title: Cross-organism analysis using InterMine.
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.
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Rachel
authors.initials: R
authors.lastname: Lyne
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Julie
authors.initials: J
authors.lastname: Sullivan
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Daniela
authors.initials: D
authors.lastname: Butano
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Sergio
authors.initials: S
authors.lastname: Contrino
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Joshua
authors.initials: J
authors.lastname: Heimbach
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Fengyuan
authors.initials: F
authors.lastname: Hu
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Alex
authors.initials: A
authors.lastname: Kalderimis
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Mike
authors.initials: M
authors.lastname: Lyne
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Richard N
authors.initials: RN
authors.lastname: Smith
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Radek
authors.initials: R
authors.lastname: Štěpán
authors.affiliation: Department of Genetics, Stanford University, Stanford, California.
authors.forename: Rama
authors.initials: R
authors.lastname: Balakrishnan
authors.affiliation: Department of Genetics, Stanford University, Stanford, California.
authors.forename: Gail
authors.initials: G
authors.lastname: Binkley
authors.affiliation: Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
authors.forename: Todd
authors.initials: T
authors.lastname: Harris
authors.affiliation: Department of Genetics, Stanford University, Stanford, California.
authors.forename: Kalpana
authors.initials: K
authors.lastname: Karra
authors.affiliation: ZFIN, University of Oregon, Eugene, Oregon.
authors.forename: Sierra A T
authors.initials: SA
authors.lastname: Moxon
authors.affiliation: The Jackson Laboratory, Bar Harbor, Maine.
authors.forename: Howie
authors.initials: H
authors.lastname: Motenko
authors.affiliation: The Jackson Laboratory, Bar Harbor, Maine.
authors.forename: Steven
authors.initials: S
authors.lastname: Neuhauser
authors.affiliation: ZFIN, University of Oregon, Eugene, Oregon.
authors.forename: Leyla
authors.initials: L
authors.lastname: Ruzicka
authors.affiliation: Department of Genetics, Stanford University, Stanford, California.
authors.forename: Mike
authors.initials: M
authors.lastname: Cherry
authors.affiliation: The Jackson Laboratory, Bar Harbor, Maine.
authors.forename: Joel
authors.initials: J
authors.lastname: Richardson
authors.affiliation: Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
authors.forename: Lincoln
authors.initials: L
authors.lastname: Stein
authors.affiliation: ZFIN, University of Oregon, Eugene, Oregon.|Institute of Neuroscience, University of Oregon, Eugene, Oregon.
authors.forename: Monte
authors.initials: M
authors.lastname: Westerfield
authors.affiliation: Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, Wisconsin.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Worthey
authors.affiliation: Cambridge Systems Biology Centre, University of Cambridge, Cambridge, United Kingdom.|Department of Genetics, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Gos
authors.initials: G
authors.lastname: Micklem
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D016208:Databases, Factual; D030541:Databases, Genetic; D023281:Genomics; D006801:Humans; D020407:Internet; D012984:Software; D018511:Systems Integration; D014584:User-Computer Interface
keywords: comparative analysis; cross-organism analysis; data analysis; data integration; genomics; integrative analysis; proteomics