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

Abstract

BackgroundInvestigating 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.DescriptionIn 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.ConclusionsIn 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/.

Bioinformatics: Basics, Development, and Future

“…Development of tools for predicting the putative protein sequences, structure, and function of proteins/genes based on DNA sequences [48][49][50][51][52][53][54][55][56][57][58], completing full genome sequences, and building web-based genome databases for many prokaryotic and eukaryotic organisms [58] has provided a great advance in the bioinformatics field. In addition, rapid genome-wide gene expression profiling and analysis opportunities [59][60][61][62], biological pathway assignment and identification, data storing, and mining and querying for large volume of biological datasets [63][64][65][66][67][68][69][70][71][72][73] have further provided unprecedented popularity of bioinformatics in the scene of world science, which has been briefly reviewed below.…”

GIW and InCoB are advancing bioinformatics in the Asia-Pacific

“…Wu et al . [20] implemented a one-stop web-based yeast-associated genes mining tool YAGM for biological associations that include TF binding, regulation, mutant phenotype, physical and genetic interactions among others.…”

An Interface for Biomedical Big Data Processing on the Tianhe-2 Supercomputer

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