Position Weight Matrix or Acyclic Probabilistic Finite Automaton: Which model to use? A decision rule inferred for the prediction of transcription factor binding sites

Autor(es)

Guilherme Miura Lavezzo ^[1] ; Marcelo de Souza Lauretto ^[2] ; Luiz Paulo Moura Andrioli ^[3] ; Ariane Machado-Lima ^[4]

Afiliação do(s) autor(es)

^[1] Universidade de São Paulo. Instituto de Matemática e Estatística. Programa Interunidades de Pós-Graduação em Bioinformática - Brasil

^[2] Universidade de São Paulo. Escola de Artes, Ciências e Humanidades - Brasil

^[3] Universidade de São Paulo. Escola de Artes, Ciências e Humanidades - Brasil

^[4] Universidade de São Paulo. Escola de Artes, Ciências e Humanidades - Brasil

• Tipo de documento: Artigo Científico
• Fonte: GENETICS AND MOLECULAR BIOLOGY; v. 46, n. 4 2024-01-19.

Resumo

Abstract Prediction of transcription factor binding sites (TFBS) is an example of application of Bioinformatics where DNA molecules are represented as sequences of A, C, G and T symbols. The most used model in this problem is Position Weight Matrix (PWM). Notwithstanding the advantage of being simple, PWMs cannot capture dependency between nucleotide positions, which may affect prediction performance. Acyclic Probabilistic Finite Automata (APFA) is an alternative model able to accommodate position dependencies. However, APFA is a more complex model, which means more parameters have to be learned. In this paper, we propose an innovative method to identify when position dependencies influence preference for PWMs or APFAs. This implied using position dependency features extracted from 1106 sets of TFBS to infer a decision tree able to predict which is the best model - PWM or APFA - for a given set of TFBSs. According to our results, as few as three pinpointed features are able to choose the best model, providing a balance of performance (average precision) and model simplicity. (AU)

• Processo FAPESP: 13/07375-0 - CeMEAI - Centro de Ciências Matemáticas Aplicadas à Indústria
• Beneficiário: Francisco Louzada Neto
• Modalidade de apoio: Auxílio à Pesquisa - Centros de Pesquisa, Inovação e Difusão - CEPIDs