Deciphering Protein Network In Systems Biology Approach
Lin, C. Y12., Lin, F.K1., Lin, C.H1., Cho, C.S1., Chen C.L1., Lo, C.Z1., Hsiung, C. A1.
1Division
of Bioinformatics and Biostatistics, National Health Research Institutes, Taiwan
2Institute
of Information Science, Academia Sinica, Taiwan
Following the completion of full genome sequences for several model
organisms, protein interaction networks of some viral, prokaryotic and
eukaryotic species have been established gradually. Many studies have
already elucidated that the functional related proteins of different species were
regulated in the similar mechanisms. Via the strategies based on evolutionary
conserved domains among living organisms, it will be possible to establish a
model to convert protein - protein interactions to domain – domain interactions
with a strict statistical evaluating mechanism. According to this model, the
novel interactions in inter-species and intra-species will be discovered with
statistically significant probabilities.
Based on the composing of Apache, PHP, MySQL, Linux, open source
software, The Helicobacter pylori and other putative protein interactions
databases will be constructed with interactive visualization and further
annotations. The interacting partners will annotate those proteins without
functional annotations. To present the enormous amount of protein interactions
in a way of protein networking maps, we provide a succinct yet comprehensive
visualization tool with detailed annotation information from Genbank, GO, and
KEGG, as well as even spatiotemporal information. The query filters of
integrated web database made by statistical estimations and biological
meanings will encourage the research community to discover the most
possible interactions for further studies and decipher the functional roles of
these proteins in the complex network.
References:
Lin, C. Y., Chen C.L., Cho, C.S., Wang L.M., Chang C. M., Chen P. Y., Lo, C.Z.,
Hsiung, C. A. 2005. hp-DPI: Helicobacter pylori Database of Protein Interactomes,
A Combined Experimental and Inferring Interactions. Bioinformatics, 21:
1288-1290.
(Advance
Access
published
on
October
28,
2004.
doi:10.1093/bioinformatics/bti101) (NSC92 – 3112 –B – 400 - 007-Y)
(http://dpi.nhri.org.tw/hp/)(SCI/ 6.701)