Abstract
Functional genomics focuses on assigning genes into functional categories and providing a comprehensive understanding of genetic networks. Genetic networks are complicated to perform complex biological tasks. Lots of works are still working on deciphering it and forcing to higher accuracy of algorithm. But there are still about one-fourth of genes in human genome functionally indistinct and are annotated to hypothetical genes. Genes involve in the same biological process are often regulated by similar transcriptional mechanism and are likely to contain similar transcription factor binding sites (TFBS) in their proximal promoters. Functional elements tend to evolve much slower than non-functional region, as they are subjected to selective pressure. Multi-species approach is come to make sense of TFBS prediction in silico, and was used with success to identify regulatory elements in various genes. The method is so-called “Phylogenetic Footprinting’’. The work flow goes through promoter extraction, prediction, and regulatory elements detection. Thus, both hypothetical genes and cancer-related genes are the inputs for testing. In this thesis, I analyzed the promoter region of hypothetical genes of Homo sapiens which are homologous to other organism, and provide a web service for biologists to analyze genetic networks between different organisms easily. Finally, the results are interesting because of discovering several conserved elements within some hypothetical genes and cancer-related genes, and supplying the highly conserved regulatory elements from different taxonomic nodes.