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 @entity66 association have not been used in these two web tools. Since the comprehensive transcription factor (TF)-gene binding data, TF-gene regulation data and @entity66 data are available in @entity375 , we developed a web tool called YAGM ( @entity375 Associated Genes Miner) which constructed the transcriptional regulation association, @entity66 association and five commonly used biological associations to mine a list of associated genes of a query @entity375 gene. DESCRIPTION: In YAGM, we collected seven kinds of datasets including TF-gene binding (TFB) data, TF-gene regulation (TFR) data, @entity66 ( @entity66 ) data, @entity177 ( @entity177 ) 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 @entity375 , we constructed seven biological associations including two transcriptional regulation associations (TFB association and TFR association), @entity66 association, @entity177 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 @entity375 . Among the eight biological associations constructed in YAGM, three (TFB association, TFR association, and @entity66 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 @entity375 biologists. YAGM is available online at http://cosbi3.ee.ncku.edu.tw/yagm/.

YAGM: a web tool for mining associated genes in XXXX based on diverse biological associations.

@entity177 :: ('MESH:D051437', 'Disease') :: ['FA', 'functional annotation'] @entity375 :: ('4932', 'Species') :: ['yeast', 'Yeast'] @entity66 :: ('MESH:D004194', 'Disease') :: ['MP', 'mutant phenotype']
@entity375 :: (4932,Species) :: ['yeast']
