Discovering genetic basis of diseases is an important goal and a challenging problem in bioinformatics research. Inspired by network-based global inference approach, Semi-global inference method is proposed to capture...Discovering genetic basis of diseases is an important goal and a challenging problem in bioinformatics research. Inspired by network-based global inference approach, Semi-global inference method is proposed to capture the complex associations between phenotypes and genes. The proposed method integrates phenotype similarities and protein-protein interactions, and it establishes the profile vectors of phenotypes and proteins. Then the relevance between each candidate gene and the target phenotype is evaluated. Candidate genes are then ranked according to relevance mark and genes that are potentially associated with target disease are identified based on this ranking. The model selects nodes in integrated phenotype-protein network for inference, by exploiting Phenotype Similarity Threshold (PST), which throws lights on selection of similar phenotypes for gene prediction problem. Different vector relevance metrics for computing the relevance marks of candidate genes are discussed. The performance of the model is evaluated on Online Mendelian Inheritance in Man (OMIM) data sets and experimental evaluation shows high performance of proposed Semi-global method outperforms existing global inference methods.展开更多
A major focus of systems biology is to characterize interactions between cellular compo- nents, in order to develop an accurate picture of the intricate networks within biological systems. Over the past decade, protei...A major focus of systems biology is to characterize interactions between cellular compo- nents, in order to develop an accurate picture of the intricate networks within biological systems. Over the past decade, protein microarrays have greatly contributed to advances in proteomics and are becoming an important platform for systems biology. Protein microarrays are highly flex- ible, ranging from large-scale proteome microarrays to smaller customizable microarrays, making the technology amenable for detection of a broad spectrum of biochemical properties of proteins. In this article, we will focus on the numerous studies that have utilized protein microarrays to recon- struct biological networks including protein-DNA interactions, posttranslational protein modifica- tions （PTMs）, lectin glycan recognition, pathogen-host interactions and hierarchical signaling cascades. The diversity in applications allows for integration of interaction data from numerous molecular classes and cellular states, providing insight into the structure of complex biological sys- tems. We will also discuss emerging applications and future directions of protein microarray tech- nology in the global frontier.展开更多
AIM:To understand the complex reaction of gastric inflammation induced by Helicobacter pylori(H pylori) in a systematic manner using a protein interaction network. METHODS:The expression of genes significantly changed...AIM:To understand the complex reaction of gastric inflammation induced by Helicobacter pylori(H pylori) in a systematic manner using a protein interaction network. METHODS:The expression of genes significantly changed on microarray during H pylori infection was scanned from the web literary database and translated into proteins.A network of protein interactions was constructed by searching the primary interactions of selected proteins.The constructed network was mathematically analyzed and its biological function was examined.In addition,the nodes on the network were checked to determine if they had any further functional importance or relation to other proteins by extending them. RESULTS:The scale-free network showing the relationship between inflammation and carcinogenesis was constructed.Mathematical analysis showed hub and bottleneck proteins,and these proteins were mostly related to immune response.The network contained pathways and proteins related to H pylori infection,such as the JAK-STAT pathway triggered by interleukins.Activation of nuclear factor (NF)-κB,TLR4,and other proteins known to function as core proteins of immune response were also found. These immune-related proteins interacted on the network with pathways and proteins related to the cell cycle,cell maintenance and proliferation,andtranscription regulators such as BRCA1,FOS,REL,and zinc finger proteins.The extension of nodes showed interactions of the immune proteins with cancer- related proteins.One extended network,the core network,a summarized form of the extended network, and cell pathway model were constructed. CONCLUSION:Immune-related proteins activated by H pylori infection interact with proto-oncogene proteins.The hub and bottleneck proteins are potential drug targets for gastric inflammation and cancer.展开更多
