Use of MESs-clustering software to compare tissues by gene expression characterized by Unigene and Homologene databases Saulo de Paula Pinto2, Elisa R. Donnard1, Gabriel Fernandes1, J. Miguel Ortega1 1 Dept. Bioquimica e Imunologia, ICB, UFMG, 2PUC MINAS Abstract NCBI Unigene database  collects occurrence of sequences per cluster of expressed sequences organized by body sites (tissues). Another resource known as Homologene  builds homology relationship between genes of diverse organisms. We set up to organize a local repository of those data in a local MySQL database. We choose to collect the information on 14 organisms spanning from man to rice. The database thus holds information from 1907 Neurospora crassa up to 116273 Homo sapiens unigenes. In order to have enough EST representation in tissue or body site samples, we concentrate our analysis on samples with over 10000 sequences, which contemplates 78, 46, 20 distinct tissues for human, mouse, and rat, respectively. Besides, we grouped unigenes under the same homologene identifier in order to enable interorganisms tissues comparison and we considered the sum of the individual unigene expressions to be the homologene expression.. After that, we applied the MESs (most expressed sequences) clustering  to the corresponding datasets. Considering unigene datasets we found out that human tissues share MESs from 62.3% for lung-uterus pair to 11.4% for tonsil-trachea whereas mouse share from 61.1% for lung-mammary gland to 6.1% for spinal cord-tongue. Rat shared much less than the others: from 39% for lung-spleen to 12.2% for pituitary gland-testis). Besides, one remarkable finding is the high occurrence of pairs involving lung and kidney among the 20 topmost ones: 11 in human, 15 in mouse, and 12 in rat, which can indicate a certain variability of the expressed sequences among the 1000 analyzed MESs, for these two tissues. On the other side, among the 20 lowermost pairs we found a prevalence of pairs involving testis and liver: 11 in human, 12 in mouse, and 17 in rat, which points to a much different set of expressed MESs. The homologene results almost repeated the unigene ones considering separated organisms. But considering the three organisms at once we found that same tissues from different organisms share MESs from 52.6% for mouse and rat liver to 6.6% for human trachea and mouse tongue. Our results are not conclusive at all, but point to a direction where the expression estimated in the way presented here can be reliably used to find out relationships among the patterns of gene expression in different tissues and organisms. References  Pontius, J. U, Wagner, L, Schuler, G. D. UniGene: a unified view of the transcriptome. In: The NCBI Handbook. Bethesda (MD): National Center for Biotechnology Information; 2003.  de Paula Pinto, S. and Ortega, J. M., An algorithm to infer similarity among cell types and organisms by examining the most expressed sequences (MESs), to appear in the Genetic and Molecular Research, special issue in Bioinformatics, 2008.