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The sophisticated process of reprogramming of adult stem cells to embryonic-like stem cells, known as cellular reprogramming, involves the risk of generation of tumorigenic cells due to the complexity involved. Oct4 protein is the inevitable element for inducing pluripotency along with Sox2 and Nanog proteins. In this study, the set of genes interacting with Oct4, Sox2 and Nanog were analyzed and categorized based on their molecular function. Later, the domains of translated products of 46 transcription factors interacting with Oct4, Sox2 and Nanog were identified, clustered them based on the nature of the domain and multiple sequence alignment was performed to find any functionally important consensus regions in the sequence. The key finding of this study is the 13 member cluster of homeo domain transcription factors exhibited some consensus in their sequence.