ATPexGen is dedicated to building a database centered on ATP-induced cell death, aiming to fill a significant gap in biomedical research. As the primary source of energy for cells, the role of ATP in regulating cell death requires further exploration. However, current databases lack the systematic and comprehensive data necessary to meet research needs. ATPexGen will integrate the latest experimental data and literature, offering a multi-dimensional information platform that advances the study of ATP's relationship with cell death, thereby facilitating drug development and progress in disease treatment. Given the high incidence of diseases related to cell death globally, the development of ATPexGen is particularly urgent and important, destined to provide robust support and reference for relevant fields.

Haolong Zhang1, Doblin Sandai1, Zhijing Song2, Wei Wang2, Zhongwen Zhang2, Rui Zhao2, Yuyao Liu3Corresponding address, Haoling Zhang1Corresponding address
1. Institute of Advanced Medicine and Dentistry, Universiti Sains Malaysia
2. Gan Su university of traditional chinese medicine
3. Bioinformatics R&D Department, Hefei GuangRe Biotechnology Co., Ltd, Hefei China

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Introduction

Graphic abstract

The ATPexGen project aims to construct a comprehensive database focused on ATP-induced cell death, concentrating on the critical role of ATP in the process of cell death. The core components of this project include data integration and standardization, mechanistic analysis, user platform development, and application promotion, all geared towards providing an efficient and thorough information platform for research in related fields. Our goal is to offer the scientific community an integrated resource that aids researchers in gaining a deeper understanding of the mechanisms underlying ATP-induced cell death, thereby promoting advancements in both basic research and clinical applications.

We aspire to establish ATPexGen as a globally recognized authoritative database for studies on ATP and cell death, which will enhance the understanding of cell death mechanisms and foster the development of therapeutic strategies for associated diseases. A key innovation of ATPexGen lies in its systematic and comprehensive approach. By consolidating diverse experimental data and literature into an integrated informational resource, and by implementing a dynamic updating mechanism, we ensure the database remains at the cutting edge and practical for users. Moreover, the platform will feature multi-dimensional data analysis and visualization capabilities, supporting customizable queries to improve user experience and enable more effective retrieval of necessary information.

To achieve these objectives, ATPexGen will actively collaborate with experts in biomedicine and drug development, driving the application of data and the translation of research findings. The ultimate aim of this research is to provide new insights for treating relevant diseases by advancing the study of ATP and cell death, thus contributing to the further development of the biomedical field. Through this project, we hope to build a bridge between scientific research, drug development, and clinical application, facilitating the progress of translational medicine.

Development and deployment

The front end of ATPexGen was developed using mainstream web development technologies, including HTML5, CSS3, and JavaScript. The web page layout utilizes Bootstrap v5 (https://getbootstrap.com/) to ensure a responsive design. The jQuery library (https://api.jquery.com/) was incorporated to extend JavaScript functionality. Interactive data tables on the web page are powered by DataTables (https://datatables.net/).
The back end of ATPexGen was built with the Python Django web framework (https://www.djangoproject.com/). Curated data are stored in an SQLite database (https://www.sqlite.org/). Gene-related data from external resources are saved in files formatted as csv, pickle, and feather. The GSEApy Python package (http://gseapy.rtfd.io/) is utilized for performing gene set enrichment analysis.
ATPexGen is deployed using the Apache HTTP server on CentOS.

