title: Public data and open source tools for multi-assay genomic investigation of disease.
abstract: Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.
authors.forename: Lavanya
authors.initials: L
authors.lastname: Kannan
authors.forename: Marcel
authors.initials: M
authors.lastname: Ramos
authors.forename: Angela
authors.initials: A
authors.lastname: Re
authors.forename: Nehme
authors.initials: N
authors.lastname: El-Hachem
authors.forename: Zhaleh
authors.initials: Z
authors.lastname: Safikhani
authors.forename: Deena M A
authors.initials: DM
authors.lastname: Gendoo
authors.forename: Sean
authors.initials: S
authors.lastname: Davis
authors.forename: David
authors.initials: D
authors.lastname: Gomez-Cabrero
authors.forename: Robert
authors.initials: R
authors.lastname: Castelo
authors.forename: Kasper D
authors.initials: KD
authors.lastname: Hansen
authors.forename: Vincent J
authors.initials: VJ
authors.lastname: Carey
authors.forename: Martin
authors.initials: M
authors.lastname: Morgan
authors.forename: Aedín C
authors.initials: AC
authors.lastname: Culhane
authors.forename: Benjamin
authors.initials: B
authors.lastname: Haibe-Kains
authors.forename: Levi
authors.initials: L
authors.lastname: Waldron
mesh_terms: D019295:Computational Biology; D023281:Genomics; D035683:MicroRNAs; D017422:Sequence Analysis, DNA
chemical_list: D035683:MicroRNAs
keywords: bioconductor; cancer; integrative genomics; multiple assays (multi-assays); omics; pharmacogenomics; public data