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| Full text | |
| Author(s): |
Chunikhina, Evgenia
;
Logan, Paul
;
Kovchegov, Yevgeniy
;
Yambartsev, Anatoly
;
Mondal, Debashis
;
Morgun, Andrey
Total Authors: 6
|
| Document type: | Journal article |
| Source: | IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS; v. 20, n. 1, p. 11-pg., 2023-01-01. |
| Abstract | |
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) | |
| FAPESP's process: | 18/07826-5 - Hydrodynamic limits of coalescent processes and minimal spanning trees with applications in mathematical biology |
| Grantee: | Anatoli Iambartsev |
| Support Opportunities: | Research Grants - Visiting Researcher Grant - International |
| FAPESP's process: | 18/14952-7 - Information content of self-similar structures |
| Grantee: | Evgenia Vladimirovna Chunikhina |
| Support Opportunities: | Scholarships in Brazil - Post-Doctoral |
| FAPESP's process: | 17/10555-0 - Stochastic modeling of interacting systems |
| Grantee: | Fabio Prates Machado |
| Support Opportunities: | Research Projects - Thematic Grants |