GEE: An Informatics Tool for Gene Expression Data Explore
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Objectives: Major public high-throughput functional genomic data repositories, including the Gene Expression Omnibus (GEO) and ArrayExpress have rapidly expanded. As a result, a large number of diverse high-throughput functional genomic data retrieval systems have been developed. However, high-throughput functional genomic data retrieval remains challenging. Methods: We developed Gene Expression data Explore (GEE), the first powerful, flexible web and mobile search application for searching whole-genome epigenetic data and microarray data in public databases, such as GEO and ArrayExpress. Results: GEE provides an elaborate, convenient interface of query generation competences not available via various highthroughput functional genomic data retrieval systems, including GEO, ArrayExpress, and Atlas. In particular, GEE provides a suitable query generator using eVOC, the Experimental Factor Ontology (EFO), which is well represented with a variety of high-throughput functional genomic data experimental conditions. In addition, GEE provides an experimental design query constructor (EDQC), which provides elaborate retrieval filter conditions when the user designs real experiments. Conclusions: The web version of GEE is available at http://www.snubi.org/software/gee, and its app version is available from the Apple App Store.
Abstract
Objectives: Major public high-throughput functional genomic data repositories, including the Gene Expression Omnibus (GEO) and ArrayExpress have rapidly expanded. As a result, a large number of diverse high-throughput functional genomic data retrieval systems have been developed. However, high-throughput functional genomic data retrieval remains challenging. Methods: We developed Gene Expression data Explore (GEE), the first powerful, flexible web and mobile search application for searching whole-genome epigenetic data and microarray data in public databases, such as GEO and ArrayExpress. Results: GEE provides an elaborate, convenient interface of query generation competences not available via various highthroughput functional genomic data retrieval systems, including GEO, ArrayExpress, and Atlas. In particular, GEE provides a suitable query generator using eVOC, the Experimental Factor Ontology (EFO), which is well represented with a variety of high-throughput functional genomic data experimental conditions. In addition, GEE provides an experimental design query constructor (EDQC), which provides elaborate retrieval filter conditions when the user designs real experiments. Conclusions: The web version of GEE is available at http://www.snubi.org/software/gee, and its app version is available from the Apple App Store.
참고문헌 (13)
- Barrett T, "NCBI GEO: archive for highthroughput functional genomic data", Nucleic Acids Res, 37, pp.D885~D890 (2009)
- Parkinson H, "ArrayExpress update:an archive of microarray and high-throughput sequencing-based functional genomics experiments", Nucleic Acids Res, 39, pp.D1002~D1004 (2011)
- Cheng WC, "Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database", BMC Bioinformatics, 11, pp.421~ (2010)
- Kapushesky M, "Gene Expression Atlas update:a value-added database of microarray and sequencingbased functional genomics experiments", Nucleic Acids Res, 40, pp.D1077~D1081 (2012)
- Coletti MH, "Medical subject headings used to search the biomedical literature", J Am Med Inform Assoc, 8(4), pp.317~323 (2001)
- Malone J, "Modeling sample variables with an Experimental Factor Ontology", Bioinformatics, 26(8), pp.1112~1118 (2010)
- Kelso J, "eVOC: a controlled vocabulary for unifying gene expression data", Genome Res, 13(6A), pp.1222~1230 (2003)
- Noy NF, "BioPortal: ontologies and integrated data resources at the click of a mouse", Nucleic Acids Res, 37, pp.W170~W173 (2009)
- Rayner TF, "A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGETAB", BMC Bioinformatics, 7, pp.489~ (2006)
- Lu Z, "Finding query suggestions for PubMed", AMIA Annu Symp Proc, 2009, pp.396~400 (2009)
- Ivliev AE, "Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data", Nucleic Acids Res, 36, pp.W327~W331 (2008)
- Zhu Y, "GEOmetadb:powerful alternative search engine for the Gene Expression Omnibus", Bioinformatics, 24(23), pp.2798~2800 (2008)
- Rhodes DR, "Oncomine 3.0:genes, pathways, and networks in a collection of 18,000cancer gene expression profiles", Neoplasia, 9(2), pp.166~180 (2007)