Identification of Disease-miRNA Networks Across Different Cancer Types Using SWIM

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  • Giulia Fiscon
  • Federica Conte
  • Lorenzo Farina
  • Marco Pellegrini
  • Russo, Francesco
  • Paola Paci

MicroRNAs (miRNAs) are small noncoding RNAs (ncRNAs) involved in several biological processes and diseases. MiRNAs regulate gene expression at the posttranscriptional level, mostly downregulating their targets by binding specific regions of transcripts through imperfect sequence complementarity. Prediction of miRNA-binding sites is challenging, and target prediction algorithms are usually based on sequence complementarity. In the last years, it has been shown that by adding miRNA and protein coding gene expression, we are able to build tissue-, cell line-, or disease-specific networks improving our understanding of complex biological scenarios. In this chapter, we present an application of a recently published software named SWIM, that allows to identify key genes in a network of interactions by defining appropriate "roles" of genes according to their local/global positioning in the overall network. Furthermore, we show how the SWIM software can be used to build miRNA-disease networks, by applying the approach to tumor data obtained from The Cancer Genome Atlas (TCGA).

Original languageEnglish
Title of host publicationMicroRNA Target Identification : Methods and Protocols
EditorsAlessandro Laganà
Number of pages13
PublisherHumana Press
Publication date2019
ISBN (Print)978-1-4939-9206-5
ISBN (Electronic)978-1-4939-9207-2
Publication statusPublished - 2019
SeriesMethods in Molecular Biology

ID: 225999122