title: Molecular interaction networks for the analysis of human disease: utility, limitations, and considerations.
abstract: High-throughput '-omics' data can be combined with large-scale molecular interaction networks, for example, protein-protein interaction networks, to provide a unique framework for the investigation of human molecular biology. Interest in these integrative '-omics' methods is growing rapidly because of their potential to understand complexity and association with disease; such approaches have a focus on associations between phenotype and "network-type." The potential of this research is enticing, yet there remain a series of important considerations. Here, we discuss interaction data selection, data quality, the relative merits of using data from large high-throughput studies versus a meta-database of smaller literature-curated studies, and possible issues of sociological or inspection bias in interaction data. Other work underway, especially international consortia to establish data formats, quality standards and address data redundancy, and the improvements these efforts are making to the field, is also evaluated. We present options for researchers intending to use large-scale molecular interaction networks as a functional context for protein or gene expression data, including microRNAs, especially in the context of human disease.
authors.affiliation: Sydney Medical School, Westmead Millennium Institute for Medical Research, The University of Sydney, Sydney, NSW, Australia; Melanoma Institute Australia, Sydney, NSW, Australia.
authors.forename: Sarah-Jane
authors.initials: SJ
authors.lastname: Schramm
authors.forename: Vivek
authors.initials: V
authors.lastname: Jayaswal
authors.forename: Apurv
authors.initials: A
authors.lastname: Goel
authors.forename: Simone S
authors.initials: SS
authors.lastname: Li
authors.forename: Yee Hwa
authors.initials: YH
authors.lastname: Yang
authors.forename: Graham J
authors.initials: GJ
authors.lastname: Mann
authors.forename: Marc R
authors.initials: MR
authors.lastname: Wilkins
mesh_terms: D057225:Data Mining; D030562:Databases, Protein / Q000592:standards; D006801:Humans; D035683:MicroRNAs / Q000235:genetics; D058977:Molecular Sequence Annotation; D009369:Neoplasms / Q000378:metabolism*; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D034622:RNA Interference
chemical_list: D035683:MicroRNAs; D020543:Proteome
keywords: Integrative omics; Interactome; Network; Protein-protein interaction; Systems biology