SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research

Area of Science:

• Stem cell biology
• Genomics
• Epigenetics
• Proteomics

Background:

• Stem cell differentiation involves complex, multi-level regulatory mechanisms.
• Existing databases often focus on single regulatory levels (e.g., mRNA) and limited stem cell types.
• Scattered data hinders comprehensive analysis of stem cell differentiation.

Purpose of the Study:

• To develop a unifying database, SyStemCell, integrating multi-level experimental data for stem cell research.
• To provide a centralized resource for diverse regulatory mechanisms in stem cell differentiation.
• To facilitate deeper understanding of stem cell biology through integrated data analysis.

Main Methods:

• Curated data from 285 peer-reviewed publications in PubMed.
• Included seven levels of regulation: DNA methylation/hydroxymethylation, histone modification, transcript products, microRNA regulation, protein products, phosphorylation, and transcription factor regulation.
• Compiled data for four organisms (human, mouse, rat, rhesus monkey) across various stem cell types.

Main Results:

• SyStemCell database contains 43,434 genes and 942,221 gene entries.
• Data covers multiple stem cell sources, including embryonic stem cells, neural stem cells, and induced pluripotent stem cells.
• Integrated an online analysis tool for exploring regulatory relationships.

Conclusions:

• SyStemCell is the first database to bridge multi-level experimental information in stem cell studies.
• It serves as a valuable reference resource for stem cell researchers.
• Facilitates mining potential relationships among different regulatory mechanisms.