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In silico Discovery of Genes Expressed in Liver, Kidney, Spleen and Small Intestine of Pigs |
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Zengxiang Pan, Honglin Liu, Jie Chen, Dan Xu, Zhihua Jiang, Zhuang Xie |
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| Abstract |
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An in silico approach was developed to survey the genes expressed in four internal organs of pig: liver, kidney, spleen and small intestine. The major procedures of the approach included: (1) BLAST searching against GenBank `est_others` database using human cDNA sequences as queries to screen the porcine orthologous expressed sequence tags (ESTs), (2) classifying the porcine ESTs records by resources according to certain criteria and (3) analyzing data for ESTs specifically expressed in each organ. In order to do so, four Java programs were developed. Based on the ESTs available in the GenBank database, it was found that there were at least 2,100 genes expressed in these four organs, including 128 in the liver, 81 in the kidney, 780 in the spleen, and 1,423 in the small intestine respectively (a few genes co-expressed in these tissues). Gene expression patterns, such as co-expressed genes, preferentially expressed genes and basic active genes were also compared and characterized among these organs. This study provides a comprehensive model on how to use the bioinformatics approach and Genbank databases to facilitate the discovery of new genes in livestock species. |
| Keywords:
In silico; Internal Organs; Gene Expression Profiling; Ests; Pig |
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