Integration of pathway and protein-protein interaction(PPI) data can provide more information that could lead to new biological insights. PPIs are usually represented by a simple binary model, whereas pathways are represented by more complicated models. We developed a series of rules for transforming protein interactions from pathway to binary model, and the protein interactions from seven pathway databases, including PID, Bio Carta, Reactome, Net Path, INOH, SPIKE and KEGG, were transformed based on these rules. These pathway-derived binary protein interactions were integrated with PPIs from other five PPI databases including HPRD, Int Act, Bio GRID, MINT and DIP, to develop integrated dataset(named Path PPI). More detailed interaction type and modification information on protein interactions can be preserved in Path PPI than other existing datasets. Comparison analysis results indicate that most of the interaction overlaps values(OAB) among these pathway databases were less than 5%, and these databases must be used conjunctively. The Path PPI data was provided at http://proteomeview. hupo.org.cn/Path PPI/Path PPI.html.
利用LC-MS/MS对F.nucleatum的蛋白质表达谱进行了深入研究,共鉴定到1198个蛋白质的表达,占基因组58%的编码基因.通过在p H 6.5(癌症组织p H环境)和p H 7.5(正常组织p H环境)两种条件下F.nucleatum蛋白质表达的定量蛋白质组学分析,发现处于癌症微环境p H条件下蛋白质表达的变化明显集中于金属离子转运,硫胺素代谢,糖代谢等过程和功能.产丁酸发酵的能量代谢通路中的七个代谢酶在蛋白质组数据中找到,其中有五个在癌症p H条件下显著下调,这五个酶包含了丁酸盐代谢的整个过程,这为结直肠癌患者肠道丁酸盐含量降低提供了新的证明.此外,癌症p H条件下F.nucleatum的丁酸代谢受到抑制,造成产丁酸能力下降,可能是其促进结直肠癌发展在代谢水平上的原因之一.
