PPIM: A Protein-Protein Interaction Database for Maize.

Maize (Zea mays) is one of the most important crops worldwide. To understand the biological processes underlying various traits of the crop (e.g. yield and response to stress), a detailed protein-protein interaction (PPI) network is highly demanded. Unfortunately, there are very few such PPIs available in the literature. Therefore, in this work, we present the Protein-Protein Interaction Database for Maize (PPIM), which covers 2,762,560 interactions among 14,000 proteins. The PPIM contains not only accurately predicted PPIs but also those molecular interactions collected from the literature. The database is freely available at http://comp-sysbio.org/ppim with a user-friendly powerful interface. We believe that the PPIM resource can help biologists better understand the maize crop.

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information.

MOTIVATION: Reconstruction of gene regulatory networks (GRNs), which explicitly represent the causality of developmental or regulatory process, is of utmost interest and has become a challenging computational problem for understanding the complex regulatory mechanisms in cellular systems. However, all existing methods of inferring GRNs from gene expression profiles have their strengths and weaknesses. In particular, many properties of GRNs, such as topology sparseness and non-linear dependence, are generally in regulation mechanism but seldom are taken into account simultaneously in one computational method. RESULTS: In this work, we present a novel method for inferring GRNs from gene expression data considering the non-linear dependence and topological structure of GRNs by employing path consistency algorithm (PCA) based on conditional mutual information (CMI). In this algorithm, the conditional dependence between a pair of genes is represented by the CMI between them. With the general hypothesis of Gaussian distribution underlying gene expression data, CMI between a pair of genes is computed by a concise formula involving the covariance matrices of the related gene expression profiles. The method is validated on the benchmark GRNs from the DREAM challenge and the widely used SOS DNA repair network in Escherichia coli. The cross-validation results confirmed the effectiveness of our method (PCA-CMI), which outperforms significantly other previous methods. Besides its high accuracy, our method is able to distinguish direct (or causal) interactions from indirect associations. AVAILABILITY: All the source data and code are available at: http://csb.shu.edu.cn/subweb/grn.htm. CONTACT: lnchen@sibs.ac.cn; zpliu@sibs.ac.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A phase II clinical trial with cytotropic heterogeneous molecular lipids (CHML) for patients with hepatic malignancies.

Hepatocellular carcinoma (HCC) and other forms of metastatic liver cancer (MLC) have poor outcomes due to the limited treatment options. Surgery, radiotherapy and chemotherapy have a limited success. Thus, there is an urgent need for novel therapies for patients with advanced HCC and MLC. The response and toxicity profile of a novel biological anticancer agent, cytotropic heterogeneous molecular lipids (CHML), in 135 Asian patients with hepatic malignancies treated at five different hospitals in China from April 1998 to August 2003 is described. This trial included 97 patients with HCC and 38 with MLC. The majority of these patients had received conventional therapies and many had failed to respond or relapsed. CHML was administered by intra-arterial (i.a.) infusion with or without simultaneous intravenous (i.v.) infusion for 25 days with a rest of 2-4 weeks between each cycle. Fifty three percent of patients received two cycles, and 47% received three cycles. The complete response (CR) rates were 23% for HCC and 29% for MLC with an overall CR of 24%. The overall partial response (PR) was 53%. The patients with earlier stages and limited tumor burden had a better response, but a few patients with advanced disease also achieved PR. The patients who achieved CR or PR had a significant increase in long-term survival for up to five years. The treatment with CHML resulted in minimal toxicity and the reported adverse reactions were not higher than grade II. CHML is an effective therapy for hepatic malignancies, showing responses and increases in survival in patients in whom other therapies have failed. CHML is well tolerated and is an excellent candidate for Phase III clinical trials.

DIPOS: database of interacting proteins in Oryza sativa.

Rice is an important crop throughout the world and is the staple food for about half the world's population. For better breeding and improved production, we need to know the function of rice molecules which facilitate their function through interactions with each other. The database of interacting proteins in Oryza sativa (DIPOS) provides comprehensive information of interacting proteins in rice, where the interactions are predicted using two computational methods, i.e., interologs and domain based methods. DIPOS contains 14 614 067 pairwise interactions among 27 746 proteins, covering about 41% of the whole Oryaza sativa proteome. Furthermore, each interaction is assigned a confidence score which further enables biologists to sort out the important proteins. Biological explanations of pathways and interactions are also provided based on the database. Public access to the DIPOS is available at and .