BACKGROUND Studies show that the antifibrotic mechanism of taurine may involve its inhibition of the activation and proliferation of hepatic stellate cells(HSCs). Since the molecular mechanism of taurine-mediated anti...BACKGROUND Studies show that the antifibrotic mechanism of taurine may involve its inhibition of the activation and proliferation of hepatic stellate cells(HSCs). Since the molecular mechanism of taurine-mediated antifibrotic activity has not been fully unveiled and is little studied, it is imperative to use "omics" methods to systematically investigate the molecular mechanism by which taurine inhibits liver fibrosis.AIM To establish a network including transcriptomic and protein-protein interaction data to elucidate the molecular mechanism of taurine-induced HSC apoptosis.METHODS We used microarrays, bioinformatics, protein-protein interaction(PPI) network,and sub-modules to investigate taurine-induced changes in gene expression in human HSCs(LX-2). Subsequently, all of the differentially expressed genes(DEGs) were subjected to gene ontology function and Kyoto encyclopedia of genes and genomes pathway enrichment analysis. Furthermore, the interactions of DEGs were explored in a human PPI network, and sub-modules of the DEGs interaction network were analyzed using Cytoscape software.RESULTS A total of 635 DEGs were identified in taurine-treated HSCs when compared with the controls. Of these, 304 genes were statistically significantly up-regulated, and 331 down-regulated. Most of these DEGs were mainly located on the membrane and extracellular region, and are involved in the biological processes of signal transduction, cell proliferation, positive regulation of extracellular regulated protein kinases 1(ERK1) and ERK2 cascade, extrinsic apoptotic signaling pathway and so on. Fifteen significantly enriched pathways with DEGs were identified, including mitogen-activated protein kinase(MAPK) signaling pathway, peroxisome proliferators-activated receptor signaling pathway,estrogen signaling pathway, Th1 and Th2 cell differentiation, cyclic adenosine monophosphate signaling pathway and so on. By integrating the transcriptomics and human PPI data, nine critical genes, including MMP2, MMP9, MMP21,TIMP3, KLF10, CX3CR1, TGFB1, VEGFB, and EGF, were identified in the PPI network analysis.CONCLUSION Taurine promotes the apoptosis of HSCs via up-regulating TGFB1 and then activating the p38 MAPK-JNK-Caspase9/8/3 pathway. These findings enhance the understanding of the molecular mechanism of taurine-induced HSC apoptosis and provide references for liver disorder therapy.展开更多
Smoking is the primary cause of lung cancer and is linked to 85% of lung cancer cases.However,how lung cancer develops in patients with smoking history remains unclear.Systems approaches that combine human protein-pro...Smoking is the primary cause of lung cancer and is linked to 85% of lung cancer cases.However,how lung cancer develops in patients with smoking history remains unclear.Systems approaches that combine human protein-protein interaction (PPI) networks and gene expression data are superior to traditional methods.We performed these systems to determine the role that smoking plays in lung cancer development and used the support vector machine (SVM) model to predict PPIs.By defining expression variance (EV),we found 520 dynamic proteins (EV>0.4) using data from the Human Protein Reference Database and Gene Expression Omnibus Database,and built 7 dynamic PPI subnetworks of lung cancer in patients with smoking history.We also determined the primary functions of each subnetwork:signal transduction,apoptosis,and cell migration and adhesion for subnetwork A;cell-sustained angiogenesis for subnetwork B;apoptosis for subnetwork C;and,finally,signal transduction and cell replication and proliferation for subnetworks D-G.The probability distribution of the degree of dynamic protein and static protein differed,clearly showing that the dynamic proteins were not the core proteins which widely connected with their neighbor proteins.There were high correlations among the dynamic proteins,suggesting that the dynamic proteins tend to form specific dynamic modules.We also found that the dynamic proteins were only correlated with the expression of selected proteins but not all neighbor proteins when cancer occurred.展开更多
It is a challenging task to investigate the different in- fluence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 t...It is a challenging task to investigate the different in- fluence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 three-state proteins were constructed by complex networks analysis at three length scales: Protein Contact Networks, Long-range Interaction Networks and Short-range Interaction Networks. To uncover the relationship between structural properties and folding kinetics of the proteins, the correlations of protein network parameters with protein folding rate and topology parameters contact order were analyzed. The results show that Protein Contact Networks and Short-range Interaction Networks (for both two-state and three-state proteins) exhibit the “small-world” property and Long-range Interaction networks indicate “scale-free” behavior. Our results further indicate that all Protein Contact Networks and Short- range Interaction networks are assortative type. While some of Long-range Interaction Networks are of assortative type, the others are of disassortative type. For two-state proteins, the clustering coefficients of Short-range Interaction Networks show prominent correlation with folding rate and contact order. The assortativity coefficients of Short-range Interaction Networks also show remarkable correlation with folding rate and contact order. Similar correlations exist in Protein Contact Networks of three-state proteins. For two-state proteins, the correlation between contact order and folding rate is determined by the numbers of local contacts. Short- range interactions play a key role in determining the connecting trend among amino acids and they impact the folding rate of two-state proteins directly. For three-state proteins, the folding rate is determined by short-range and long-range interactions among residues together.展开更多
