在酵母菌中，各種重要的調節特徵包括DNA彎曲性、核小體的佔有率、5'UTR的長度、和轉錄因子與基因調控的證據可以拿到。但目前尚未有任何的伺服器加以使用。因此我們開發酵母菌基因分析的平台，整合了調控特徵 (DNA彎曲性、核小體佔有率、5'UTR長度、轉錄因子與基因結合與調控證據)與功能特徵 (蛋白質交互作用、生物反應路徑、GO terms、與功能群組)並可以同時分析兩群基因，使用統計測試來分析此特徵在兩群基因之間是否有顯著差異性。
與現有的伺服器相比，我們平台的分析檢驗更為全面，除此之外，我們平台根據不同的生物學特徵而選擇最適合的統計測試，以提供客觀的比較。我們希望藉由整合分析酵母菌各種特徵，提供生物學家觀察兩群基因之間的差異性，甚至進而形成新的假說。

In yeast, various important regulatory features, including promoter bendability, nucleosome occupancy, 5’UTR length, and transcription factor (TF)-gene regulatory evidence, are available but have not been used in any enrichment analysis servers. This study presents the Yeast Genes Analyzer, a web server that simultaneously analyzes various biological (regulatory/functional) features of two yeast gene sets and performs statistical tests to identify the distinct features between them. In comparison with existing enrichment analysis servers, our server tests more comprehensive regulatory features (e.g. promoter bendability, nucleosome occupancy, 5’UTR length, experiment evidence of TF binding and TF 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, our server uses various statistical tests to provide objective comparison measures. The analysis results help biologists to form new hypotheses about the underlying biological mechanisms responsible for the observed difference between two yeast gene sets.

1. Basehoar AD, Z.S., Identification and distinct regulation of yeast TATA box-containing genes. Cell, 2004: p. 116(5):699-709.
2. Gasch AP, S.P., Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO, Genomic expression programs in the response of yeast cells to environmental changes. Science's STKE, 2000: p. 11(12):4241.
3. Antonov, A.V., et al., ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data. Nucleic Acids Res, 2008. 36(Web Server issue): p. W347-51.
4. Vencio, R.Z., et al., BayGO: Bayesian analysis of ontology term enrichment in microarray data. BMC Bioinformatics, 2006. 7: p. 86.
5. Zheng, Q. and X.J. Wang, GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res, 2008. 36(Web Server issue): p. W358-63.
6. Lawless, C., et al., Upstream sequence elements direct post-transcriptional regulation of gene expression under stress conditions in yeast. BMC Genomics, 2009. 10: p. 7.
7. Tirosh, I., J. Berman, and N. Barkai, The pattern and evolution of yeast promoter bendability. Trends Genet, 2007. 23(7): p. 318-21.
8. Lin, Z., et al., The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation. BMC Genomics, 2010. 11: p. 581.
9. Wu, W.S., Different Functional Gene Clusters in Yeast have Different Spatial Distributions of the Transcription Factor Binding Sites. Bioinform Biol Insights, 2011. 5: p. 1-11.
10. Chang, D.T., et al., YPA: an integrated repository of promoter features in Saccharomyces cerevisiae. Nucleic Acids Res, 2011. 39(Database issue): p. D647-52.
11. Tirosh, I. and N. Barkai, Two strategies for gene regulation by promoter nucleosomes. Genome Res, 2008. 18(7): p. 1084-91.
12. Pachkov, M., et al., SwissRegulon: a database of genome-wide annotations of regulatory sites. Nucleic Acids Res, 2007. 35(Database issue): p. D127-31.
13. Brukner, I., et al., Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J, 1995. 14(8): p. 1812-8.
14. Kaplan, N., et al., The DNA-encoded nucleosome organization of a eukaryotic genome. Nature, 2009. 458(7236): p. 362-6.
15. Nagalakshmi, U., et al., The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 2008. 320(5881): p. 1344-9.
16. Teixeira, M.C., et al., The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res, 2006. 34(Database issue): p. D446-51.
17. Stark, C., et al., BioGRID: a general repository for interaction datasets. Nucleic Acids Res, 2006. 34(Database issue): p. D535-9.
18. Kanehisa, M. and S. Goto, KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res, 2000. 28(1): p. 27-30.
19. Spellman, P.T., et al., Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell, 1998. 9(12): p. 3273-97.
20. Carbon, S., et al., AmiGO: online access to ontology and annotation data. Bioinformatics, 2009. 25(2): p. 288-9.
21. Cherry, J.M., et al., SGD: Saccharomyces Genome Database. Nucleic Acids Res, 1998. 26(1): p. 73-9.
22. Reimand, J., et al., g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res, 2007. 35(Web Server issue): p. W193-200.
23. Al-Shahrour, F., et al., FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res, 2007. 35(Web Server issue): p. W91-6.