СONSECUTIVE INTEGRATION OF AVAILABLE MICROARRAY DATA FOR ANALYSIS OF DIFFERENTIAL GENE EXPRESSION IN HUMAN PLACENTA

• Main Authors: O. Lykhenko, A. Frolova, M. Obolenska
• Format: Article
• Language: English
• Published: National Academy of Sciences of Ukraine and Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine. 2021-02-01
• Series: Biotechnologia Acta
• Subjects: microarray; transcript; integrative analysis; bayesian empirical method; meta-analysis; differentially expressed genes; placenta.
• Online Access: http://biotechnology.kiev.ua/images/1_2021/lykhenko_1_2021.pdf
• ISSN: 2410-7751; 2410-776X

The purpose of the study was to provide the pipeline for processing of publicly available unprocessed data on gene expression via integration and differential gene expression analysis. Data collection from open gene expression databases, normalization and integration into a single expression matrix in accordance with metadata and determination of differentially expressed genes were fulfilled. To demonstrate all stages of data processing and integrative analysis, there were used the data from gene expression in the human placenta from the first and second trimesters of normal pregnancy. The source code for the integrative analysis was written in the R programming language and publicly available as a repository on GitHub. Four clusters of functionally enriched differentially expressed genes were identified for the human placenta in the interval between the first and second trimester of pregnancy. Immune processes, developmental processes, vasculogenesis and angiogenesis, signaling and the processes associated with zinc ions varied in the considered interval between the first and second trimester of placental development. The proposed sequence of actions for integrative analysis could be applied to any data obtained by microarray technology.