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Duhuo-Jisheng-Tang is a Chinese herbal formula designed to treat rheumatoid arthritis (RA) with syndrome dual deficiency of liver and kidney. Although its therapeutic clinical effect is widely accepted over one thousand years, its therapeutic agents are still obscure. In this study, we explored the potential therapeutic agents of Duhuo-Jisheng-Tang for RA by integrating leading knowledge databases...
A network motif is defined as an over-represented subgraph pattern in a network and has been widely applied in analyses of biological networks. The detection of network motifs involves the computationally expensive enumeration of subgraphs, NP-complete graph isomorphism testing, and significance testing through the generation of many random graphs to determine the statistical uniqueness of a given...
With tandem mass spectrometry (MS/MS), spectra can be generated by various methods including collision-induced dissociation (CID), higher-energy collisional dissociation (HCD), electron capture dissociation (ECD) and electron transfer dissociation (ETD). At the same time, de novo sequencing using multiple spectra from the same peptide is becoming popular in proteomics studies. The focus of this work...
Lactobacillus delbrueckii has been widely used in combination with Streptococcus thermophilus for yogurt fermentation. It has genes encoding both D- and L-type lactate dehydrogenase (LDH) that catalyze the production of L (+) or D (−) stereoisomer of lactic acid, respectively. D-lactic acid is the primary lactate product by L. delbrueckii, yet it cannot be metabolized by human intestine. Since L....
Essential proteins are crucial to cellular survival and development. Traditionally, essential proteins are identified by knock-out experiments, which are expensive and often fatal to the target organisms. Regarding this, an important approach to essential protein identification is through computational prediction. In this research, we present a novel computational method, Integrated Edge Weights (IEW),...
PROSITE provides rich documentation entries describing protein domains, families and functional sites, associated patterns as well as generalized profiles to identify them. Generalized profiles in PROSITE are often used to detect distantly related proteins by doing sequence comparison. The developments of the PROSITE have increased the discriminatory power of generalized profiles. However in practice,...
Fang-Feng-Tang is a Chinese herbal formula which is designed to treat syndrome Feng-Han-Shi-Bi for rheumatoid arthritis (RA). Although its therapeutic effects are widely accepted, its mechanism is still obscure. In this study, by integrating leading knowledge databases of associated different domains, we explored Fang-Feng-Tang's potential therapeutic agents for RA through targeted pathway hierarchies...
Da-Fang-Feng-Tang is a Chinese herbal formula designed to treat syndrome Feng-Han-Shi-Bi for rheumatoid arthritis (RA). Although it's clinical effect have been accepted through 1000 years' clinical practises, its molecule mechanism is still obscure. In this study, by integrating powerful knowledge databases, though bioinformatics analysis, we explored the potential molecular mechanism of Da-Fang-Feng-Tang...
Tinnitus is the most common medical symptom that can be debilitating. Chinese herbal medicines (CHMs) play important roles in tinnitus treatment. This study analyzed the most frequently prescribed herbs used to treat tinnitus and the molecular mechanisms of therapeutic effects of these CHMs by text mining and bioinformatics technique. Results showed that pinellia ternate (Banxia) and gastrodin (Tianma)...
The Gene Ontology (GO) is used to achieve information about gene and protein functions by using a structured vocabulary of terms (GO Terms). GO Terms are related to biological concepts such as proteins or genes through the annotation process. There exist many different annotation processes identified by different evidence codes (EC). Annotated data are stored in public databases such as the Gene Ontology...
Protein-protein interaction (PPI) networks are crucial for organisms. Many research efforts have thus been devoted to the study on the topological properties PPI networks. However, existing studies did not always report consistent results on the topological properties of PPI networks. This situation is primarily caused by the incompleteness of current PPI datasets. To solve this problem, in this paper...
Breast cancer is a leading cause of cancer-related deaths in women worldwide. Discovery of breast cancer-related disease genes is becoming very important to researcher and opens a new way to investigate pathogenic mechanism of breast cancer. Many studies have shown that the availability of human genome-wide protein-protein interactions (PPI) provides us with new opportunity for discovering disease-genes...
Predicting drug-target interaction using computational approaches is an important step in drug discovery and repositioning. To predict whether there will be an interaction between a drug and a target, most existing methods identify similar drugs and targets in the database. The prediction is then made based on the known interactions of these drugs and targets. This idea is promising. However, there...
Shuang-Huang-Lian (SHL) is a famous modern formula prepared from three medicinal herbs including Flos Lonicerae, Radix Scutellariae and Fructus Forsythiae. Currently, SHL has been developed a variety of dosage forms due to its proved clinical efficacy. However, the in-depth research on targets and pharmacological mechanisms of SHL preparations was scarce. In the presented study, the bioinformatics...
Major depression (MD) is a major public health problem which has a substantial impact on individuals and society. Although it is usually treated with antidepressant in primary care, these therapies accompanied with serious side effects. In the clinic of Chinese medicine, Xiao-Yao-San is the first option for MD with little side effects. Although with clear therapeutic effects, its therapeutic mechanism...
Proteins are macromolecules that have a high molecular weight, and make up, along with water, most of the composition of cells. The functions they perform are extremely important, such as the catalysis of biochemical reactions, cytoskeleton formation, and the transportation and storage of substances. With the completion of genome sequencing, protein discovery has been growing exponentially, and the...
Many methods have been published to prioritize genes using network theory. By using protein-protein interaction (PPI) data, it is possible to use mathematical features to rank and prioritize genes products in the network. Taking into account that genes related to the same diseases tend to connect, in the network structure, the prioritization methods search for candidate genes in the neighborhood of...
Protein sub network biomarkers for 144 diseases and pathways are analyzed in terms of protein-protein interaction (PPI) score available in STRING database. Most of the sub network biomarker (SNB) studies are to classify disease samples from the control. But no de novo algorithm is available to identify SNB from the whole genome PPI network without the knowledge of differentially expressed genes. Recently,...
Various statistical and machine learning based algorithms have been proposed in literature for selecting an informative subset of genes from micro array data sets. The recent trend is to use functional knowledge to aid the gene selection process. In this paper we propose a clustering algorithm which generates multiple views (clusters) from the micro array expression profiles, each representing a particular...
Multiple biological sequences alignment like protein sequences or DNA/RNA in order to discover the functions, structures and evolutionary relationships among species and also discovering drugs is a fundamental study in bioinformatics. Unfortunately the multiple sequence alignment is a NP-complete problem and the reliability of the existing algorithms is not so high. The objective of our study was...
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