Our Team

Haoling Zhang

Haoling Zhang, PHD

Institute of Advanced Medicine and Dentistry, Universiti Sains Malaysia

Email: zhanghaolingedu@163.com

Research Areas: ATP Cellotoxicity; ATP-induced cell death; ATP depletion

Main Contributions: Database Paper Writing | Project Lead
Yuyao Liu

Yuyao Liu, Postgraduate

Bioinformatics R&D Department, Hefei GuangRe Biotechnology Co., Ltd

Hefei, China

Email: ahmulyy@163.com

Research Areas: Skin Melanoma | R Package Development | R Language Web Scraping | Database Setup

Main Contributions: Database Development | Database Operation | Project Lead
Doblin Sandai

Doblin Sandai, Associate Professor

Institute of Advanced Medicine and Dentistry, Universiti Sains Malaysia

Email: doblin@usm.my

Research Areas: Molecular Medical Mycology

Main Contributions: Database Development | Database Operation | Project Lead
Zhijing Song

Zhijing Song, Professor

Gansu University of Chinese Medicine

Email: Songzhijing2020@163.com

Research Areas: Traditional Chinese Medicine Orthopedics and Traumatology

Main Contributions: Database Development
Wei Wang

Wei Wang, Associate Professor

Gansu University of Chinese Medicine

Email: wangwei@gszy.edu.cn

Research Areas: Acupuncture and Tuina

Main Contributions: Database Development
Zhongwen Zhang

Zhongwen Zhang, Associate Professor

Gansu University of Chinese Medicine

Email: zrkeyan@163.com

Research Areas: Gene Dynamics

Main Contributions: Database Operation
Rui Zhao

Rui Zhao, PHD

Gansu University of Chinese Medicine

Email: 3080691523@qq.com

Research Areas: Traditional Chinese Medicine Orthopedics and Traumatology

Main Contributions: Database Development
Haolong Zhang

Haolong Zhang, PHD

Institute of Advanced Medicine and Dentistry, Universiti Sains Malaysia

Email: zhaohaoling-student@student.usm.my

Research Areas: Bioinformatics

Main Contributions: Database Operation

Help

Introduction

ATPexGen is the world's first database dedicated to ATP-induced cell death regulators and ATP-induced cell death-disease associations. There are two secondary categories of ATP-induced cell death regulators: (1) genes and (2) substances. Gene regulators encompass drivers, suppressors, markers, and unclassified regulators. Substances span a broad range of chemical entities, including pure substances (e.g., specific ATP analogs, small molecule inhibitors) and mixtures (e.g., synthetic compounds, natural product extracts). Substance regulators include inducers and inhibitors of ATP-induced cell death. Based on this concept, ATPexGen consists of seven independently curated data sets.

Data collection and processing

Function of ATPexGen

Abbreviations

FAQ

Download

1. Is there a way to download all datasets in a batch?
Reply: Unfortunately, we cannot provide the raw data download since we don't own these data. Users could download the related data with the 'analysis' menu.

2. How to download the pictures of high resolution in ATPexGen?
ATPexGen offers vector graphics in PDF format, allowing users to download and display them with clarity. Additionally, users can freely adjust the resolution of the images according to their needs.

Acknowledgements

Thanks

We would like to express our sincere gratitude to all the researchers and contributors who have made their data openly available. The success of this study would not have been possible without the generous sharing of datasets, which has greatly facilitated our research and analysis. We are deeply appreciative of the commitment and dedication of the scientific community to open science, which fosters collaboration and accelerates scientific progress.

Author contributions

  • Haolong Zhang: Responsible for the structural design and optimization of the database. Leads the team in data integration, ensuring data consistency and integrity.
  • Doblin Sandai: Ensures the database has robust security mechanisms to protect sensitive data. Formulates and enforces project security policies, ensuring strict adherence to security standards.
  • Zhijing Song: Ensures data accuracy and reliability through data management and quality control. Establishes and executes data cleaning processes, enhancing data quality.
  • Wei Wang: Ensures projects are completed on time and delivered promptly through project management and coordination. Optimizes resource allocation and tracks progress, ensuring smooth progression at each project stage.
  • Zhongwen Zhang: Ensures database stability and functionality through testing and debugging. Conducts performance optimization, improving the database's response speed and processing capacity.
  • Rui Zhao: Enhances the database's usability through documentation and user guides. Provides user training and support, ensuring users have necessary technical assistance.
  • Yuyao Liu: Responsible for developing the user interface and improving the overall user experience of the database. Leverages expertise in data analysis and visualization to create insightful and interactive data representations.
  • Haoling Zhang: Supports the data validation process, ensuring data accuracy. Provides valuable feedback and suggestions during the development process, contributing to the continuous improvement of the database.

