PUBLICATION

Cross-Organism Analysis Using InterMine

Authors
Lyne, R., Sullivan, J., Butano, D., Contrino, S., Heimbach, J., Hu, F., Kalderimis, A., Lyne, M., Smith, R.N., Štěpán, R., Balakrishnan, R., Binkley, G., Harris, T., Karra, K., Moxon, S.A., Motenko, H., Neuhauser, S., Ruzicka, L., Cherry, M., Richardson, J., Stein, L., Westerfield, M., Worthey, E., Micklem, G.
ID
ZDB-PUB-150623-5
Date
2015
Source
Genesis (New York, N.Y. : 2000)   53(8): 547-60 (Review)
Registered Authors
Moxon, Sierra (fka Taylor), Ruzicka, Leyla, Westerfield, Monte
Keywords
Comparative analysis, Cross-organism analysis, Data analysis, Data integration, Genomics, Integrative analysis, Proteomics
MeSH Terms
  • Animals
  • Computational Biology/methods
  • Databases, Factual*
  • Databases, Genetic
  • Genomics
  • Humans
  • Internet
  • Software*
  • Systems Integration
  • User-Computer Interface
PubMed
26097192 Full text @ Genesis
Abstract
InterMine is a data integration warehouse and analysis software system developed for large and complex biological datasets. 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, summarised 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 the paper are resources freely available to the scientific community. This article is protected by copyright. All rights reserved.
Genes / Markers
Figures
Show all Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes