ILDGDB: a manually curated database of genomics, transcriptomics, proteomics and drug information for interstitial lung
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ILDGDB: a manually curated database of genomics, transcriptomics, proteomics and drug information for interstitial lung diseases Yupeng Li1†, Gangao Wu2†, Yu Shang3†, Yue Qi2, Xue Wang1, Shangwei Ning2* and Hong Chen1*
Abstract Background: Interstitial lung diseases (ILDs), a diverse group of diffuse lung diseases, mainly affect the lung parenchyma. The low-throughput ‘omics’ technologies (genomics, transcriptomics, proteomics) and relative drug information have begun to reshaped our understanding of ILDs, whereas, these data are scattered among massive references and are difficult to be fully exploited. Therefore, we manually mined and summarized these data at a database (ILDGDB, http://ildgdb.org/) and will continue to update it in the future. Main body: The current version of ILDGDB incorporates 2018 entries representing 20 ILDs and over 600 genes obtained from over 3000 articles in four species. Each entry contains detailed information, including species, disease type, detailed description of gene (e.g. official symbol of gene), and the original reference etc. ILDGDB is free, and provides a user-friendly web page. Users can easily search for genes of interest, view their expression pattern and detailed information, manage genes sets and submit novel ILDs-gene association. Conclusion: The main principle behind ILDGDB’s design is to provide an exploratory platform, with minimum filtering and interpretation, while making the presentation of the data very accessible, which will provide great help for researchers to decipher gene mechanisms and improve the prevention, diagnosis and therapy of ILDs. Keywords: Interstitial lung disease, Gene, ILDGDB, Drug
Background Interstitial lung diseases (ILDs), a diverse group of diffuse lung diseases, mainly affect the lung parenchyma, some of which are characterized by high disabilities and mortality. For instance, idiopathic pulmonary fibrosis (IPF), a common ILD of unknown etiology with repeated acute lung injury, causes gradually progressive lung * Correspondence: [email protected]; [email protected] † Yupeng Li, Gangao Wu and Yu Shang contributed equally to this work. 2 College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China 1 Department of Respiratory and Critical Care Medicine, the Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China Full list of author information is available at the end of the article
fibrosis leading to rapidly deteriorated lung function, with mortality of 50% of patients 3–5 years after diagnosis [1–3]. Other ILDs, such as pulmonary sarcoidosis [4, 5], pneumoconiosis [6, 7], connective tissue diseaseassociated interstitial lung disease (CTD-ILD) [8] and so on also require more healthcare utilization. The pathophysiological mechanism of ILDs is remarkably complex, therefore, it is the primary challenge to discover the precise molecular mechanisms according to genomics, transcriptomics, proteomics etc. Through the past decades, rapid advances in g
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