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

Autor(es)

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

• Tipo de documento: Artigo Científico
• Fonte: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES; v. 18, n. 2 FEB 2017.
• Citações Web of Science: 13

Resumo

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)

• Processo FAPESP: 15/07925-5 - Softwares de código aberto contendo ferramentas estatísticas para análise e integração de conjuntos de dados epigenômicos produzidos em alta escala, a fim de decifrar e entender redes reguladoras de câncer
• Beneficiário: Houtan Noushmehr
• Linha de fomento: Auxílio à Pesquisa - Apoio a Jovens Pesquisadores
• Processo FAPESP: 16/01389-7 - Ferramenta de bioinformática para integrar e compreender as mudanças epigenômicas e genômicas aberrantes associadas com câncer: métodos, desenvolvimento e análise
• Beneficiário: Tiago Chedraoui Silva
• Linha de fomento: Bolsas no Brasil - Doutorado Direto