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Abstract
- In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues
In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues
Sheng-Ying Pao1 ,2 , Win-Li Lin1  and Ming-Jing Hwang2 
1Institute of Biomedical Engineering, National Taiwan University, Taipei, Taiwan
2Institute of BiomedicalSciences, Academia Sinica, Taipei, Taiwan
Background
Screening for differentially expressed genes on the genomic scale and comparative analysis of the expression profiles of orthologous genes between species to study gene function and regulation are becoming increasingly feasible. Expressed sequence tags (ESTs) are an excellent source of data for such studies using bioinformatic approachesbecause of the rich libraries and tremendous amount of data now available in the public domain. However, any large-scale EST-based bioinformatics analysis must deal with the heterogeneous, and often ambiguous, tissue and organ terms used to describe EST libraries.
Results
To deal with the issue of tissue source, in this work, we carefully screened and organized more than 8 million human and mouseESTs into 157 human and 108 mouse tissue/organ categories, to which we applied an established statistic test using different thresholds of the p value to identify genes differentially expressed in different tissues. Further analysis of the tissue distribution and level of expression of human and mouse orthologous genes showed that tissue-specific orthologs tended to have more similar expressionpatterns than those lacking significant tissue specificity. On the other hand, a number of orthologs were found to have significant disparity in their expression profiles, hinting at novel functions, divergent regulation, or new ortholog relationships.
Conclusion
Comprehensive statistics on the tissue-specific expression of human and mouse genes were obtained in this very large-scale, EST-basedanalysis. These statistical results have been organized into a database, freely accessible at our website http://gln.ibms.sinica.edu.tw/product/HMDEG/EST/index.php, for easy searching of human and mouse tissue-specific genes and for investigating gene expression profiles in the context of comparative genomics. Comparative analysis showed that, although highly tissue-specific genes tend to exhibitsimilar expression profiles in human and mouse, there are significant exceptions, indicating that orthologous genes, while sharing basic genomic properties, could result in distinct phenotypes.
Source: BMC Genomics 2006, 7:86
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricteduse, distribution, and reproduction in any medium, provided the original work is properly cited.
Background
- In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues
High-throughput analysis of gene expression offers a powerful means of studying how genes work and of uncovering the secrets encoded in genome sequences. Differential geneexpression, which plays a key role in various cellular processes, can be quantified by analyzing a large number of transcription products. To do so, several large-scale transcript detection technologies have been developed, chief among which are variants of microarray technology [1,2], expressed sequence tags (ESTs) [3], and serial analysis of gene expression (SAGE) [4]. Although each of these has itsown limitations [5-10], combined with bioinformatics and statistical analysis, they have been successful in revealing genes expressed differentially in different tissues or in different physiological or phenotypical states and in yielding unprecedented insights into the complicated interactions of expressed genes and their cellular functions [10-12].
In this work, the EST database for human...
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