Analysis of Regulatory motif binding site - an effective approach for identifying upregulated genes in the human oncogenome

¹Sanga Mitra, ¹Arpita Basu, ¹Debipriya Banerjee, ¹Manjita Mazumdar, ¹Sambit Basu, ¹Sananda Chakraborty, ¹Satabdi Kundu, ¹Jyotirmoy Ghosh, ¹Subhankar Paul, ¹Satarupa Chatterjee, ¹Urmimala Sen, ²Sayak Ganguli
¹Indian Institute of Social Welfare and Business Management, Kolkata - 700073, India, ²BIF - Presidency College, Kolkata - 700073, India

Current trends in the analysis of cancer genomics have involved approaches for identifying the expression levels of the oncogenome in specific types of cancer and to locate the genes that are upregulated in specific cancer phenotypes. The experimental protocols mostly involve SAGE and microarray based approaches, which are both time consuming and expensive. Moreover the analysis involves a huge amount of starting gene sets which may or may not respond evenly in each experimental cascade. In this work we report for the first time an in silico approach for the detection and screening of genes which might be upregulated in cancer. The approach involves the identification and analyses of regulatory motif binding sites in the genes implicated in various human carcinomas and correlating them with the reported expression patterns of the genes. The results indicate that the genes reported to be upregulated in cancer possess a specific pattern of regulatory motif binding sites and future cancer biomarkers can be screened and tested with the presence of the same set of regulatory motif binding sites. A correspondence analysis was also performed along with a correlation analysis to further establish our findings. This approach could prove to be beneficial for screening of the specific genes before workers embark upon wet lab experiments.