Identification of Disease-miRNA Networks Across Different Cancer Types Using SWIM
Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
Giulia Fiscon, Federica Conte, Lorenzo Farina, Marco Pellegrini, Francesco Russo, 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).
|Title of host publication||MicroRNA Target Identification : Methods and Protocols|
|Number of pages||13|
|Publication status||Published - 2019|
|Series||Methods in Molecular Biology|