title: SpidermiR: An R/Bioconductor Package for Integrative Analysis with miRNA Data.
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.
authors.affiliation: Institute of Molecular Bioimaging and Physiology National Research Council (IBFM-CNR), Segrate (Mi) 20090, Italy. claudia.cava@ibfm.cnr.it.
authors.forename: Claudia
authors.initials: C
authors.lastname: Cava
authors.affiliation: Interuniversity Institute of Bioinformatics in Brussels (IB)2, Brussels 1050, Belgium. antonio.colaprico@ulb.ac.be.|Machine Learning Group (MLG), Department d'Informatique, Universite libre de Bruxelles (ULB), Brussels 1050, Belgium. antonio.colaprico@ulb.ac.be.
authors.forename: Antonio
authors.initials: A
authors.lastname: Colaprico
authors.affiliation: Institute of Molecular Bioimaging and Physiology National Research Council (IBFM-CNR), Segrate (Mi) 20090, Italy. gloria.bertoli@ibfm.cnr.it.
authors.forename: Gloria
authors.initials: G
authors.lastname: Bertoli
authors.affiliation: Institute of Molecular Bioimaging and Physiology National Research Council (IBFM-CNR), Segrate (Mi) 20090, Italy. alex.graudenzi@unimib.it.
authors.forename: Alex
authors.initials: A
authors.lastname: Graudenzi
authors.affiliation: Department of Genetics Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil. tiagochst@gmail.com.
authors.forename: Tiago C
authors.initials: TC
authors.lastname: Silva
authors.affiliation: Interuniversity Institute of Bioinformatics in Brussels (IB)2, Brussels 1050, Belgium. colsen@ulb.ac.be.|Machine Learning Group (MLG), Department d'Informatique, Universite libre de Bruxelles (ULB), Brussels 1050, Belgium. colsen@ulb.ac.be.
authors.forename: Catharina
authors.initials: C
authors.lastname: Olsen
authors.affiliation: Department of Genetics Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo 14049-900, Brazil. houtana@gmail.com.|Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA. houtana@gmail.com.
authors.forename: Houtan
authors.initials: H
authors.lastname: Noushmehr
authors.affiliation: Interuniversity Institute of Bioinformatics in Brussels (IB)2, Brussels 1050, Belgium. gbonte@ulb.ac.be.|Machine Learning Group (MLG), Department d'Informatique, Universite libre de Bruxelles (ULB), Brussels 1050, Belgium. gbonte@ulb.ac.be.
authors.forename: Gianluca
authors.initials: G
authors.lastname: Bontempi
authors.affiliation: Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan 20125, Italy. mauri@disco.unimib.it.|SYSBIO Centre of Systems Biology (SYSBIO), Milan 20126, Italy. mauri@disco.unimib.it.
authors.forename: Giancarlo
authors.initials: G
authors.lastname: Mauri
authors.affiliation: Institute of Molecular Bioimaging and Physiology National Research Council (IBFM-CNR), Segrate (Mi) 20090, Italy. isabella.castiglioni@ibfm.cnr.it.
authors.forename: Isabella
authors.initials: I
authors.lastname: Castiglioni
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics; D005260:Female; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000378:metabolism*; D009363:Neoplasm Proteins / Q000378:metabolism; D011471:Prostatic Neoplasms / Q000235:genetics; D011485:Protein Binding; D012984:Software; D013223:Statistics as Topic
chemical_list: D035683:MicroRNAs; D009363:Neoplasm Proteins
keywords: gene; microRNA; network; protein