Biosom: gene synonym analysis by self-organizing map.
There are several guidelines for gene nomenclature, but they are not always applied to the names of newly identified genes. The lack of standardization in naming genes generates inconsistent databases with errors such as genes with the same function and different names, genes with different functions and the same name, and use of an abbreviated name. This paper presents a methodology for predicting synonyms in a given gene nomenclature, thereby detecting and minimizing naming redundancy and inconsistency and facilitating the annotation of new genes and data mining in public databases. To identify gene synonyms, i.e., gene ambiguity, the methodology proposed begins by grouping genes according to their names using a Kohonen self-organizing map artificial neural network. Afterwards, it identifies the groups generated employing the Matrix-U technique. The employment of such techniques allows one to infer the synonyms of genes, to predict probable hypothetical gene names and to point out possible errors in a database record. Many mistakes related to gene nomenclature were detected in this research, demonstrating the importance of predicting synonyms. The methodology developed is applicable for describing hypothetical, putative and other types of genes without a known function. Moreover, it can also indicate a possible function for genes after grouping them.
Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, PR, Brasil.
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KR
Otemaier
Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, PR, Brasil.
M B R
MB
Steffens
Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, PR, Brasil raittz@gmail.com.
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RT
Raittz
Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, PR, Brasil.
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A
Brawerman
Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, PR, Brasil.
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JN
Marchaukoski
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030541:Databases, Genetic; D005796:Genes; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D016571:Neural Networks, Computer; D015203:Reproducibility of Results; D016415:Sequence Alignment; D012984:Software; D009626:Terminology as Topic
D000596:Amino Acids