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Nucleic Acids Res. 2015 Jul 1;43(W1):W98-103. doi: 10.1093/nar/gkv511. Epub 2015 May 18.

Multidimensional gene search with Genehopper.

Author information

1
Institute for Information Systems, Technische Universität Braunschweig, Braunschweig 38106, Germany.
2
Target Discovery Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, Biberach (Riss) 88397, Germany eric.simon@boehringer-ingelheim.com.

Abstract

The high abundance of genetic information enables researchers to gain new insights from the comparison of human genes according to their similarities. However, existing tools that allow the exploration of such gene-to-gene relationships, apply each similarity independently. To make use of multidimensional scoring, we developed a new search engine named Genehopper. It can handle two query types: (i) the typical use case starts with a term-to-gene search, i.e. an optimized full-text search for an anchor gene of interest. The web-interface can handle one or more terms including gene symbols and identifiers of Ensembl, UniProt, EntrezGene and RefSeq. (ii) When the anchor gene is defined, the user can explore its neighborhood by a gene-to-gene search as the weighted sum of nine normalized gene similarities based on sequence homology, protein domains, mRNA expression profiles, Gene Ontology Annotation, gene symbols and other features. Each weight can be adjusted by the user, allowing flexible customization of the gene search. All implemented similarities have a low pairwise correlation (max r(2) = 0.4) implying a low linear dependency, i.e. any change in a single weight has an effect on the ranking. Thus, we treated them as separate dimensions in the search space. Genehopper is freely available at http://genehopper.ifis.cs.tu-bs.de.

PMID:
25990726
PMCID:
PMC4489220
DOI:
10.1093/nar/gkv511
[Indexed for MEDLINE]
Free PMC Article

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