In this paper, we attempt to understand complex network evolution from the underlying evolutionary relationship between biological organisms. Firstly, we construct a Pfam domain interaction network for each of the 470...In this paper, we attempt to understand complex network evolution from the underlying evolutionary relationship between biological organisms. Firstly, we construct a Pfam domain interaction network for each of the 470 completely sequenced organisms, and therefore each organism is correlated with a specific Pfam domain interaction network; secondly, we infer the evolutionary relationship of these organisms with the nearest neighbour joining method; thirdly, we use the evolutionary relationship between organisms constructed in the second step as the evolutionary course of the Pfam domain interaction network constructed in the first step. This analysis of the evolutionary course shows： （i） there is a conserved sub-network structure in network evolution; in this sub-network, nodes with lower degree prefer to maintain their connectivity invariant, and hubs tend to maintain their role as a hub is attached preferentially to new added nodes; （ii） few nodes are conserved as hubs; most of the other nodes are conserved as one with very low degree; （iii） in the course of network evolution, new nodes are added to the network either individually in most cases or as clusters with relative high clustering coefficients in a very few cases.展开更多
Background:To develop a protein-protein interaction network of Paroxysmal nocturnal hemoglobinuria(PNH)and Aplastic anemia(AA)based on genetic genes and to predict pathways underlying the molecular complexes in the ne...Background:To develop a protein-protein interaction network of Paroxysmal nocturnal hemoglobinuria(PNH)and Aplastic anemia(AA)based on genetic genes and to predict pathways underlying the molecular complexes in the network.Methods:In this research,the PNH and AA-related genes were screened through Online Mendelian Inheritance in Man(OMIM).The plugins and Cytoscape were used to search literature and build a protein-protein interaction network.Results:The protein-protein interaction network contains two molecular complexes that are five higher than the correlation integral values.The target genes of this study were obtained:CD59,STAT3,TERC,TNF,AKT1,C5AR1,EPO,IL6,IL10 and so on.We also found that many factors regulate biological behaviors:neutrophils,macrophages,vascular endothelial growth factor,immunoglobulin,interleukin,cytokine receptor,interleukin-6 receptor,tumor necrosis factor,and so on.This research provides a bioinformatics foundation for further explaining the mechanism of common development of both.Conclusion:This indicates that the PNH and AA is a complex process regulated by many cellular pathways and multiple genes.展开更多
Objective Oral squamous cell carcinoma(OSCC)is an aggressive cancer with a high mortality rate.San-Zhong-Kui-Jian-Tang(SZKJT),a Chinese herbal formula,has long been used as an adjuvant therapy in cancer clinical pract...Objective Oral squamous cell carcinoma(OSCC)is an aggressive cancer with a high mortality rate.San-Zhong-Kui-Jian-Tang(SZKJT),a Chinese herbal formula,has long been used as an adjuvant therapy in cancer clinical practice.Although its therapeutic effects and molecular mechanisms in OSCC have been previously elucidated,the potential interactions and mechanisms between the active phytochemicals and their therapeutic targets are still lacking.Methods The present study employed network pharmacology and topology approaches to establish a“herbal ingredients–active phytochemicals–target interaction”network to explore the potential therapeutic targets of SZKJT-active phytochemicals in the treatment of OSCC.The role of the target proteins in oncogenesis was assessed via GO and KEGG enrichment analyses,and their interactions with the active phytochemicals of SZKJT were calculated via molecular docking and dynamic simulations.The pharmacokinetic properties and toxicity of the active phytochemicals were also predicted.Results A total of 171 active phytochemicals of SZKJT fulfilled the bioavailability and drug-likeness screening criteria,with the flavonoids quercetin,kaempferol,and naringenin having the greatest potential.The 4 crucial targets of these active phytochemicals are PTGS2,TNF,BCL2,and CASP3,which encode cyclooxygenase-2,tumor necrosis factor(TNF),BCL-2 apoptosis regulator,and caspase-3,respectively.The interactions between phytochemicals and target proteins were predicted to be thermodynamically feasible and stable via molecular docking and dynamics simulations.Finally,the results revealed that the IL-6/JAK/STAT3 pathway and TNF signaling via NF-κB are the two prominent pathways targeted by SZKJT.Conclusion In summary,this study provides computational data for in-depth exploration of the mechanism by which SZKJT activates phytochemicals to treat OSCC.展开更多
