Clustering of Human Gene Expression Stimulated by Bacterial Infection from Microarray Analysis

Abstract

Gene expression profiling of human cells against bacterial infection has become a major tool that allows explaining genome-wide expression changes in health and disease, which is important for the diagnosis and prognosis of diseases. A good way to identify human genes with similar biological activities or functions when stimulated by bacteria injection is by clustering. The objective of this research is to cluster human gene expression stimulated by wide-type (WS) and mutant strain (MS) of Burkholderia pseudomallei compared to controls via microarray transcriptional profile. K-means clustering algorithm was used to cluster human gene expression based on the fold change (FC) values of primary human monocytes (PHM) stimulated by both strains. In the phase of determining k-cluster experimented on PHM genes stimulated with WS, with MS and without strains stimulation (control), it results were 7, 7 and 7 clusters, respectively. According to three clustering patterns based on bacterial strain of stimulation, genes in cluster in the same ranked level reveals the similar molecular functions whereas different levels have different functions. Moreover, the clusters with highest FC values are also crucial. In the first top cluster, gene expression in PHM stimulated with WS and MS compared to the control, the cytokine genes especially csf2, csf3, il23A, il6 and stat4 were found in all bacterial stimulation. These gene clusters showed the molecular functions in PHM including cytokine activity, growth receptor binding, growth factor activity and cytokine receptor binding. These results indicated that the cluster of human genes infected by B. pseudomallei revealed the association between immune response genes and their molecular functions. These clusters of PHM genes might be the important biomarker genes which related for understanding the human immune response against B. pseudomallei infection and prognosis the melioidosis patients.