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Genesis. 2015 Aug;53(8):547-60. doi: 10.1002/dvg.22869. Epub 2015 Jul 8.

Cross-organism analysis using InterMine.

Author information

1
Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.
2
Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
3
Department of Genetics, Stanford University, Stanford, California.
4
Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
5
ZFIN, University of Oregon, Eugene, Oregon.
6
The Jackson Laboratory, Bar Harbor, Maine.
7
Institute of Neuroscience, University of Oregon, Eugene, Oregon.
8
Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin.

Abstract

InterMine is a data integration warehouse and analysis software system developed for large and complex biological data sets. Designed for integrative analysis, it can be accessed through a user-friendly web interface. For bioinformaticians, extensive web services as well as programming interfaces for most common scripting languages support access to all features. The web interface includes a useful identifier look-up system, and both simple and sophisticated search options. Interactive results tables enable exploration, and data can be filtered, summarized, and browsed. A set of graphical analysis tools provide a rich environment for data exploration including statistical enrichment of sets of genes or other entities. InterMine databases have been developed for the major model organisms, budding yeast, nematode worm, fruit fly, zebrafish, mouse, and rat together with a newly developed human database. Here, we describe how this has facilitated interoperation and development of cross-organism analysis tools and reports. InterMine as a data exploration and analysis tool is also described. All the InterMine-based systems described in this article are resources freely available to the scientific community.

KEYWORDS:

comparative analysis; cross-organism analysis; data analysis; data integration; genomics; integrative analysis; proteomics

PMID:
26097192
PMCID:
PMC4545681
DOI:
10.1002/dvg.22869
[Indexed for MEDLINE]
Free PMC Article

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