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Title: An in silico approach to identify novel genes preferentially expressed in the eye
Author: Patel, Sapna P.
Awarding Body: University of Edinburgh
Current Institution: University of Edinburgh
Date of Award: 2004
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Specific or preferential expression of a gene in a particular tissue or organ is often indicative of its importance in function or development. It would be beneficial to discover novel genes with preferential expression to enhance understanding of the tissue or organ in question. In this thesis, an in silico method was employed to find novel genes preferentially expressed in the mouse eye. The chosen in silico method was digital differential display (DDD), which utilises the publicly available UniGene database as a resource. UniGene is composed of expressed sequence tag (EST) sequences that are clustered by homology, such that each cluster is considered to represent a gene. Crucially, ESTs in UniGene are traceable to their library of origin. This allows DDD to statistically compare, for each cluster, the proportional representation of ESTs in different user-defined pools of libraries. Using an eye pool and a non-eye pool of libraries, DDD was performed on the mouse, human and rat UniGene sets. The production amongst the DDD results of genes homologous between mouse and human, both those known to be eye relevant as well as those not recognised as having preferential expression, supports the validity of the genes produced. The DDD results used for further analysis comprised 292 mouse UniGene clusters that were more highly represented in the eye pool than in the non-eye pool. Of the 154 clusters that represented known genes, 48% were known to be eye relevant. Thirty-one of the 138 novel clusters were selected for expression studies. Ten of these were later recognised as known genes, with 5 having eye relevance. Fifteen of the 31 novel clusters were confirmed by RT-PCR to show preferential expression, with 4 appearing eye specific. Three of the 15 genes are known (Aip11, Crygf and Otx2) and another 9 putative genes show expression in various regions of the eye. These novel genes may well have a role in eye development or function and are candidates for mouse and human eye mutations.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available