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Drug Target Identification Using Gene Expression Microarray Data of Toxoplasma Gondii
Budhayash Gautam, Pramod Katara, Satendra Singh, Rohit Farmer
Pages - 113 - 124     |    Revised - 30-06-2010     |    Published - 10-08-2010
Volume - 4   Issue - 3    |    Publication Date - July 2010  Table of Contents
Toxoplasma gondii, Toxoplasmosis, Microarray data analysis, Co-expression
Toxoplasma gondii is an obligate intracellular Apicomplexan parasite that can infect a wide range of warmblooded animals including humans. This pathogen is one of the most common in humans due to many contributing factors that include: (1) its complex life cycle allows it to be transmitted both sexually via felid fecal matter and asexually via carnivorism. (2) Toxoplasma has an extremely wide host cell tropism that includes most nucleated cells. (3) In humans and other intermediate hosts, Toxoplasma develops into a chronic infection that cannot be eliminated by the host’s immune response or by currently used drugs. In most cases, chronic infections are largely asymptomatic unless the host becomes immune compromised and often suffer from life threatening encephalitis. Unfortunately, owing to the toxic side effects and general low efficacy of all known drugs for toxoplasmosis, new chemotherapeutic agents are urgently required. The mechanisms by which Toxoplasma grows within its host cell, encysts, and interacts with the host’s immune system are important questions. The use of DNA microarrays in transcriptional profiling, genotyping, and epigenetic experiments has impacted our understanding of these processes. In the past years, many existing data analysis methods from other fields have been applied to gene expression data. Among these, clustering methods are a large family of commonly used data analysis methods. Clustering methods are particularly useful in the analysis of gene expression data and organization of gene expression data. In present work Hierarchical and kmeans clustering methods have been used for the analysis of microarray gene expression data of Toxoplasma gondii with the help of Genesis tool. On the basis of coexpression, some probable gene targets in Toxoplasma gondii have been found (IL-16 and Inhibitor of kappa light chain Epsilon etc.). Their promoters have been predicted with Neural Network Promoter Predictor, of BDGP. Predicted promoters were aligned using ClustalW to SAG family members, (which are related to the invasion or surface attachment of the parasite to the host cell) to see common regulation. They showed good amount of sequence similarity with the already known targeted genes of SAG family. These probable targets have important functions in the case of encephalitis in AIDS patient caused by Toxoplasma gondii, as these targets play major role in prevention of AIDS.
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Mr. Budhayash Gautam
SHIATS, Allahabad - India
Mr. Pramod Katara
Banasthali University, - India
Mr. Satendra Singh
- India
Mr. Rohit Farmer
- India