YGA: Identifying distinct biological features between yeast gene sets

The advance of high-throughput experimental technologies generates many gene sets with different biological meanings, where many important insights can only be extracted by identifying the biological (regulatory/functional) features that are distinct between different gene sets (e.g. essential vs. non-essential genes, TATA box-containing vs. TATA box-less genes, induced vs. repressed genes under certain biological conditions). Although many servers have been developed to identify enriched features in a gene set, most of them were designed to analyze one gene set at a time but cannot compare two gene sets. Moreover, the features used in existing servers were mainly focused on functional annotations (GO terms), pathways, transcription factor binding sites (TFBSs) and/or protein–protein interactions (PPIs). In yeast, various important regulatory features, including promoter bendability, nucleosome occupancy, 5′-UTR length, and TF–gene regulation evidence, are available but have not been used in any enrichment analysis servers. This motivates us to develop the Yeast Genes Analyzer (YGA), a web server that simultaneously analyzes various biological (regulatory/functional) features of two gene sets and performs statistical tests to identify the distinct features between them. Many well-studied gene sets such as essential, stress-response, TATA box-containing and cell cycle genes were pre-compiled in YGA for users, if they have only one gene set, to compare with. In comparison with the existing enrichment analysis servers, YGA tests more comprehensive regulatory features (e.g. promoter bendability, nucleosome occupancy, 5′-UTR length, experimental evidence of TF–gene binding and TF–gene regulation) and functional features (e.g. PPI, GO terms, pathways and functional groups of genes, including essential/non-essential genes, stress-induced/-repressed genes, TATA box-containing/-less genes, occupied/depleted proximal-nucleosome genes and cell cycle genes). Furthermore, YGA uses various statistical tests to provide objective comparison measures. The two major contributions of YGA, comprehensive features and statistical comparison, help to mine important information that cannot be obtained from other servers. The sophisticated analysis tools of YGA can identify distinct biological features between two gene sets, which help biologists to form new hypotheses about the underlying biological mechanisms responsible for the observed difference between these two gene sets. YGA can be accessed from the following web pages: http://cosbi.ee.ncku.edu.tw/yga/ and http://yga.ee.ncku.edu.tw/ . ► YGA can compare various biological features between two yeast gene sets. ► YGA includes six unique regulatory features and one unique functional feature. ► YGA provides an overall index for biological features with multiple tests. ► YGA proposes a novel procedure to compare two profiles. ► YGA can form hypotheses responsible for the observed difference between gene sets.