Duplication and divergence have been widely recognized as the two domi- nant evolutionary forces in shaping biological networks, e.g., gene regulatory networks and protein-protein interaction （PPI） networks. It has ...Duplication and divergence have been widely recognized as the two domi- nant evolutionary forces in shaping biological networks, e.g., gene regulatory networks and protein-protein interaction （PPI） networks. It has been shown that the network growth models constructed on the principle of duplication and divergence can recapture the topo- logical properties of real PPI networks. However, such network models only consider the evolution processes. How to select the model parameters with the real biological experi- mental data has not been presented. Therefore, based on the real PPI network statistical data, a yeast PPI network model is constructed. The simulation results indicate that the topological characteristics of the constructed network model are well consistent with those of real PPI networks, especially on sparseness, scale-free, small-world, hierarchical modularity, and disassortativity.展开更多
Inferring causal protein signalling networks from human immune system cell data is a promising approach to unravel the underlying tissue signalling biology and dysfunction in diseased cells,which has attracted conside...Inferring causal protein signalling networks from human immune system cell data is a promising approach to unravel the underlying tissue signalling biology and dysfunction in diseased cells,which has attracted considerable attention within the bioinformatics field.Recently,Bayesian network(BN)techniques have gained significant popularity in inferring causal protein signalling networks from multiparameter single-cell data.However,current BN methods may exhibit high computational complexity and ignore interactions among protein signalling molecules from different single cells.A novel BN method is presented for learning causal protein signalling networks based on parallel discrete artificial bee colony(PDABC),named PDABC.Specifically,PDABC is a score-based BN method that utilises the parallel artificial bee colony to search for the global optimal causal protein signalling networks with the highest discrete K2 metric.The experimental results on several simulated datasets,as well as a previously published multi-parameter fluorescence-activated cell sorter dataset,indicate that PDABC surpasses the existing state-of-the-art methods in terms of performance and computational efficiency.展开更多
The advantages and disadvantages of genetic algorithm and BP algorithm are introduced. A neural network based on GA-BP algorithm is proposed and applied in the prediction of protein secondary structure, which combines...The advantages and disadvantages of genetic algorithm and BP algorithm are introduced. A neural network based on GA-BP algorithm is proposed and applied in the prediction of protein secondary structure, which combines the advantages of BP and GA. The prediction and training on the neural network are made respectively based on 4 structure classifications of protein so as to get higher rate of predication---the highest prediction rate 75.65%,the average prediction rate 65.04%.展开更多
Searching the maximum bicliques or bipartite subgraphs in a graph is a tough question. We proposed a new and efficient method, Searching Quasi-Bicliques (SQB) algorithm, to detect maximum quasi-bicliques from protein-...Searching the maximum bicliques or bipartite subgraphs in a graph is a tough question. We proposed a new and efficient method, Searching Quasi-Bicliques (SQB) algorithm, to detect maximum quasi-bicliques from protein-protein interaction network. As a Divide-and-Conquer method, SQB consists of three steps: first, it divides the protein-protein interaction network into a number of Distance-2-Subgraphs;second, by combining top-down and branch-and-bound methods, SQB seeks quasi-bicliques from every Distance-2-Subgraph;third, all the redundant results are removed. We successfully applied our method on the Saccharomyces cerevisiae dataset and obtained 2754 distinct quasi-bicliques.展开更多
A new method was described for using a recurrent neural network with bias units to predict contact maps in proteins. The main inputs to the neural network include residues pairwise, residue classification according to...A new method was described for using a recurrent neural network with bias units to predict contact maps in proteins. The main inputs to the neural network include residues pairwise, residue classification according to hydrophobicity, polar, acidic, basic and secondary structure information and residue separation between two residues. In our work, a dataset was used which was composed of 53 globulin proteins of known 3D structure. An average predictive accuracy of 0.29 was obtained. Our results demonstrate the viability of the approach for predicting contact maps.展开更多
