BackgroundRecently, high-throughput experimental techniques have generated a large amount of protein-protein interaction (PPI) data which can construct large complex PPI networks for numerous organisms. System biology attempts to understand cellular organization and function by analyzing these PPI networks. However, most studies still focus on static PPI networks which neglect the dynamic information of PPI.ResultsThe gene expression data under different time points and conditions can reveal the dynamic information of proteins. In this study, we used an active probability-based method to distinguish the active level of proteins at different active time points. We constructed dynamic probabilistic protein networks (DPPN) to integrate dynamic information of protein into static PPI networks. Based on DPPN, we subsequently proposed a novel method to identify protein complexes, which could effectively exploit topological structure as well as dynamic information of DPPN. We used three different yeast PPI datasets and gene expression data to construct three DPPNs. When applied to three DPPNs, many well-characterized protein complexes were accurately identified by this method.ConclusionThe shift from static PPI networks to dynamic PPI networks is essential to accurately identify protein complex. This method not only can be applied to identify protein complex, but also establish a framework to integrate dynamic information into static networks for other applications, such as pathway analysis.

BackgroundAccurate determination of protein complexes has become a key task of system biology for revealing cellular organization and function. Up to now, the protein complex prediction methods are mostly focused on static protein protein interaction (PPI) networks. However, cellular systems are highly dynamic and responsive to cues from the environment. The shift from static PPI networks to dynamic PPI networks is essential to accurately predict protein complex.ResultsThe gene expression data contains crucial dynamic information of proteins and PPIs, along with high-throughput experimental PPI data, are valuable for protein complex prediction. Firstly, we exploit gene expression data to calculate the active time point and the active probability of each protein and PPI. The dynamic active information is integrated into high-throughput PPI data to construct dynamic PPI networks. Secondly, a novel method for predicting protein complexes from the dynamic PPI networks is proposed based on core-attachment structural feature. Our method can effectively exploit not only the dynamic active information but also the topology structure information based on the dynamic PPI networks.ConclusionsWe construct four dynamic PPI networks, and accurately predict many well-characterized protein complexes. The experimental results show that (i) the dynamic active information significantly improves the performance of protein complex prediction; (ii) our method can effectively make good use of both the dynamic active information and the topology structure information of dynamic PPI networks to achieve state-of-the-art protein complex prediction capabilities.

BackgroundGenetic susceptibility plays an important role in the risk of developing pain in individuals with cancer. As a complex trait, multiple genes underlie this susceptibility. We used gene network analyses to identify novel target genes associated with pain in patients newly diagnosed with squamous cell carcinoma of the head and neck (HNSCC).ResultsWe first identified 36 cancer pain-related genes (i.e., focus genes) from 36 publications based on a literature search. The Ingenuity Pathway Analysis (IPA) analysis identified additional genes that are functionally related to the 36 focus genes through pathway relationships yielding a total of 82 genes. Subsequently, 800 SNPs within the 82 IPA-selected genes on the Illumina HumanOmniExpress-12v1 platform were selected from a large-scale genotyping effort. Association analyses between the 800 candidate SNPs (covering 82 genes) and pain in a patient cohort of 1368 patients with HNSCC (206 patients with severe pain vs. 1162 with non-severe pain) showed the highest significance for MAPK1/ERK2, a gene belonging to the MAP kinase family (rs8136867, p value = 8.92 × 10−4; odds ratio [OR] = 1.33, 95 % confidence interval [CI]: 1.13–1.58). Other top genes were PIK3C2G (a member of PI3K [complex], rs10770367, p value = 1.10 × 10−3; OR = 1.46, 95 % CI: 1.16–1.82), TCRA (the alpha chain of T-cell receptor, rs6572493, p value = 2.84 × 10−3; OR = 0.70, 95 % CI: 0.55–0.88), PDGFC (platelet-derived growth factor C, rs6845322, p value = 4.88 × 10−3; OR = 1.32, 95 % CI: 1.09–1.60), and CD247 (a member of CD3, rs2995082, p value = 7.79 × 10−3; OR = 0.76, 95 % CI: 0.62–0.93).ConclusionsOur findings provide novel candidate genes and biological pathways underlying pain in cancer patients. Further study of the variations of these candidate genes could inform clinical decision making when treating cancer pain.

