ArticleBMC bioinformatics2016
GEMINI: a computationally-efficient search engine for large gene expression datasets.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- SNPnexus: a web server for functional annotation of human genome sequence variation (2020 update).Nucleic acids research · 2020Article
- Stems cells, big data and compendium-based analyses for identifying cell types, signalling pathways and gene regulatory networks.Biophysical reviews · 2019Review
- Both rare and common genetic variants contribute to autism in the Faroe Islands.NPJ genomic medicine · 2019Article
- CellAtlasSearch: a scalable search engine for single cells.Nucleic acids research · 2018Article
- Bystro: rapid online variant annotation and natural-language filtering at whole-genome scale.Genome biology · 2018Article
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3 authors.
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Abstract
backgroundLow-cost DNA sequencing allows organizations to accumulate massive amounts of genomic data and use that data to answer a diverse range of research questions. Presently, users must search for relevant genomic data using a keyword, accession number of meta-data tag. However, in this search paradigm the form of the query - a text-based string - is mismatched with the form of the target - a genomic profile.
resultsTo improve access to massive genomic data resources, we have developed a fast search engine, GEMINI, that uses a genomic profile as a query to search for similar genomic profiles. GEMINI implements a nearest-neighbor search algorithm using a vantage-point tree to store a database of n profiles and in certain circumstances achieves an [Formula: see text] expected query time in the limit. We tested GEMINI on breast and ovarian cancer gene expression data from The Cancer Genome Atlas project and show that it achieves a query time that scales as the logarithm of the number of records in practice on genomic data. In a database with 10(5) samples, GEMINI identifies the nearest neighbor in 0.05 sec compared to a brute force search time of 0.6 sec.
conclusionsGEMINI is a fast search engine that uses a query genomic profile to search for similar profiles in a very large genomic database. It enables users to identify similar profiles independent of sample label, data origin or other meta-data information.
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