Yeast Protein Interactomes: The Novel Platform and Value-Added Database
Chung-Yen Lin1, Chi-Shang Cho2, Chen-Zen Lo, Chao A. Hsiung
1cylin@nhri.org.tw, National Health Research Institutes; 2vecstar@nhri.org.tw, National Health Research Institutes
We propose an interactive, fast, and easy way to use web database system as platform of Interactomes for yeast interlogs based on known protein interaction networks. In this system, we can search the protein-protein interaction in two conditions via the composing of php, Mysql, Linux. The first is key word search, and the second is specific search by entering gene number, orf, and protein id or accession number. And following the web links, more details of interested proteins will be shown. We also provide the three layers (i.e. 2, 3, 4) choice of protein-protein interaction and implement the interaction as both normal text and graphical interface. Through visualized presentation in web-based interface, it will be easy to get the whole picture of protein interactions network. The benefit of this system combines convenience (since it’s web based, you can use it worldwide if your computer is connecting internet), speed (we optimize the code and other software), and friendly user interface (The query result is implemented as graphical interaction).
Using the platform described above, we construct the S. cerevisiae (15,000 entries) and putative C. elegans protein interactions database. This database can add more annotations on novel proteins by the interacting partners, can map regulatory and metabolic pathways for analysis of gene expression, and also provide proper candidates to narrow down the scale of further high-throughput screening experiments.