BackgroundThis study aimed to investigate the reliability and validity of the Chinese version of the Patient Health Questionnaire (PHQ-15) in a tertiary hospital.MethodsUsing a cross-sectional study design, the Chinese version of the PHQ-15 was administered to a total of 1329 inpatients. To examine the discriminant validity of this questionnaire, we investigated the correlation of the PHQ-15 score with sociodemographic data and the PHQ-9 and GAD-7 scale scores. Exploratory factor analysis was performed to assess the internal consistency of the PHQ-15. To evaluate the consistency of this questionnaire with item response theory (IRT), IRT analysis was performed.ResultsThe Chinese version of the PHQ-15 showed good reliability (Cronbach’s alpha = 0.83). The correlations of the PHQ-15 scores with the PHQ-9 depression scale scores (r = 0.565) and the GAD-7 anxiety scale scores (r = 0.512) were moderate; these results suggested that the PHQ-15 had discriminant validity. We identified three factors, referred to as “cardiopulmonary,” “gastrointestinal,” and “pain/neurological,” which explained 56 % of the total variance. A second-order factor analysis including these three factors produced an acceptable model. Several items (4, 8 and 11) displayed extreme floor effects. Additionally, item 4 displayed a very small variance of 0.35 and showed very small differences in its thresholds based on IRT analysis.ConclusionsThe PHQ-15 scale had good reliability and high validity to detect patients with high somatic symptom severity in a Chinese tertiary hospital. Several of the current findings were consistent with previous research on the PHQ-15 in Western countries and in China. To improve the diagnostic quality of this questionnaire, items 4, 8 and 11 can be omitted.

BackgroundIn pancreaticobiliary maljunction (PBM), the sphincter of Oddi can not control bile and pancreatic juice flow, which may lead to two-way reflux of bile and pancreatic juice, thus causing chronic inflammation, thickening, fibrosis and metaplasia of the common bile duct wall. These pathophysiological changes have been linked to disruption of the epithelium barrier in the common bile duct. We hypothesized that the expression of tight junction-associated proteins may be dysregulated in the common bile duct in PBM. In the current study, we sought to analyze the expression of tight junction-associated proteins in the common bile duct epithelium of pediatric patients with PBM.MethodsSpecimens of the common bile duct were collected from 12 pediatric patients with PBM and 10 non-PBM controls. The expression of the tight junction-associated proteins occludin and claudin-1 in the epithelium was examined by immunohistochemistry. The Image-Pro Plus v. 6.0 image analysis software was used to calculate the mean qualifying score (MQS) of imunostained sections of common bile duct epithelium. Total protein extracts of common bile duct were analyzed by Western blotting assays to examine expression of occludin, claudin-1 and myosin light chain kinase (MLCK). Spearman correlation analysis was used to analyze the relation between MLCK and occludin, MLCK and claudin-1.ResultsImmunostained sections of the common bile duct epithelium showed significantly higher MQS in pediatric patients than controls for occludin (44.11 ± 13.82 vs. 11.30 ± 9.58, P = 0.0034) and claudin-1 (63.44 ± 23.59 vs. 46.10 ± 7.84, P = 0.0384). Western blotting also showed significantly higher expression of occludin, claudin-1 and MLCK in the common bile duct of patients than of controls (P = 0.0023, 0.0015, 0.0488). Spearman correlation analysis showed that MLCK expression correlated positively with the expression of occludin (rs = 0.61538, P = 0.0032) and claudin-1 (rs = 0.7972, P = 0.0019).ConclusionsOccludin and claudin-1 are up-regulated in the common bile duct epithelium of pediatric PBM patients. MLCK may be involved in the process of up-regulation of the tight junction-associated proteins in PBM.

BackgroundFundamental researches suggest that ileum presents greater adaptive potential than the jejunum. However, few studies estimate the association between ileum and adaptive potential in human. To discover the association, we conducted this matched case-control study.MethodsA 1:2 pair-matched, case-control study was conducted from January 1, 2001 to January 1, 2015 in Intestinal Rehabilition and Transplant Center. The case group was ileum predominated (IP) group and the control group was jejunum predominated (JP) group. Demographic data, medical history and progression of each patient were collected.ResultsThere were 24 IP cases and 48 JP controls in this study. The cumulative probabilities of parenteral nutrition (PN) weaning in IP group were higher than that in JP group. The Bristol stool scale scores of IP group were lower than that of JP group at third month. The Cox proportional hazards regression model confirmed that IP had a higher odds of PN weaning (OR = 2.69; 95 % CI: 1.27, 5.70, p = 0.01) as compared with JP group. The conditional logistic regression with 1:2 matching also confirmed IP group had a higher odds (OR = 4.84; 95 % CI: 2.02, 11.56, p <0.01).ConclusionsOur results indicated that ileum presents greater adaptive potential than the jejunum in nutrition and fluid absorption. And a potential anatomic subtype of short bowel syndrome was proposed. Further research need to be conducted to more fully understand the adaptive potential of ileum besides nutrition and fluid absorption.