title: YAGM: a web tool for mining associated genes in yeast based on diverse biological associations.
abstract: BACKGROUND
  Investigating association between genes can be used in understanding the relations of genes in biological processes. STRING and GeneMANIA are two well-known web tools which can provide a list of associated genes of a query gene based on diverse biological associations such as co-expression, co-localization, co-citation and so on. However, the transcriptional regulation association and mutant phenotype association have not been used in these two web tools. Since the comprehensive transcription factor (TF)-gene binding data, TF-gene regulation data and mutant phenotype data are available in yeast, we developed a web tool called YAGM (Yeast Associated Genes Miner) which constructed the transcriptional regulation association, mutant phenotype association and five commonly used biological associations to mine a list of associated genes of a query yeast gene.
  
  
  METHODS
  In YAGM, we collected seven kinds of datasets including TF-gene binding (TFB) data, TF-gene regulation (TFR) data, mutant phenotype (MP) data, functional annotation (FA) data, physical interaction (PI) data, genetic interaction (GI) data, and literature evidence (LE) data. Then by using the hypergeometric test to calculate the association scores of all gene pairs in yeast, we constructed seven biological associations including two transcriptional regulation associations (TFB association and TFR association), MP association, FA association, PI association, GI association, and LE association. Moreover, the expression profile association from SPELL database was also included in YAGM. When using YAGM, users can input a query gene and choose any possible subsets of the eight biological associations, then a list of associated genes of the query gene will be returned based on the chosen biological associations.
  
  
  CONCLUSIONS
  In this study, we presented the YAGM which provides eight biological associations for mining associated genes of a query gene in yeast. Among the eight biological associations constructed in YAGM, three (TFB association, TFR association, and MP association) are novel ones. By comparing the query results of two well-known web tools (STRING and GeneMANIA), we found that YAGM can find out distinct associated genes of a query gene. That is, YAGM can provide alternative candidates of associated genes for biologists to do further experimental investigation. We believe that YAGM will be a useful web tool for yeast biologists. YAGM is available online at http://cosbi3.ee.ncku.edu.tw/yagm/.
authors.forename: Wei-Sheng
authors.initials: WS
authors.lastname: Wu
authors.forename: Chung-Ching
authors.initials: CC
authors.lastname: Wang
authors.forename: Meng-Jhun
authors.initials: MJ
authors.lastname: Jhou
authors.forename: Yu-Cheng
authors.initials: YC
authors.lastname: Wang
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D020407:Internet; D009154:Mutation; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014584:User-Computer Interface; D015003:Yeasts / Q000235:genetics* / Q000378:metabolism
chemical_list: D014157:Transcription Factors