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ORIO (Online Resource for Integrative Omics): a web-based platform for rapid
integration of next generation sequencing data
#MMPMID28402545
Lavender CA
; Shapiro AJ
; Burkholder AB
; Bennett BD
; Adelman K
; Fargo DC
Nucleic Acids Res
2017[Jun]; 45
(10
): 5678-5690
PMID28402545
show ga
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.
|*Transcription Initiation Site
[MESH]
|*User-Computer Interface
[MESH]
|Animals
[MESH]
|Chromatin Immunoprecipitation
[MESH]
|Data Interpretation, Statistical
[MESH]
|Enhancer Elements, Genetic
[MESH]
|Genomics/methods/*statistics & numerical data
[MESH]
|High-Throughput Nucleotide Sequencing/*statistics & numerical data
[MESH]
free
free
free