Protein Secondary Structure Prediction (PSSP) is considered as one of the major challenging tasks in bioinformatics, so many solutions have been proposed to solve that problem via trying to achieve more accurate predi...Protein Secondary Structure Prediction (PSSP) is considered as one of the major challenging tasks in bioinformatics, so many solutions have been proposed to solve that problem via trying to achieve more accurate prediction results. The goal of this paper is to develop and implement an intelligent based system to predict secondary structure of a protein from its primary amino acid sequence by using five models of Neural Network (NN). These models are Feed Forward Neural Network (FNN), Learning Vector Quantization (LVQ), Probabilistic Neural Network (PNN), Convolutional Neural Network (CNN), and CNN Fine Tuning for PSSP. To evaluate our approaches two datasets have been used. The first one contains 114 protein samples, and the second one contains 1845 protein samples.展开更多
文摘Discovering genetic basis of diseases is an important goal and a challenging problem in bioinformatics research. Inspired by network-based global inference approach, Semi-global inference method is proposed to capture the complex associations between phenotypes and genes. The proposed method integrates phenotype similarities and protein-protein interactions, and it establishes the profile vectors of phenotypes and proteins. Then the relevance between each candidate gene and the target phenotype is evaluated. Candidate genes are then ranked according to relevance mark and genes that are potentially associated with target disease are identified based on this ranking. The model selects nodes in integrated phenotype-protein network for inference, by exploiting Phenotype Similarity Threshold (PST), which throws lights on selection of similar phenotypes for gene prediction problem. Different vector relevance metrics for computing the relevance marks of candidate genes are discussed. The performance of the model is evaluated on Online Mendelian Inheritance in Man (OMIM) data sets and experimental evaluation shows high performance of proposed Semi-global method outperforms existing global inference methods.
基金the Grants awarded to HZ (Grant No. RR020839, DK082840,RO1GM076102, CA125807, CA160036 and HG006434)an F31 NRSA Predoctoral Fellowship to IU (Grant No.5F31GM096716)
文摘A major focus of systems biology is to characterize interactions between cellular compo- nents, in order to develop an accurate picture of the intricate networks within biological systems. Over the past decade, protein microarrays have greatly contributed to advances in proteomics and are becoming an important platform for systems biology. Protein microarrays are highly flex- ible, ranging from large-scale proteome microarrays to smaller customizable microarrays, making the technology amenable for detection of a broad spectrum of biochemical properties of proteins. In this article, we will focus on the numerous studies that have utilized protein microarrays to recon- struct biological networks including protein-DNA interactions, posttranslational protein modifica- tions （PTMs）, lectin glycan recognition, pathogen-host interactions and hierarchical signaling cascades. The diversity in applications allows for integration of interaction data from numerous molecular classes and cellular states, providing insight into the structure of complex biological sys- tems. We will also discuss emerging applications and future directions of protein microarray tech- nology in the global frontier.
文摘AIM:To understand the complex reaction of gastric inflammation induced by Helicobacter pylori(H pylori) in a systematic manner using a protein interaction network. METHODS:The expression of genes significantly changed on microarray during H pylori infection was scanned from the web literary database and translated into proteins.A network of protein interactions was constructed by searching the primary interactions of selected proteins.The constructed network was mathematically analyzed and its biological function was examined.In addition,the nodes on the network were checked to determine if they had any further functional importance or relation to other proteins by extending them. RESULTS:The scale-free network showing the relationship between inflammation and carcinogenesis was constructed.Mathematical analysis showed hub and bottleneck proteins,and these proteins were mostly related to immune response.The network contained pathways and proteins related to H pylori infection,such as the JAK-STAT pathway triggered by interleukins.Activation of nuclear factor (NF)-κB,TLR4,and other proteins known to function as core proteins of immune response were also found. These immune-related proteins interacted on the network with pathways and proteins related to the cell cycle,cell maintenance and proliferation,andtranscription regulators such as BRCA1,FOS,REL,and zinc finger proteins.The extension of nodes showed interactions of the immune proteins with cancer- related proteins.One extended network,the core network,a summarized form of the extended network, and cell pathway model were constructed. CONCLUSION:Immune-related proteins activated by H pylori infection interact with proto-oncogene proteins.The hub and bottleneck proteins are potential drug targets for gastric inflammation and cancer.
