YSGM: an integrative repository of diverse biological features for mining similar genes in yeast

  • 王 鐘慶

Student thesis: Master's Thesis


Investigating gene similarity can be used in understanding the relations of genes in biological processes Determining similar genes by calculating the similarity between them can substantially improve knowledge of biological behavior Moreover interpret biological processes participated by similar genes and in turn predicts similar mechanisms in other species Previous related studies of similar genes have primarily concentrated on the association of biological function in cross species However few studies have thoroughly investigated the resemblance between genes which exist in the same species such as yeast Although several databases and web tools exist they have not collected adequate databases about yeast or considered various conditions of yeast mechanisms Therefore we developed a web tool YSGM (Yeast Similar Genes Miner) that intends to fully represent similarity between yeast genes and exploited more distinctive data to explore yeast similar genes Here we have integrated various databases which involve protein-protein interaction genetic interaction transcription factor(TF)-gene binding pairs TF-gene regulatory pairs expression profiles mutant phenotypes functional description and literature evidence And then we have used hypergeometric test to calculate the score of gene similarity in seven biological data including protein-protein interactions genetic interactions TF-gene binding pairs TF-gene regulatory pairs mutant phenotypes functional descriptions and evidences from the literature and retrieved and scaled the correlation score from the result of Hibbs et al who identified similar gene expression profiles between yeast genes and developed serial pattern of expression levels locator(SPELL) as the similarity score of expression profiles of yeast Subsequently we combined these similarity scores as the similarity score Through giving a yeast gene of interest choosing specific gene similarity features and measuring yeast gene similarity YSGM can extract similar yeast genes for specified yeast genes under different gene similarity features In this study we presented the YSGM database that provides unique biological information for searching similar yeast genes Furthermore investigating yeast similarity with YSGM can obtain correct and complete prediction of similar genes of yeast because the biological information in YSGM including many aspects of biological behavior and evidence such as TF-gene binding TF-gene regulatory and mutant phenotypes for querying similar yeast genes are more distinctive than other database We believe that the diversity of biological information accumulated in YSGM will drastically enhance the usefulness of data for yeast biologists to study similarity between yeast genes
Date of Award2014 Jul 16
Original languageEnglish
SupervisorWei-Sheng Wu (Supervisor)

Cite this