Postdoc - Biomedicine

Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data.


Journal article


Mahmoud Ahmed, Huynh Quoc Nguyen, Jin Seok Hwang, Sahib Zada, Trang Huyen Lai, Sang Soo Kang, Deok Ryong Kim
Oncotarget, vol. 9(21), 2018 Jan 15, pp. 15526-15541

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APA
Ahmed, M., Nguyen, H. Q., Hwang, J. S., Zada, S., Lai, T. H., Kang, S. S., & Kim, D. R. (2018). Systematic characterization of autophagy-related genes during the adipocyte differentiation using public-access data. Oncotarget, 9(21), 15526–15541.

Chicago/Turabian
Ahmed, Mahmoud, Huynh Quoc Nguyen, Jin Seok Hwang, Sahib Zada, Trang Huyen Lai, Sang Soo Kang, and Deok Ryong Kim. “Systematic Characterization of Autophagy-Related Genes during the Adipocyte Differentiation Using Public-Access Data.” Oncotarget 9, no. 21 (January 15, 2018): 15526–15541.

MLA
Ahmed, Mahmoud, et al. “Systematic Characterization of Autophagy-Related Genes during the Adipocyte Differentiation Using Public-Access Data.” Oncotarget, vol. 9, no. 21, Jan. 2018, pp. 15526–41.


Abstract

Autophagy contributes to reorganizing intracellular components and forming fat droplets during the adipocyte differentiation. Here, we systematically describe the role of autophagy-related genes and gene sets during the differentiation of adipocytes. We used a public dataset from the European Nucleotide Archive from an RNA-seq experiment in which 3T3-L1 cells were induced by a differentiation induction medium, total RNA was extracted and sequenced at four different time points. Raw reads were aligned to the UCSC mouse reference genome (mm10) using HISAT2, and aligned reads were summarized at the gene or exon level using HTSeq. DESeq2 and DEXSeq were used to model the gene and exon counts and test for differential expression and relative exon usage, respectively. After applying the appropriate transformation, gene counts were used to perform the gene set and pathway enrichment analysis. Data were obtained, processed and annotated using R and Bioconductor. Several autophagy-related genes and autophagy gene sets, as defined in the Gene Ontology, were actively regulated during the course of the adipocyte differentiation. We further characterized these gene sets by clustering their members to a few distinct temporal profiles. Other potential functionally related genes were identified using a machine learning procedure. In summary, we characterized the autophagy gene sets and their members to biologically meaningful groups and elected a number of genes to be functionally related based on their expression patterns, suggesting that autophagy plays a critical role in removal of some intracellular components and supply of energy sources for lipid biogenesis during adipogenesis.

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