title: GoGene: gene annotation in the fast lane.
abstract: High-throughput screens such as microarrays and RNAi screens produce huge amounts of data. They typically result in hundreds of genes, which are often further explored and clustered via enriched GeneOntology terms. The strength of such analyses is that they build on high-quality manual annotations provided with the GeneOntology. However, the weakness is that annotations are restricted to process, function and location and that they do not cover all known genes in model organisms. GoGene addresses this weakness by complementing high-quality manual annotation with high-throughput text mining extracting co-occurrences of genes and ontology terms from literature. GoGene contains over 4,000,000 associations between genes and gene-related terms for 10 model organisms extracted from more than 18,000,000 PubMed entries. It does not cover only process, function and location of genes, but also biomedical categories such as diseases, compounds, techniques and mutations. By bringing it all together, GoGene provides the most recent and most complete facts about genes and can rank them according to novelty and importance. GoGene accepts keywords, gene lists, gene sequences and protein sequences as input and supports search for genes in PubMed, EntrezGene and via BLAST. Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene.
authors.affiliation: Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany. conrad.plake@biotec.tu-dresden.de
authors.forename: Conrad
authors.initials: C
authors.lastname: Plake
authors.forename: Loic
authors.initials: L
authors.lastname: Royer
authors.forename: Rainer
authors.initials: R
authors.lastname: Winnenburg
authors.forename: Jörg
authors.initials: J
authors.lastname: Hakenberg
authors.forename: Michael
authors.initials: M
authors.lastname: Schroeder
mesh_terms: D000818:Animals; D001862:Bone Resorption / Q000235:genetics; D020869:Gene Expression Profiling; D005796:Genes; D006801:Humans; D051379:Mice; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D010024:Osteoporosis / Q000235:genetics; D010190:Pancreatic Neoplasms / Q000235:genetics; D017121:Porphyria, Hepatoerythropoietic / Q000235:genetics; D039781:PubMed; D051381:Rats; D012984:Software; D018875:Vocabulary, Controlled