SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data

Author(s)

Cava, Claudia ; Colaprico, Antonio ; Bertoli, Gloria ; Graudenzi, Alex ; Silva, Tiago C. ; Olsen, Catharina ; Noushmehr, Houtan ; Bontempi, Gianluca ; Mauri, Giancarlo ; Castiglioni, Isabella

• Document type: Journal article
• Source: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES; v. 18, n. 2 FEB 2017.
• Web of Science Citations: 19

Abstract

Gene Regulatory Networks (GRNs) control many biological systems, but how such network coordination is shaped is still unknown. GRNs can be subdivided into basic connections that describe how the network members interact e.g., co-expression, physical interaction, co-localization, genetic influence, pathways, and shared protein domains. The important regulatory mechanisms of these networks involve miRNAs. We developed an R/Bioconductor package, namely SpidermiR, which offers an easy access to both GRNs and miRNAs to the end user, and integrates this information with differentially expressed genes obtained from The Cancer Genome Atlas. Specifically, SpidermiR allows the users to: (i) query and download GRNs and miRNAs from validated and predicted repositories; (ii) integrate miRNAs with GRNs in order to obtain miRNA-gene-gene and miRNA-protein-protein interactions, and to analyze miRNA GRNs in order to identify miRNA-gene communities; and (iii) graphically visualize the results of the analyses. These analyses can be performed through a single interface and without the need for any downloads. The full data sets are then rapidly integrated and processed locally. (AU)

• FAPESP's process: 15/07925-5 - Open source software statistical tools to aid in analyzing and integrating large cancer epigenomic datasets in order to decipher and understand regulatory networks
• Grantee: Houtan Noushmehr
• Support Opportunities: Research Grants - Young Investigators Grants
• FAPESP's process: 16/01389-7 - Bioinformatic tool to integrate and understand aberrant epigenomic and genomic changes associated with cancer: methods, development and analysis
• Grantee: Tiago Chedraoui Silva
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)