Computational techniques to recover missing gene expression data

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Authors
Fraidouni, Negin
Záruba, Gergely V.
Advisors
Issue Date
2018
Type
Article
Keywords
Gene expression prediction , Pearson correlation coefficient , Cosine similarity , Robust principal component analysis , Alternating direction , Method of multiplier
Research Projects
Organizational Units
Journal Issue
Citation
Fraidouni, Negin; Zaruba, Gergely V. 2018. Computational techniques to recover missing gene expression data. Advances in Science, Technology and Engineering Systems, vol. 3:no. 6:pp 233-242
Abstract

Almost every cells in human's body contain the same number of genes so what makes them different is which genes are expressed at any time. Measuring gene expression can be done by measuring the amount of mRNA molecules. However, it is a very expensive and time consuming task. Using computational methods can help biologists to perform gene expression measurements more efficiently by providing prediction techniques based on partial measurements. In this paper we describe how we can recover a gene expression dataset by employing Euclidean distance, Pearson correlation coefficient, Cosine similarity and Robust PCA. To do this, we can assume that the gene expression data is a matrix that has missing values. In that case the rows of the matrix are different genes and columns are different subjects. In order to find missing values, we assume that the data matrix is low rank. We then used different correlation metrics to find similar genes. In another approach, we employed RPCA method to differentiate the underlying low rank matrix from the sparse noise. We used existing implementations of state-of-the-art algorithms to compare their accuracy. We describe that RPCA approach outperforms the other approaches with reaching improvement factors beyond 4.8 in mean squared error.

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Publisher
Elsevier
Journal
Book Title
Series
Technology and Engineering Systems;v.3:no.6
PubMed ID
DOI
ISSN
2415-6698
EISSN