1. AddictGene: An integrated knowledge base for differentially expressed genes associated with addictive substance
- Author
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Kunlin Zhang, Mei Zhao, Quansheng Du, Yan Wang, Chong Li, and Leisheng Shi
- Subjects
media_common.quotation_subject ,Biophysics ,Druggability ,Addiction ,Computational biology ,Biology ,Drug abuse ,Biochemistry ,Database ,03 medical and health sciences ,0302 clinical medicine ,Structural Biology ,Gene expression ,Genetics ,medicine ,Northern blot ,Epigenetics ,Gene ,Data Article ,030304 developmental biology ,media_common ,0303 health sciences ,Substance dependence ,medicine.disease ,Computer Science Applications ,Drug dependence ,030220 oncology & carcinogenesis ,DNA methylation ,TP248.13-248.65 ,Biotechnology - Abstract
Graphical abstract AddictGene and its easy-to-use web interface was built by integrating gene expression, gene-gene interaction, gene-drug interaction and epigenetic regulatory annotation of differentially expressed genes associated with abused substances. The common pathways and genes of multiple drugs irrespective of stages of addiction was identified., Addiction, a disorder of maladaptive brain plasticity, is associated with changes in numerous gene expressions. Nowadays, high-throughput sequencing data on addictive substance-induced gene expression have become widely available. A resource for comprehensive annotation of genes that show differential expression in response to commonly abused substances is necessary. So, we developed AddictGene by integrating gene expression, gene-gene interaction, gene-drug interaction and epigenetic regulatory annotation for over 70,156 items of differentially expressed genes associated with 7 commonly abused substances, including alcohol, nicotine, cocaine, morphine, heroin, methamphetamine, and amphetamine, across three species (human, mouse, rat). We also collected 1,141 addiction-related experimentally validated genes by techniques such as RT-PCR, northern blot and in situ hybridization. The easy-to-use web interface of AddictGene (http://159.226.67.237/sun/addictgedb/) allows users to search and browse multidimensional data on DEGs of their interest: 1) detailed gene-specific information extracted from the original studies; 2) basic information about the specific gene extracted from NCBI; 3) SNP associated with substance dependence and other psychiatry disorders; 4) expression alteration of specific gene in other psychiatric disorders; 5) expression patterns of interested gene across 31 primary and 54 secondary human tissues; 6) functional annotation of interested gene; 7) epigenetic regulators involved in the alteration of specific genes, including histone modifications and DNA methylation; 8) protein–protein interaction for functional linkage with interested gene; 9) drug-gene interaction for potential druggability. AddictGene offers a valuable repository for researchers to study the molecular mechanisms underlying addiction, and might provide valuable insights into potential therapies for drug abuse and relapse.
- Published
- 2021