基金the National Natural Science Foundation of China,No.81360595 and No.81860790Guangxi Natural Science Foundation Program,No.KJT13066+2 种基金the Bagui Scholars Foundation Program of Guangxithe Special-term Experts Foundation Program of Guangxithe Project of Guangxi Young Teacher Fundamental Ability Promotion,No.2017KY0298
文摘BACKGROUND Studies show that the antifibrotic mechanism of taurine may involve its inhibition of the activation and proliferation of hepatic stellate cells(HSCs). Since the molecular mechanism of taurine-mediated antifibrotic activity has not been fully unveiled and is little studied, it is imperative to use "omics" methods to systematically investigate the molecular mechanism by which taurine inhibits liver fibrosis.AIM To establish a network including transcriptomic and protein-protein interaction data to elucidate the molecular mechanism of taurine-induced HSC apoptosis.METHODS We used microarrays, bioinformatics, protein-protein interaction(PPI) network,and sub-modules to investigate taurine-induced changes in gene expression in human HSCs(LX-2). Subsequently, all of the differentially expressed genes(DEGs) were subjected to gene ontology function and Kyoto encyclopedia of genes and genomes pathway enrichment analysis. Furthermore, the interactions of DEGs were explored in a human PPI network, and sub-modules of the DEGs interaction network were analyzed using Cytoscape software.RESULTS A total of 635 DEGs were identified in taurine-treated HSCs when compared with the controls. Of these, 304 genes were statistically significantly up-regulated, and 331 down-regulated. Most of these DEGs were mainly located on the membrane and extracellular region, and are involved in the biological processes of signal transduction, cell proliferation, positive regulation of extracellular regulated protein kinases 1(ERK1) and ERK2 cascade, extrinsic apoptotic signaling pathway and so on. Fifteen significantly enriched pathways with DEGs were identified, including mitogen-activated protein kinase(MAPK) signaling pathway, peroxisome proliferators-activated receptor signaling pathway,estrogen signaling pathway, Th1 and Th2 cell differentiation, cyclic adenosine monophosphate signaling pathway and so on. By integrating the transcriptomics and human PPI data, nine critical genes, including MMP2, MMP9, MMP21,TIMP3, KLF10, CX3CR1, TGFB1, VEGFB, and EGF, were identified in the PPI network analysis.CONCLUSION Taurine promotes the apoptosis of HSCs via up-regulating TGFB1 and then activating the p38 MAPK-JNK-Caspase9/8/3 pathway. These findings enhance the understanding of the molecular mechanism of taurine-induced HSC apoptosis and provide references for liver disorder therapy.
基金supported by grants from the National Natural Science Foundation of China (No. 91130009)Science and Technology Planning Project of Guangdong Province of China (No. 2003A3080503)
文摘Smoking is the primary cause of lung cancer and is linked to 85% of lung cancer cases.However,how lung cancer develops in patients with smoking history remains unclear.Systems approaches that combine human protein-protein interaction (PPI) networks and gene expression data are superior to traditional methods.We performed these systems to determine the role that smoking plays in lung cancer development and used the support vector machine (SVM) model to predict PPIs.By defining expression variance (EV),we found 520 dynamic proteins (EV>0.4) using data from the Human Protein Reference Database and Gene Expression Omnibus Database,and built 7 dynamic PPI subnetworks of lung cancer in patients with smoking history.We also determined the primary functions of each subnetwork:signal transduction,apoptosis,and cell migration and adhesion for subnetwork A;cell-sustained angiogenesis for subnetwork B;apoptosis for subnetwork C;and,finally,signal transduction and cell replication and proliferation for subnetworks D-G.The probability distribution of the degree of dynamic protein and static protein differed,clearly showing that the dynamic proteins were not the core proteins which widely connected with their neighbor proteins.There were high correlations among the dynamic proteins,suggesting that the dynamic proteins tend to form specific dynamic modules.We also found that the dynamic proteins were only correlated with the expression of selected proteins but not all neighbor proteins when cancer occurred.
