Abstract
Arsenic is a toxic metalloid. Moderate levels of arsenic exposure from drinking water can cause various human health problems such as skin lesions, circulatory disorders and cancers. Thus, arsenic toxicity is a key focus area for environmental and toxicological investigations. Many arsenic-related genes in yeast have been identified by experimental strategies such as phenotypic screening and transcriptional profiling. These identified arsenic-related genes are valuable information for studying arsenic toxicity. However, the literature about these identified arsenic-related genes is widely dispersed and cannot be easily acquired by researchers. This prompts us to develop YARG (Yeast Arsenic-Related Genes) database, which comprehensively collects 3396 arsenic-related genes in the literature. For each arsenic-related gene, the number and types of experimental evidence (phenotypic screening and/or transcriptional profiling) are provided. Users can use both search and browse modes to query arsenic-related genes in YARG. We used two case studies to show that YARG can return biologically meaningful arsenic-related information for the query gene(s). We believe that YARG is a useful resource for arsenic toxicity research. YARG is available at http://cosbi4.ee.ncku.edu.tw/YARG/.
Highlights
Arsenic (As), the 20th most abundant element on earth, is a toxic metalloid
Arr1Δ of S. cerevisiae BY4741 (MATa, his3Δ, 100 μM sodium arsenite for 2 h leu2Δ0, met15Δ0, uraΔ0). These 7 arsenic-related gene lists consist of (i) 3 lists of genes which are differentially expressed between WT and WT under arsenic exposure and (ii) 4 lists of genes which are differentially expressed between WT and the transcription factor mutants both under arsenic exposure. aA gene was considered differentially expressed if the fold-change value was greater than or equal to twofold and if the p-value was less than 0.001 or 0.01
YARG is a useful resource of arsenic research since it provides arsenic-related genes supported by transcriptional profiling or/and phenotypic screening evidence from the literature
Summary
Arsenic (As), the 20th most abundant element on earth, is a toxic metalloid. In nature, arsenic is found in two chemical forms: inorganic species [arsenite (As3+) and arsenate (As5+)] and organic species [monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA)]. Thousands of arsenic-related genes in yeast have been identified by many experimental studies using either phenotypic screening or transcriptional profiling, or both [7,8,9,10,11,12,13,14,15]. Users can search YARG by gene names and get the information about their arsenic-related correlation with collective evidence from phenotypic screening and/or transcriptional profiling. We collected 20 gene lists in nine existing studies [7,8,9,10,11,12,13,14,15] which experimentally identified arsenic-related genes by phenotypic screening (PS) or transcriptional profiling (TP).
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