The recent explosion in the number of gene expression experiments and the need to extract useful biological information from the resulting volumes of data has presented a new challenge, that is, to identify the most significant changes in gene expression and to interpret the results in terms of biological relationships. There are a number of web resources that provide data annotation services for gene expression datasets. Microarray Analysis has become a huge widely used tool for the generation of gene expression data on functional genomic scale. The information gained offers an unprecedented opportunity to fully characterize biological processes. The global burden of cancer continues to increase largely because of the aging and growth of the world population alongside an increasing adoption of cancer-causing behaviours, particularly smoking, in economically developing countries. Mainly the Head and Neck squamous cell carcinoma, and is one of the leading causes of human death worldwide and the deaths from cancer are projected to continue rising. With the help of Bioinformatics techniques the analysis of gene expression data is done through BRB Array tool .Microarray data is analysed using PAM and Hierarchical clustering. The two genes i.e. Keratin 4 and Mal, Tcell differentiation protein are predicted through PAM. These genes can have important role in the Head and Neck squamous cell carcinoma.