文摘It is a challenging task to investigate the different in- fluence of long-range and short-range interactions on two-state and three-state folding kinetics of protein. The networks of the 30 two-state proteins and 15 three-state proteins were constructed by complex networks analysis at three length scales: Protein Contact Networks, Long-range Interaction Networks and Short-range Interaction Networks. To uncover the relationship between structural properties and folding kinetics of the proteins, the correlations of protein network parameters with protein folding rate and topology parameters contact order were analyzed. The results show that Protein Contact Networks and Short-range Interaction Networks (for both two-state and three-state proteins) exhibit the “small-world” property and Long-range Interaction networks indicate “scale-free” behavior. Our results further indicate that all Protein Contact Networks and Short- range Interaction networks are assortative type. While some of Long-range Interaction Networks are of assortative type, the others are of disassortative type. For two-state proteins, the clustering coefficients of Short-range Interaction Networks show prominent correlation with folding rate and contact order. The assortativity coefficients of Short-range Interaction Networks also show remarkable correlation with folding rate and contact order. Similar correlations exist in Protein Contact Networks of three-state proteins. For two-state proteins, the correlation between contact order and folding rate is determined by the numbers of local contacts. Short- range interactions play a key role in determining the connecting trend among amino acids and they impact the folding rate of two-state proteins directly. For three-state proteins, the folding rate is determined by short-range and long-range interactions among residues together.
基金Project supported by the National Natural Science Foundation of China (Grant Nos. 70671089 and 30871521)the State Key Program of National Natural Science of China (Grant No. 10635040)
文摘In this paper, we attempt to understand complex network evolution from the underlying evolutionary relationship between biological organisms. Firstly, we construct a Pfam domain interaction network for each of the 470 completely sequenced organisms, and therefore each organism is correlated with a specific Pfam domain interaction network; secondly, we infer the evolutionary relationship of these organisms with the nearest neighbour joining method; thirdly, we use the evolutionary relationship between organisms constructed in the second step as the evolutionary course of the Pfam domain interaction network constructed in the first step. This analysis of the evolutionary course shows： （i） there is a conserved sub-network structure in network evolution; in this sub-network, nodes with lower degree prefer to maintain their connectivity invariant, and hubs tend to maintain their role as a hub is attached preferentially to new added nodes; （ii） few nodes are conserved as hubs; most of the other nodes are conserved as one with very low degree; （iii） in the course of network evolution, new nodes are added to the network either individually in most cases or as clusters with relative high clustering coefficients in a very few cases.
文摘Background:To develop a protein-protein interaction network of Paroxysmal nocturnal hemoglobinuria(PNH)and Aplastic anemia(AA)based on genetic genes and to predict pathways underlying the molecular complexes in the network.Methods:In this research,the PNH and AA-related genes were screened through Online Mendelian Inheritance in Man(OMIM).The plugins and Cytoscape were used to search literature and build a protein-protein interaction network.Results:The protein-protein interaction network contains two molecular complexes that are five higher than the correlation integral values.The target genes of this study were obtained:CD59,STAT3,TERC,TNF,AKT1,C5AR1,EPO,IL6,IL10 and so on.We also found that many factors regulate biological behaviors:neutrophils,macrophages,vascular endothelial growth factor,immunoglobulin,interleukin,cytokine receptor,interleukin-6 receptor,tumor necrosis factor,and so on.This research provides a bioinformatics foundation for further explaining the mechanism of common development of both.Conclusion:This indicates that the PNH and AA is a complex process regulated by many cellular pathways and multiple genes.
文摘Objective Oral squamous cell carcinoma(OSCC)is an aggressive cancer with a high mortality rate.San-Zhong-Kui-Jian-Tang(SZKJT),a Chinese herbal formula,has long been used as an adjuvant therapy in cancer clinical practice.Although its therapeutic effects and molecular mechanisms in OSCC have been previously elucidated,the potential interactions and mechanisms between the active phytochemicals and their therapeutic targets are still lacking.Methods The present study employed network pharmacology and topology approaches to establish a“herbal ingredients–active phytochemicals–target interaction”network to explore the potential therapeutic targets of SZKJT-active phytochemicals in the treatment of OSCC.The role of the target proteins in oncogenesis was assessed via GO and KEGG enrichment analyses,and their interactions with the active phytochemicals of SZKJT were calculated via molecular docking and dynamic simulations.The pharmacokinetic properties and toxicity of the active phytochemicals were also predicted.Results A total of 171 active phytochemicals of SZKJT fulfilled the bioavailability and drug-likeness screening criteria,with the flavonoids quercetin,kaempferol,and naringenin having the greatest potential.The 4 crucial targets of these active phytochemicals are PTGS2,TNF,BCL2,and CASP3,which encode cyclooxygenase-2,tumor necrosis factor(TNF),BCL-2 apoptosis regulator,and caspase-3,respectively.The interactions between phytochemicals and target proteins were predicted to be thermodynamically feasible and stable via molecular docking and dynamics simulations.Finally,the results revealed that the IL-6/JAK/STAT3 pathway and TNF signaling via NF-κB are the two prominent pathways targeted by SZKJT.Conclusion In summary,this study provides computational data for in-depth exploration of the mechanism by which SZKJT activates phytochemicals to treat OSCC.
