Physiome II : use of PPI databases to determine the significance of decorin on cartilage degeneration

• Main Author: Chew, Grace Huizhen.
• Other Authors: Goh Kheng Lim
• Format: Final Year Project
• Language: English
• Published: 2009
• Subjects: DRNTU::Engineering::Chemical engineering::Biotechnology
• Online Access: http://hdl.handle.net/10356/16594
• Institution: Nanyang Technological University

With significant resources being allocated to the conduct of biomedical research, there exists a need for a more effective use of these available resources. This project seeks the use of databases documenting protein-protein interactions to study the impact of DCN proteoglycans with ECM proteins in cartilage degeneration. It is also hoped that a definitive link can be drawn from DCN association with its protein neighbours to cartilage degenerative diseases such as Osteoarthritis, Ehlers-Danlos Syndrome and the Marfan Syndrome. Three databases were used in this experiment for the prediction of protein interactions, they are: (i) STRING 8.0; (ii) iHOP; and (iii) HPRD. Genenames was used to provide the necessary UniProt ID that was required by STRING 8.0. An experimental methodology was designed for this project, encompassing the use of the aforementioned databases. It was found that of the top ten functional associations proposed by STRING 8.0, only eight of them were further confirmed with iHOP; and subsequently only three of them (TGFB3, COL1A2 and COL5A1) demonstrated evidence relevancy of greater than 50%. Further review only confirmed TGFB3 and COL1A2 as true interactions, providing an accuracy of 20% with the use of the databases. It was also shown that it is still not possible to definitively link the various interactions proposed to causal diseases. Evidences produced by STRING 8.0 and iHOP were not able to definitively conclude that the associations of DCN with TGFB3, COL1A2 and COL5A1 contributed to degenerative cartilage diseases.