GEM-TREND

GEM-TREND is a web tool that allows users to search for gene expression data from the Gene Expression Omnibus (GEO) database by comparing query gene expression patterns with those of GEO gene expression data. It utilizes a nonparametric, rank-based pattern matching approach with statistical significance calculation. GEM-TREND was tested using gene expression ratio data randomly extracted from the GEO and in-house microarray data, and it was validated for its ability to retrieve gene expression entries biologically related to a query from GEO. GEM-TREND provides a network visualization interface for further analysis and dynamic linking of genes and gene annotations to external data repositories. It is user-friendly and expected to support knowledge discovery.

Topic

Data mining;Systems biology;Gene expression

Detail

  • Operation: Query;Search

  • Software interface: Command-line user interface

  • Language: PHP;Java;R

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: Kakenhi from the Ministry of Education, Culture, Sports, Science and Technology of Japan, by Industrial Technology Research Grant Program from NEDO of Japan, Suntory Institute for Bioorganic Research and ONO PHARMACEUTICAL CO., LTD.

  • Input: -

  • Output: -

  • Contact: -

  • Collection: -

  • Maturity: -

Publications

  • GEM-TREND: a web tool for gene expression data mining toward relevant network discovery.
  • Feng C, et al. GEM-TREND: a web tool for gene expression data mining toward relevant network discovery. GEM-TREND: a web tool for gene expression data mining toward relevant network discovery. 2009; 10:411. doi: 10.1186/1471-2164-10-411
  • https://doi.org/10.1186/1471-2164-10-411
  • PMID: 19728865
  • PMC: PMC2748096

Download and documentation

    Currently not available or not maintained.

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