| Texto completo | |
| Autor(es): |
Chunikhina, Evgenia
;
Logan, Paul
;
Kovchegov, Yevgeniy
;
Yambartsev, Anatoly
;
Mondal, Debashis
;
Morgun, Andrey
Número total de Autores: 6
|
| Tipo de documento: | Artigo Científico |
| Fonte: | IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS; v. 20, n. 1, p. 11-pg., 2023-01-01. |
| Resumo | |
Omics technologies are powerful tools for analyzing patterns in gene expression data for thousands of genes. Due to a number of systematic variations in experiments, the raw gene expression data is often obfuscated by undesirable technical noises. Various normalization techniques were designed in an attempt to remove these non-biological errors prior to any statistical analysis. One of the reasons for normalizing data is the need for recovering the covariance matrix used in gene network analysis. In this paper, we introduce a novel normalization technique, called the covariance shift (C-SHIFT) method. This normalization algorithm uses optimization techniques together with the blessing of dimensionality philosophy and energy minimization hypothesis for covariance matrix recovery under additive noise (in biology, known as the bias). Thus, it is perfectly suited for the analysis of logarithmic gene expression data. Numerical experiments on synthetic data demonstrate the method's advantage over the classical normalization techniques. Namely, the comparison is made with Rank, Quantile, cyclic LOESS (locally estimated scatterplot smoothing), and MAD (median absolute deviation) normalization methods. We also evaluate the performance of C-SHIFTalgorithm on real biological data. (AU) | |
| Processo FAPESP: | 18/07826-5 - Limites hidrodinâmicos de processos coalescentes e árvores de extensão mínima com aplicações em biologia matemática |
| Beneficiário: | Anatoli Iambartsev |
| Modalidade de apoio: | Auxílio à Pesquisa - Pesquisador Visitante - Internacional |
| Processo FAPESP: | 18/14952-7 - Componente de informação de estruturas auto-similares |
| Beneficiário: | Evgenia Vladimirovna Chunikhina |
| Modalidade de apoio: | Bolsas no Brasil - Pós-Doutorado |
| Processo FAPESP: | 17/10555-0 - Modelagem estocástica de sistemas interagentes |
| Beneficiário: | Fabio Prates Machado |
| Modalidade de apoio: | Auxílio à Pesquisa - Temático |