A Validity Measure for Fuzzy Clustering
IEEE Transactions on Pattern Analysis and Machine Intelligence
A new approach to analyzing gene expression time series data
Proceedings of the sixth annual international conference on Computational biology
A Convergence Theorem for the Fuzzy ISODATA Clustering Algorithms
IEEE Transactions on Pattern Analysis and Machine Intelligence
Computational Statistics & Data Analysis
Clustering Time-Series Gene Expression Data with Unequal Time Intervals
Transactions on Computational Systems Biology X
Clustering of gene expression data based on shape similarity
EURASIP Journal on Bioinformatics and Systems Biology - Special issue on applications of signal procesing techniques to bioinformatics, genomics, and proteomics
Microarray Time-Series Data Clustering via Multiple Alignment of Gene Expression Profiles
PRIB '09 Proceedings of the 4th IAPR International Conference on Pattern Recognition in Bioinformatics
A novel HMM-based clustering algorithm for the analysis of gene expression time-course data
Computational Statistics & Data Analysis
Autocorrelation-based fuzzy clustering of time series
Fuzzy Sets and Systems
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
A General Framework for Analyzing Data from Two Short Time-Series Microarray Experiments
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
ICANN'06 Proceedings of the 16th international conference on Artificial Neural Networks - Volume Part II
Computer Methods and Programs in Biomedicine
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Time course measurements are becoming a common type of experiment in the use of microarrays. The temporal order of the data and the varying length of sampling intervals are important and should be considered in clustering time-series. However, the shortness of gene expression time-series data limits the use of conventional statistical models and techniques for time-series analysis. To address this problem, this paper proposes the fuzzy short time-series (FSTS) clustering algorithm, which clusters profiles based on the similarity of their relative change of expression level and the corresponding temporal information. One of the major advantages of fuzzy clustering is that genes can belong to more than one group, revealing distinctive features of each gene's function and regulation. Several examples are provided to illustrate the performance of the proposed algorithm. In addition, we present the validation of the algorithm by clustering the genes which define the model profiles in Chu et al. (Science, 282 (1998) 699). The fuzzy c-means, k-means, average linkage hierarchical algorithm and random clustering are compared to the proposed FSTS algorithm. The performance is evaluated with a well-established cluster validity measure proving that the FSTS algorithm has a better performance than the compared algorithms in clustering similar rates of change of expression in successive unevenly distributed time points. Moreover, the FSTS algorithm was able to cluster in a biologically meaningful way the genes defining the model profiles.