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GSuite HyperBrowser: integrative analysis of dataset collections across the genome and epigenome
- Source :
- GigaScience
- Publication Year :
- 2017
- Publisher :
- Oxford University Press (OUP), 2017.
-
Abstract
- Background: Recent large-scale undertakings such as ENCODE and Roadmap Epigenomics have generated experimental data mapped to the human reference genome (as genomic tracks) representing a variety of functional elements across a large number of cell types. Despite the high potential value of these publicly available data for a broad variety of investigations, little attention has been given to the analytical methodology necessary for their widespread utilisation. Findings: We here present a first principled treatment of the analysis of collections of genomic tracks. We have developed novel computational and statistical methodology to permit comparative and confirmatory analyses across multiple and disparate data sources. We delineate a set of generic questions that are useful across a broad range of investigations and discuss the implications of choosing different statistical measures and null models. Examples include contrasting analyses across different tissues or diseases. The methodology has been implemented in a comprehensive open-source software system, the GSuite HyperBrowser. To make the functionality accessible to biologists, and to facilitate reproducible analysis, we have also developed a web-based interface providing an expertly guided and customizable way of utilizing the methodology. With this system, many novel biological questions can flexibly be posed and rapidly answered. Conclusions: Through a combination of streamlined data acquisition, interoperable representation of dataset collections, and customizable statistical analysis with guided setup and interpretation, the GSuite HyperBrowser represents a first comprehensive solution for integrative analysis of track collections across the genome and epigenome. The software is available at: https://hyperbrowser.uio.no.<br />This work was supported by the Research Council of Norway (under grant agreements 221580, 218241, and 231217/F20), by the Norwegian Cancer Society (under grant agreements 71220’PR-2006-0433 and 3485238-2013), and by the South-Eastern Norway Regional Health Authority (under grant agreement 2014041).
- Subjects :
- 0301 basic medicine
Epigenomics
statistical genomics
Computer science
Gagnasöfn
Interface (computing)
Datasets as Topic
Health Informatics
Genomics
ENCODE
computer.software_genre
Epigenesis, Genetic
03 medical and health sciences
Genamengi
Technical Note
genomics
Humans
Statistical genomics
Software system
data integration
genome analysis
Tölfræði
Whole Genome Sequencing
Genome, Human
genomic track
Genomic track
Epigenome
Genome analysis
Data science
Computer Science Applications
Galaxy
030104 developmental biology
Disparate system
Data integration
computer
Software
Reference genome
Subjects
Details
- Language :
- English
- ISSN :
- 2047217X
- Database :
- OpenAIRE
- Journal :
- GigaScience
- Accession number :
- edsair.doi.dedup.....869c75074dd5fae6117e5904942f97e1