FM-test: a fuzzy-set-theory-based approach to differential gene expression data analysis

Water quality evaluation of Haihe River with fuzzy similarity measure methods

Fuzzy similarity measures, which are used to judge the closeness of two fuzzy sets, are presented to evaluate the water quality of the Haihe River. Based on the membership functions and coefficient of variation as the weights, four fuzzy similarity measures (including Lattice similarity measure, Hamming similarity measure, Euclidean similarity measure and the max-min similarity measure) are used to classify the 299 samples into the proper water quality standard ranks. The results are compared with the traditional distance discriminant methods. The calculation of two traditional distance discriminant methods (both Euclidean distance and absolute value distance) is also based on the use of coefficients of variation as the weights. Without the Lattice similarity measure, for this method loses some information, the correct assignment of samples classified into the same water quality ranks is 75.92% with the other three similarity measures and two distance discriminant methods. This result shows the reliability of the five methods. Only considering the three similarity measures, there were only 1.01% of the samples that did not classify to the same ranks, while the corresponding ratio of the two distance discriminant methods was 5.69%. The results of leave-one-out cross validation show that more than 88% of the samples are classified to the proper ranks, which demonstrates that the similarity measures are suitable to evaluate the water quality of the Haihe River.

A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding

Reliable assignment of an unknown query sequence to its correct species remains a methodological problem for the growing field of DNA barcoding. While great advances have been achieved recently, species identification from barcodes can still be unreliable if the relevant biodiversity has been insufficiently sampled. We here propose a new notion of species membership for DNA barcoding-fuzzy membership, based on fuzzy set theory-and illustrate its successful application to four real data sets (bats, fishes, butterflies and flies) with more than 5000 random simulations. Two of the data sets comprise especially dense species/population-level samples. In comparison with current DNA barcoding methods, the newly proposed minimum distance (MD) plus fuzzy set approach, and another computationally simple method, 'best close match', outperform two computationally sophisticated Bayesian and BootstrapNJ methods. The new method proposed here has great power in reducing false-positive species identification compared with other methods when conspecifics of the query are absent from the reference database.

MCM-test: a fuzzy-set-theory-based approach to differential analysis of gene pathways

Background

Gene pathway can be defined as a group of genes that interact with each other to perform some biological processes. Along with the efforts to identify the individual genes that play vital roles in a particular disease, there is a growing interest in identifying the roles of gene pathways in such diseases.

Results

This paper proposes an innovative fuzzy-set-theory-based approach, Multi-dimensional Cluster Misclassification test (MCM-test), to measure the significance of gene pathways in a particular disease. Experiments have been conducted on both synthetic data and real world data. Results on published diabetes gene expression dataset and a list of predefined pathways from KEGG identified OXPHOS pathway involved in oxidative phosphorylation in mitochondria and other mitochondrial related pathways to be deregulated in diabetes patients. Our results support the previously supported notion that mitochondrial dysfunction is an important event in insulin resistance and type-2 diabetes.

Conclusion

Our experiments results suggest that MCM-test can be successfully used in pathway level differential analysis of gene expression datasets. This approach also provides a new solution to the general problem of measuring the difference between two groups of data, which is one of the most essential problems in most areas of research.

Development of computations in bioscience and bioinformatics and its application: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB06)

The first symposium of computations in bioinformatics and bioscience (SCBB06) was held in Hangzhou, China on June 21–22, 2006. Twenty-six peer-reviewed papers were selected for publication in this special issue of BMC Bioinformatics. These papers cover a broad range of topics including bioinformatics theories, algorithms, applications and tool development. The main technical topics contain gene expression analysis, sequence analysis, genome analysis, phylogenetic analysis, gene function prediction, molecular interaction and system biology, genetics and population study, immune strategy, protein structure prediction and proteomics.