize and navigate current knowledge of the noncoding RNA component of cell death and autophagy, to uncover the generic organizing principles of ncRNA-associated cell death systems, and to generate valuable biological hypotheses.

Keywords: autophagy; cell death; crosstalk; database; ncRNA; network.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Apoptosis / genetics*
  • Autophagy / genetics*
  • Computational Biology*
  • Databases, Genetic*
  • Humans
  • Proteins / metabolism
  • RNA, Untranslated / genetics*
  • Signal Transduction / genetics

Substances

  • Proteins
  • RNA, Untranslated