Differentially expressed genes

Screening for key genes associated with invasive ductal carcinoma of the breast via microarray data analysis

J. L. Huan, Gao, X., Xing, L., Qin, X. J., Qian, H. X., Zhou, Q., and Zhu, L., Screening for key genes associated with invasive ductal carcinoma of the breast via microarray data analysis, vol. 13, pp. 7919-7925, 2014.

The aim of this study was to identify key genes related to invasive ductal carcinoma (IDC) of the breast by analyzing gene expression data with bioinformatic tools. Microarray data set GSE31138 was downloaded from Gene Expression Omnibus, including 3 breast cancer tissue samples and 3 normal controls. Differentially expressed genes (DEGs) between breast cancer and normal control were screened out (FDR 2). Coexpression between genes was examined with String, and a network was then constructed. Relevant pathways and diseases were retrieved with KOBAS.

Functional analysis of differentially expressed genes associated with glaucoma from DNA microarray data

Y. Wu, Zang, W. D., and Jiang, W., Functional analysis of differentially expressed genes associated with glaucoma from DNA microarray data, vol. 13, pp. 9421-9428, 2014.

Microarray data of astrocytes extracted from the optic nerves of donors with and without glaucoma were analyzed to screen for differentially expressed genes (DEGs). Functional exploration with bioinformatic tools was then used to understand the roles of the identified DEGs in glaucoma. Microarray data were downloaded from the Gene Expression Omnibus (GEO) database, which contains 13 astrocyte samples, 6 from healthy subjects and 7 from patients suffering from glaucoma. Data were pre-processed, and DEGs were screened out using R software packages.

Identification of differently expressed genes in leukemia using multiple microarray datasets

Z. Y. Zhang, Xu, R. Q., Guo, T. J., Zhang, M., Li, D. X., and Lu, X. Y., Identification of differently expressed genes in leukemia using multiple microarray datasets, vol. 13, pp. 10482-10489, 2014.

The purpose of this study was to identify differentially expressed genes and analyze biological processes related to leukemia. A meta-analysis was performed using the Rank Product package of Gene Expression Omnibus datasets for leukemia. Next, Gene Ontology-enrichment analysis and pathway analysis were performed using the Gene Ontology website and Kyoto Encyclopedia of Genes and Genomes. A protein-protein interaction network was constructed using the Cytoscape software.

Comparative and joint analyses of gene expression profiles under drought and rewatering in Arabidopsis

Z. H. Xu and Wu, W. R., Comparative and joint analyses of gene expression profiles under drought and rewatering in Arabidopsis, vol. 12, pp. 3622-3629, 2013.

Drought is a major limiting factor in crop production. Rewatering is a process opposite to drought, allowing plants to recover to their normal physiological state. To understand more thoroughly the set of genes involved in plant response to drought, we comparatively and jointly analyzed the microarray data of drought and rewatering experiments in Arabidopsis. A total of 3833 differentially expressed genes (DEGs) were identified. Among them, ~74% were proven to be co-regulated by drought and rewatering.

Regulation network analysis of testicular seminoma at various stages of progression

J. - J. Sha, Dong, Y. - H., Liu, D. - M., Bo, J. - J., Huang, Y. - R., Li, Z., and Ping, P., Regulation network analysis of testicular seminoma at various stages of progression, vol. 12, pp. 4297-4307, 2013.

Testicular seminoma has become the most common solid malignancy in young men, especially in the 20s group. We obtained the gene expression profile of human testicular seminoma cells from NCBI, identified the differentially expressed genes of testicular seminoma cells of different stages, and constructed the regulation networks of different stages of testicular seminoma using bioinformatics methodology. Forty differentially expressed genes of testicular seminoma cells of different stages were identified.

Expression profiling analysis of hypoxic pulmonary disease

L. Zhou, Wang, L. M., Song, H. M., Shen, Y. Q., Xu, W. J., Xu, J. H., Liu, Y., Yan, W. W., and Jiang, J. F., Expression profiling analysis of hypoxic pulmonary disease, vol. 12, pp. 4162-4170, 2013.

Exposure of humans to low levels of environmental oxygen results in alveolar hypoxia and normally causes chronic pulmonary hypertension and morphological alterations of precapillary pulmonary vessels. In this study, the microarray dataset GSE11341 was used to identify potential differentially expressed genes related with human lung microvascular endothelial cell hypoxia. In addition, gene ontology term enrichment analysis was performed to explore their underlying functions. In addition, we also investigated the small molecules by comparing with the Connectivity Map.

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