基金Project supported by the National Natural Science Foundation of China(No.11172158)
文摘Duplication and divergence have been widely recognized as the two domi- nant evolutionary forces in shaping biological networks, e.g., gene regulatory networks and protein-protein interaction （PPI） networks. It has been shown that the network growth models constructed on the principle of duplication and divergence can recapture the topo- logical properties of real PPI networks. However, such network models only consider the evolution processes. How to select the model parameters with the real biological experi- mental data has not been presented. Therefore, based on the real PPI network statistical data, a yeast PPI network model is constructed. The simulation results indicate that the topological characteristics of the constructed network model are well consistent with those of real PPI networks, especially on sparseness, scale-free, small-world, hierarchical modularity, and disassortativity.
基金National Natural Science Foundation of China,Grant/Award Numbers:62106009,62276010R&D Program of Beijing Municipal Education Commission,Grant/Award Numbers:KM202210005030,KZ202210005009。
文摘Inferring causal protein signalling networks from human immune system cell data is a promising approach to unravel the underlying tissue signalling biology and dysfunction in diseased cells,which has attracted considerable attention within the bioinformatics field.Recently,Bayesian network(BN)techniques have gained significant popularity in inferring causal protein signalling networks from multiparameter single-cell data.However,current BN methods may exhibit high computational complexity and ignore interactions among protein signalling molecules from different single cells.A novel BN method is presented for learning causal protein signalling networks based on parallel discrete artificial bee colony(PDABC),named PDABC.Specifically,PDABC is a score-based BN method that utilises the parallel artificial bee colony to search for the global optimal causal protein signalling networks with the highest discrete K2 metric.The experimental results on several simulated datasets,as well as a previously published multi-parameter fluorescence-activated cell sorter dataset,indicate that PDABC surpasses the existing state-of-the-art methods in terms of performance and computational efficiency.
文摘The advantages and disadvantages of genetic algorithm and BP algorithm are introduced. A neural network based on GA-BP algorithm is proposed and applied in the prediction of protein secondary structure, which combines the advantages of BP and GA. The prediction and training on the neural network are made respectively based on 4 structure classifications of protein so as to get higher rate of predication---the highest prediction rate 75.65%,the average prediction rate 65.04%.
文摘Searching the maximum bicliques or bipartite subgraphs in a graph is a tough question. We proposed a new and efficient method, Searching Quasi-Bicliques (SQB) algorithm, to detect maximum quasi-bicliques from protein-protein interaction network. As a Divide-and-Conquer method, SQB consists of three steps: first, it divides the protein-protein interaction network into a number of Distance-2-Subgraphs;second, by combining top-down and branch-and-bound methods, SQB seeks quasi-bicliques from every Distance-2-Subgraph;third, all the redundant results are removed. We successfully applied our method on the Saccharomyces cerevisiae dataset and obtained 2754 distinct quasi-bicliques.
文摘A new method was described for using a recurrent neural network with bias units to predict contact maps in proteins. The main inputs to the neural network include residues pairwise, residue classification according to hydrophobicity, polar, acidic, basic and secondary structure information and residue separation between two residues. In our work, a dataset was used which was composed of 53 globulin proteins of known 3D structure. An average predictive accuracy of 0.29 was obtained. Our results demonstrate the viability of the approach for predicting contact maps.
文摘Protein Secondary Structure Prediction (PSSP) is considered as one of the major challenging tasks in bioinformatics, so many solutions have been proposed to solve that problem via trying to achieve more accurate prediction results. The goal of this paper is to develop and implement an intelligent based system to predict secondary structure of a protein from its primary amino acid sequence by using five models of Neural Network (NN). These models are Feed Forward Neural Network (FNN), Learning Vector Quantization (LVQ), Probabilistic Neural Network (PNN), Convolutional Neural Network (CNN), and CNN Fine Tuning for PSSP. To evaluate our approaches two datasets have been used. The first one contains 114 protein samples, and the second one contains 1845 protein samples.
