Background: Selecting an appropriate similarity measurement method is crucial for obtaining biologically meaningful clustering modules. Commonly used measurement methods are insufficient in capturing the complexity of biological systems and fail to accurately represent their intricate interactions.
Objective: This study aimed to obtain biologically meaningful gene modules by using the clustering algorithm based on a similarity measurement method.
Methods: A new algorithm called the Dual-Index Nearest Neighbor Similarity Measure (DINNSM) was proposed. This algorithm calculated the similarity matrix between genes using Pearson's or Spearman's correlation. It was then used to construct a nearest-neighbor table based on the similarity matrix. The final similarity matrix was reconstructed using the positions of shared genes in the nearest neighbor table and the number of shared genes.
Results: Experiments were conducted on five different gene expression datasets and compared with five widely used similarity measurement techniques for gene expression data. The findings demonstrate that when utilizing DINNSM as the similarity measure, the clustering results performed better than using alternative measurement techniques.
Conclusions: DINNSM provided more accurate insights into the intricate biological connections among genes, facilitating the identification of more accurate and biological gene co-expression modules.
Keywords: Clustering; co-expression module; gene expression data; similarity measure.