FerrDb


36305834	FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations. [PMID: 36305834] Nan Zhou, Xiaoqing Yuan, Qingsong Du, Zhiyu Zhang, Xiaolei Shi, Jinku Bao, Yuping Ning, Li Peng Abstract Ferroptosis is a mode of regulated cell death characterized by iron-dependent accumulation of lipid peroxidation. It is closely linked to the pathophysiological processes in many diseases. Since our publication of the first ferroptosis database in 2020 (FerrDb V1), many new findings have been published. To keep up with the rapid progress in ferroptosis research and to provide timely and high-quality data, here we present the successor, FerrDb V2. It contains 1001 ferroptosis regulators and 143 ferroptosis-disease associations manually curated from 3288 articles. Specifically, there are 621 gene regulators, of which 264 are drivers, 238 are suppressors, 9 are markers, and 110 are unclassified genes; and there are 380 substance regulators, with 201 inducers and 179 inhibitors. Compared to FerrDb V1, curated articles increase by >300%, ferroptosis regulators increase by 175%, and ferroptosis-disease associations increase by 50.5%. Circular RNA and pseudogene are novel regulators in FerrDb V2, and the percentage of non-coding RNA increases from 7.3% to 13.6%. External gene-related data were integrated, enabling thought-provoking and gene-oriented analysis in FerrDb V2. In conclusion, FerrDb V2 will help to acquire deeper insights into ferroptosis. FerrDb V2 is freely accessible at http://www.zhounan.org/ferrdb/. Nucleic Acids Res. 2023:51(D1) \| 156 Citations (from Europe PMC, 2025-03-22)
32219413	FerrDb: a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations. [PMID: 32219413] Nan Zhou, Jinku Bao Abstract Ferroptosis is a mode of regulated cell death that depends on iron. Cells die from the toxic accumulation of lipid reactive oxygen species. Ferroptosis is tightly linked to a variety of human diseases, such as cancers and degenerative diseases. The ferroptotic process is complicated and consists of a wide range of metabolites and biomolecules. Although great progress has been achieved, the mechanism of ferroptosis remains enigmatic. We have currently entered an era of extensive knowledge advancement, and thus, it is important to find ways to organize and utilize data efficiently. We have observed a high-quality knowledge base of ferroptosis research is lacking. In this study, we downloaded 784 ferroptosis articles from the PubMed database. Ferroptosis regulators and markers and associated diseases were extracted from these articles and annotated. In summary, 253 regulators (including 108 drivers, 69 suppressors, 35 inducers and 41 inhibitors), 111 markers and 95 ferroptosis-disease associations were found. We then developed FerrDb, the first manually curated database for regulators and markers of ferroptosis and ferroptosis-disease associations. The database has a user-friendly interface, and it will be updated every 6 months to offer long-term service. FerrDb is expected to help researchers acquire insights into ferroptosis. Database URL: http://www.zhounan.org/ferrdb. Database (Oxford). 2020:2020() \| 469 Citations (from Europe PMC, 2025-03-22)

FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations. [PMID: 36305834]

Nan Zhou, Xiaoqing Yuan, Qingsong Du, Zhiyu Zhang, Xiaolei Shi, Jinku Bao, Yuping Ning, Li Peng

Abstract

Ferroptosis is a mode of regulated cell death characterized by iron-dependent accumulation of lipid peroxidation. It is closely linked to the pathophysiological processes in many diseases. Since our publication of the first ferroptosis database in 2020 (FerrDb V1), many new findings have been published. To keep up with the rapid progress in ferroptosis research and to provide timely and high-quality data, here we present the successor, FerrDb V2. It contains 1001 ferroptosis regulators and 143 ferroptosis-disease associations manually curated from 3288 articles. Specifically, there are 621 gene regulators, of which 264 are drivers, 238 are suppressors, 9 are markers, and 110 are unclassified genes; and there are 380 substance regulators, with 201 inducers and 179 inhibitors. Compared to FerrDb V1, curated articles increase by >300%, ferroptosis regulators increase by 175%, and ferroptosis-disease associations increase by 50.5%. Circular RNA and pseudogene are novel regulators in FerrDb V2, and the percentage of non-coding RNA increases from 7.3% to 13.6%. External gene-related data were integrated, enabling thought-provoking and gene-oriented analysis in FerrDb V2. In conclusion, FerrDb V2 will help to acquire deeper insights into ferroptosis. FerrDb V2 is freely accessible at http://www.zhounan.org/ferrdb/.

Nucleic Acids Res. 2023:51(D1) | 156 Citations (from Europe PMC, 2025-03-22)

FerrDb: a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations. [PMID: 32219413]

Nan Zhou, Jinku Bao

Abstract

Ferroptosis is a mode of regulated cell death that depends on iron. Cells die from the toxic accumulation of lipid reactive oxygen species. Ferroptosis is tightly linked to a variety of human diseases, such as cancers and degenerative diseases. The ferroptotic process is complicated and consists of a wide range of metabolites and biomolecules. Although great progress has been achieved, the mechanism of ferroptosis remains enigmatic. We have currently entered an era of extensive knowledge advancement, and thus, it is important to find ways to organize and utilize data efficiently. We have observed a high-quality knowledge base of ferroptosis research is lacking. In this study, we downloaded 784 ferroptosis articles from the PubMed database. Ferroptosis regulators and markers and associated diseases were extracted from these articles and annotated. In summary, 253 regulators (including 108 drivers, 69 suppressors, 35 inducers and 41 inhibitors), 111 markers and 95 ferroptosis-disease associations were found. We then developed FerrDb, the first manually curated database for regulators and markers of ferroptosis and ferroptosis-disease associations. The database has a user-friendly interface, and it will be updated every 6 months to offer long-term service. FerrDb is expected to help researchers acquire insights into ferroptosis.
Database URL: http://www.zhounan.org/ferrdb.

Database (Oxford). 2020:2020() | 469 Citations (from Europe PMC, 2025-03-22)

URL:	http://www.zhounan.org/ferrdb
Full name:	A manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations
Description:	FerrDb is a database of ferroptosis regulators and markers and ferroptosis-disease associations.
Year founded:	2020
Last update:	2020-01-01
Version:	1.0
Accessibility:	Accessible
Country/Region:	China

Data type:	DNA
Data object:	NA
Database category:	Health and medicine Literature
Major species:	NA
Keywords:	ferroptosis

University/Institution:	Sichuan University
Address:	Key Laboratory of the State Ministry of Education for Bio-Resources and Ecologic Environment, College of Life Sciences, Sichuan University, 29 Wangjiang Rd, Chengdu, 610064, China
City:	Chengdu
Province/State:	Sichuan
Country/Region:	China
Contact name (PI/Team):	Jinku Bao
Contact email (PI/Helpdesk):	baojinku@scu.edu.cn

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Database Commons a catalog of worldwide biological databases