title: ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data.
abstract: Established and emerging next generation sequencing (NGS)-based technologies allow for genome-wide interrogation of diverse biological processes. However, accessibility of NGS data remains a problem, and few user-friendly resources exist for integrative analysis of NGS data from different sources and experimental techniques. Here, we present Online Resource for Integrative Omics (ORIO; https://orio.niehs.nih.gov/), a web-based resource with an intuitive user interface for rapid analysis and integration of NGS data. To use ORIO, the user specifies NGS data of interest along with a list of genomic coordinates. Genomic coordinates may be biologically relevant features from a variety of sources, such as ChIP-seq peaks for a given protein or transcription start sites from known gene models. ORIO first iteratively finds read coverage values at each genomic feature for each NGS dataset. Data are then integrated using clustering-based approaches, giving hierarchical relationships across NGS datasets and separating individual genomic features into groups. In focusing its analysis on read coverage, ORIO makes limited assumptions about the analyzed data; this allows the tool to be applied across data from a variety of experiments and techniques. Results from analysis are presented in dynamic displays alongside user-controlled statistical tests, supporting rapid statistical validation of observed results. We emphasize the versatility of ORIO through diverse examples, ranging from NGS data quality control to characterization of enhancer regions and integration of gene expression information. Easily accessible on a public web server, we anticipate wide use of ORIO in genome-wide investigations by life scientists.
authors.affiliation: Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Lavender
authors.affiliation: Program Operations Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Shapiro
authors.affiliation: Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
authors.forename: Adam B
authors.initials: AB
authors.lastname: Burkholder
authors.affiliation: Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Bennett
authors.affiliation: Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.|Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Adelman
authors.affiliation: Office of Scientific Computing, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
authors.forename: David C
authors.initials: DC
authors.lastname: Fargo
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation; D003627:Data Interpretation, Statistical; D004742:Enhancer Elements, Genetic; D023281:Genomics / Q000379:methods / Q000706:statistics & numerical data*; D059014:High-Throughput Nucleotide Sequencing / Q000706:statistics & numerical data*; D006657:Histones / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D020407:Internet; D051379:Mice; D017422:Sequence Analysis, DNA; D024363:Transcription Initiation Site; D014584:User-Computer Interface
chemical_list: D006657:Histones