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Public data and open source tools for multi-assay genomic investigation of disease.

TitlePublic data and open source tools for multi-assay genomic investigation of disease.
Publication TypeReview
Year of Publication2016
AuthorsKannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DMA, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L
Secondary TitleBrief Bioinform
Volume17
Issue4
Pagination603-15
Date Published2016 Jul
Publication LanguageENG
ISSN Number1477-4054
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.

DOI10.1093/bib/bbv080
Custom 1

http://www.ncbi.nlm.nih.gov/pubmed/26463000?dopt=Abstract

Alternate TitleBrief. Bioinformatics
Citation Key1989
PubMed ID26463000
PubMed Central IDPMC4945830
Grant ListG12 MD007599 / MD / NIMHD NIH HHS / United States
U19 AI111224 / AI / NIAID NIH HHS / United States
U24 CA180996 / CA / NCI NIH HHS / United States