Funding information

  1. This research was funded in part by the Sparkle Database (Internal Grant No. GRSWSCITOP202404). More details can be found at https://grswsci.top/.

Competing Interests

We have declared that no competing interest exists.

Public Databases integrated

References

  1. Wang W, Zhang H, Sandai D, et al. ATP-induced cell death: a novel hypothesis for osteoporosis. Frontiers in cell and developmental biology, 2023, 11: 1324213.
  2. Zhang H L, Sandai D, Zhang Z W, et al. Adenosine triphosphate induced cell death: Mechanisms and implications in cancer biology and therapy. World journal of clinical oncology, 2023, 14(12): 549.
  3. Zhang H L, Doblin S, Zhang Z W, et al. Elucidating the molecular basis of ATP-induced cell death in breast cancer: Construction of a robust prognostic model. World Journal of Clinical Oncology, 2024, 15(2): 208.
  4. Zhang H, Sandai D, Zhang Z, et al. ATP-induced Cell Death Mechanism. International Journal of Biology and Life Sciences, 2023, 4(1): 15-16.
  5. Wang W, Wang X M, Zhang H L, et al. Molecular and metabolic landscape of adenosine triphosphate-induced cell death in cardiovascular disease. World Journal of Cardiology, 2024, 16(12): 689-706.
  6. Zhang Z, Zhang H, Zhang Z, et al. Identification and validation of mRNA profiles linked to ATP-induced cell death represent a novel prognostic model for breast cancer. Frontiers in Immunology, 2024, 15: 1483498.
  7. Zhang H, Zhang H, Zhao R, et al. ATP Cellotoxicity, ATP-Induced Cell Death and ATP Depletion. International Journal of Public Health and Medical Research, 2024, 1(2): 35-38.

Updates

Terms of Use

ATPexGen is a database maintained by The Sparkle Research Network, providing comprehensive expression resources and functional analysis for transcriptional regulation. The Sparkle Research Network may update the content on https://www.grswsci.top/ATPexGen/ ("Content") from time to time. The Sparkle Research Network makes no warranties or representations, express or implied, regarding any of the Content, including but not limited to its current accuracy, completeness, timeliness, adequacy, or usefulness. By using this website, you agree that The Sparkle Research Network will not be liable for any losses or damages arising from your use of or reliance on the Content, or other websites or information to which this website may be linked.

ATPexGen is freely accessible for research use in an academic setting. You may view the Content solely for your own personal reference or for research in an academic setting. All academic research use of the Content must credit ATPexGen as the source and reference these Terms of Use. Outside of scientific publications, you may not redistribute or share the Content, in part or in whole, with any third party for any purpose without the express permission of The Sparkle Research Network.

Unless you have signed a license agreement with The Sparkle Research Network, you may not use any part of the Content for any of the following purposes:

  1. Use or incorporation into a commercial product or towards the performance of a commercial service;
  2. Research use in a commercial setting;
  3. Use for patient services; or
  4. Generation of reports in a hospital or other patient care setting. You may not copy, transfer, reproduce, modify, or create derivative works of ATPexGen for any commercial purpose without the express permission of Sparkle Network. If you seek to use ATPexGen for such purposes, please request the appropriate license below:
  5. Research use in a commercial setting
  6. Use in a commercial product
  7. Use for patient services or reports in a hospital setting. Please contact us at ahmulyy@163.com.

Start preparation time 2024-11-01
Pilot run time 2024-11-20
Formal running time 2024-12-01

This study is part of the Sparkle Platform and operates as a dedicated sub-project within its ecosystem
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