EBD: an eye biomarker database

Zhang, Xueli; Kong, Lingcong; Liu, Shunming; Zhang, Xiayin; Shang, Xianwen; Zhu, Zhuoting; Huang, Yu Huei; Ma, Shuo; Jason, Ha; Kiburg, Katerina; Zheng, Chunwen; Hu, Yunyan; Liu, Cong; Wu, Guanrong; Liang, Yingying; He, Mengxia; Wang, Yan; Bai, Xiaohe; Shi, Danli; Wang, Wei; Zhang, Chi; Zhao, Ke; Yuan, Haining; Hu, Guang; Hu, Yijun; Liang, Huiying; Yu, Honghua; Zhang, Lei; He, Mingguang

doi:10.1093/bioinformatics/btad194

Cited by 3 publications

(3 citation statements)

References 18 publications

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“…tw/LiverCancerMarkerRIF/) [20]. An eye biomarker database released by us provided a standardized platform for ocular biomarkers, and a driving force for future ophthalmic precision medicine [21]. These platforms offer invaluable insights for both the research community and clinical practitioners.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, for oncology‐centric research, there is the Gastric Cancer (Biomarkers) Knowledgebase for gastric cancer ( http://biomarkers.bii.a-star.edu.sg/background/gastricCancerBiomarkersKb.php ) [ 19 ], and the Liver Cancer Biomarker Reference Into Function (LiverCancerMarkerRIF) tailored for liver cancer ( http://btm.tmu.edu.tw/LiverCancerMarkerRIF/ ) [ 20 ]. An eye biomarker database released by us provided a standardized platform for ocular biomarkers, and a driving force for future ophthalmic precision medicine [ 21 ]. These platforms offer invaluable insights for both the research community and clinical practitioners.…”

Section: Discussionmentioning

confidence: 99%

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CBD2: A functional biomarker database for colorectal cancer

Zhang,

Li,

et al. 2023

iMeta

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The rapidly evolving landscape of biomarkers for colorectal cancer (CRC) necessitates an integrative, updated repository. In response, we constructed the Colorectal Cancer Biomarker Database (CBD), which collected and displayed the curated biomedicine information for 870 CRC biomarkers in the previous study. Building on CBD, we have now developed CBD2, which includes information on 1569 newly reported biomarkers derived from different biological sources (DNA, RNA, protein, and others) and clinical applications (diagnosis, treatment, and prognosis). CBD2 also incorporates information on nonbiomarkers that have been identified as unsuitable for use as biomarkers in CRC. A key new feature of CBD2 is its network analysis function, by which users can investigate the visible and topological network between biomarkers and identify their relevant pathways. CBD2 also allows users to query a series of chemicals, drug combinations, or multiple targets, to enable multidrug, multitarget, multipathway analyses, toward facilitating the design of polypharmacological treatments for CRC. CBD2 is freely available at http://www.eyeseeworld.com/cbd.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

CBD2: A functional biomarker database for colorectal cancer

Zhang,

Li,

et al. 2023

iMeta

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“…In addition to these universal databases, specialized databases containing miRNAbased prognostic signatures are available. An example of such a database is EBD, which contains 35 miRNA-based predictive signatures [149], and miRNeye, which contains 285 predictive signatures but focuses on eye diseases in mice [150]. Information on gene expression in relation to eye diseases is also available.…”

Section: Data Governancementioning

confidence: 99%

miRNA Studies in Glaucoma: A Comprehensive Review of Current Knowledge and Future Perspectives

Dobrzycka,

Sulewska,

Biecek

et al. 2023

IJMS

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Glaucoma, a neurodegenerative disorder that leads to irreversible blindness, remains a challenge because of its complex nature. MicroRNAs (miRNAs) are crucial regulators of gene expression and are associated with glaucoma and other diseases. We aimed to review and discuss the advantages and disadvantages of miRNA-focused molecular studies in glaucoma through discussing their potential as biomarkers for early detection and diagnosis; offering insights into molecular pathways and mechanisms; and discussing their potential utility with respect to personalized medicine, their therapeutic potential, and non-invasive monitoring. Limitations, such as variability, small sample sizes, sample specificity, and limited accessibility to ocular tissues, are also addressed, underscoring the need for robust protocols and collaboration. Reproducibility and validation are crucial to establish the credibility of miRNA research findings, and the integration of bioinformatics tools for miRNA database creation is a valuable component of a comprehensive approach to investigate miRNA aberrations in patients with glaucoma. Overall, miRNA research in glaucoma has provided significant insights into the molecular mechanisms of the disease, offering potential biomarkers, diagnostic tools, and therapeutic targets. However, addressing challenges such as variability and limited tissue accessibility is essential, and further investigations and validation will contribute to a deeper understanding of the functional significance of miRNAs in glaucoma.

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BioKA: a curated and integrated biomarker knowledgebase for animals

Wang,

Lin,

et al. 2023

Nucleic Acids Research

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Biomarkers play an important role in various area such as personalized medicine, drug development, clinical care, and molecule breeding. However, existing animals’ biomarker resources predominantly focus on human diseases, leaving a significant gap in non-human animal disease understanding and breeding research. To address this limitation, we present BioKA (Biomarker Knowledgebase for Animals, https://ngdc.cncb.ac.cn/bioka), a curated and integrated knowledgebase encompassing multiple animal species, diseases/traits, and annotated resources. Currently, BioKA houses 16 296 biomarkers associated with 951 mapped diseases/traits across 31 species from 4747 references, including 11 925 gene/protein biomarkers, 1784 miRNA biomarkers, 1043 mutation biomarkers, 773 metabolic biomarkers, 357 circRNA biomarkers and 127 lncRNA biomarkers. Furthermore, BioKA integrates various annotations such as GOs, protein structures, protein–protein interaction networks, miRNA targets and so on, and constructs an interactive knowledge network of biomarkers including circRNA–miRNA–mRNA associations, lncRNA–miRNA associations and protein–protein associations, which is convenient for efficient data exploration. Moreover, BioKA provides detailed information on 308 breeds/strains of 13 species, and homologous annotations for 8784 biomarkers across 16 species, and offers three online application tools. The comprehensive knowledge provided by BioKA not only advances human disease research but also contributes to a deeper understanding of animal diseases and supports livestock breeding.

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EBD: an eye biomarker database

Cited by 3 publications

References 18 publications

CBD2: A functional biomarker database for colorectal cancer

CBD2: A functional biomarker database for colorectal cancer

miRNA Studies in Glaucoma: A Comprehensive Review of Current Knowledge and Future Perspectives

BioKA: a curated and integrated biomarker knowledgebase for animals

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