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iPCD: A Comprehensive Data Resource of Regulatory Proteins in Programmed Cell Death
Dachao Tang1, Cheng Han1, Shaofeng Lin1
1Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
Cells
|July 9, 2022
Summary
A new database, iPCD, catalogs over a million proteins regulating programmed cell death (PCD) across eukaryotes. This resource integrates extensive annotations, aiding research into PCD mechanisms and related human diseases.
Area of Science:
- Molecular Biology
- Genomics
- Biochemistry
Background:
- Programmed cell death (PCD) is crucial in human diseases, with numerous regulatory proteins identified.
- Post-translational modifications significantly influence PCD, and proteomics advances reveal new PCD proteins.
- Existing public databases lack comprehensive integration of PCD regulatory proteins.
Purpose of the Study:
- To establish an integrated resource for curated and annotated PCD regulatory proteins.
- To develop the iPCD database, consolidating information on PCD proteins across eukaryotic species.
Main Methods:
- Summarized mainstream PCD forms and current database development.
- Manually collected experimentally identified PCD proteins from literature.
- Performed orthologous searches to identify additional PCD proteins.
- Integrated data from 102 resources for in-depth annotation in model organisms.
Main Results:
- Developed the iPCD database containing 1,091,014 regulatory proteins across 30 PCD forms and 562 species.
- Manually curated 6,493 experimentally identified PCD proteins.
- Provided comprehensive annotations for PCD proteins in eight model organisms, covering 16 aspects.
- The database has a data volume of 125 GB.
Conclusions:
- The iPCD database serves as a valuable, comprehensive resource for studying programmed cell death in eukaryotes.
- Facilitates further analysis of PCD mechanisms, protein regulation, and potential therapeutic targets.
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