Open Access

Differential co‑expression analysis of venous thromboembolism based on gene expression profile data

  • Authors:
    • Zhibing Ming
    • Wenbin Ding
    • Ruifan Yuan
    • Jie Jin
    • Xiaoqiang Li
  • View Affiliations

  • Published online on: March 30, 2016     https://doi.org/10.3892/etm.2016.3208
  • Pages: 2193-2200
  • Copyright: © Ming et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

The aim of the present study was to screen differentially co‑expressed genes and the involved transcription factors (TFs) and microRNAs (miRNAs) in venous thromboembolism (VTE). Microarray data of GSE19151 were downloaded from Gene Expression Omnibus, including 70 patients with VTE and 63 healthy controls. Principal component analysis (PCA) was performed using R software. Differential co‑expression analysis was performed using R, followed by screening of modules using Cytoscape. Functional annotation was performed using Database for Annotation, Visualization, and Integrated Discovery. Moreover, Fisher test was used to screen key TFs and miRNAs for the modules. PCA revealed the disease and healthy samples could not be distinguished at the gene expression level. A total of 4,796 upregulated differentially co‑expressed genes (e.g. zinc finger protein 264, electron‑transfer‑flavoprotein, beta polypeptide and Janus kinase 2) and 3,629 downregulated differentially co‑expressed genes (e.g. adenylate cyclase 7 and single‑stranded DNA binding protein 2) were identified, which were further mined to obtain 17 and eight modules separately. Functional annotation revealed that the largest upregulated module was primarily associated with acetylation and the largest downregulated module was mainly involved in mitochondrion. Moreover, 48 TFs and 62 miRNA families were screened for the 17 upregulated modules, such as E2F transcription factor 4, miR‑30 and miR‑135 regulating the largest module. Conversely, 35 TFs and 18 miRNA families were identified for the 8 downregulated modules, including mitochondrial ribosomal protein S12 and miR‑23 regulating the largest module. Differentially co‑expressed genes regulated by TFs and miRNAs may jointly contribute to the abnormal acetylation and mitochondrion presentation in the progression of VTE.

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June-2016
Volume 11 Issue 6

Print ISSN: 1792-0981
Online ISSN:1792-1015

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Copy and paste a formatted citation
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Spandidos Publications style
Ming Z, Ding W, Yuan R, Jin J and Li X: Differential co‑expression analysis of venous thromboembolism based on gene expression profile data. Exp Ther Med 11: 2193-2200, 2016
APA
Ming, Z., Ding, W., Yuan, R., Jin, J., & Li, X. (2016). Differential co‑expression analysis of venous thromboembolism based on gene expression profile data. Experimental and Therapeutic Medicine, 11, 2193-2200. https://doi.org/10.3892/etm.2016.3208
MLA
Ming, Z., Ding, W., Yuan, R., Jin, J., Li, X."Differential co‑expression analysis of venous thromboembolism based on gene expression profile data". Experimental and Therapeutic Medicine 11.6 (2016): 2193-2200.
Chicago
Ming, Z., Ding, W., Yuan, R., Jin, J., Li, X."Differential co‑expression analysis of venous thromboembolism based on gene expression profile data". Experimental and Therapeutic Medicine 11, no. 6 (2016): 2193-2200. https://doi.org/10.3892/etm.2016.3208