Abstract
Aim:
To study and establish a proteome reference map and regulation network of neonatal rat cardiomyocyte.
Methods:
Cultured cardiomyocytes of neonatal rats were used. All proteins expressed in the cardiomyocytes were separated and identified by two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Biological networks and pathways of the neonatal rat cardiomyocytes were analyzed using the Ingenuity Pathway Analysis (IPA) program (www.ingenuity.com). A 2-DE database was made accessible on-line by Make2ddb package on a web server.
Results:
More than 1000 proteins were separated on 2D gels, and 148 proteins were identified. The identified proteins were used for the construction of an extensible markup language-based database. Biological networks and pathways were constructed to analyze the functions associate with cardiomyocyte proteins in the database. The 2-DE database of rat cardiomyocyte proteins can be accessed at http://2d.bjmu.edu.cn.
Conclusion:
A proteome reference map and regulation network of the neonatal rat cardiomyocytes have been established, which may serve as an international platform for storage, analysis and visualization of cardiomyocyte proteomic data.
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Acknowledgements
This work was supported by grants from Major State Basic Research Development Program of China (973 Program, 2011CB503903), the National Natural Science Foundation of China (81070078 and 81030001) and Beijing Municipal Natural Science Foundation (7102158).
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Supplementary information
Supplementary Figure 1
A merge network for direct interaction functional networks of the cardiomyocyte proteins in the database. (PPT 3018 kb)
Supplementary Figure 2
Functions and canonical pathways for the direct interaction merge network. (PPT 1217 kb)
Supplementary Figure 3
The indirect interaction functional networks map of the cardiomyocyte proteins in the database. (PPT 3159 kb)
Supplementary Figure 4
Functions and canonical pathways for the indirect interaction merge network (PPT 1217 kb)
Supplementary Table 1
The top functions table for indirect interaction networks (GIF 41 kb)
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Li, Zj., Liu, N., Han, Qd. et al. Proteome reference map and regulation network of neonatal rat cardiomyocyte. Acta Pharmacol Sin 32, 1116–1127 (2011). https://doi.org/10.1038/aps.2011.86
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DOI: https://doi.org/10.1038/aps.2011.86
