Network Meta-Analysis of Chicken Microarray Data following Avian Influenza Challenge—A Comparison of Highly and Lowly Pathogenic Strains

Genes

卷:13

Saeid Kadkhodaei¹  Azadeh Moradi Pirbaluty²  Hossein Mehrban²  Mostafa Ghaderi-Zefrehei³  Ahmad Oryan⁴  Rudabeh Ravash⁵  Jacqueline Smith⁶ 

[1] Agricultural Biotechnology Research Institute of Iran (ABRII), Center of Iran, Isfahan 14968-13151, Iran;

[2] Department of Genetics and Animal Breeding, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran;

[3] Department of Genetics and Animal Breeding, Faculty of Agriculture, Yasouj University, Yasouj 75918-74831, Iran;

[4] Department of Pathology, School of Veterinary Medicine, Shiraz University, Shiraz 71557-13876, Iran;

[5] Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord 88186-34141, Iran;

[6] The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK;

关键词: microarray;    network;    meta-analysis;    Python;    influenza;    chicken;   

DOI  :  10.3390/genes13030435

来源: DOAJ

【 摘 要 】

The current bioinformatics study was undertaken to analyze the transcriptome of chicken (Gallus gallus) after influenza A virus challenge. A meta-analysis was carried out to explore the host expression response after challenge with lowly pathogenic avian influenza (LPAI) (H1N1, H2N3, H5N2, H5N3 and H9N2) and with highly pathogenic avian influenza (HPAI) H5N1 strains. To do so, ten microarray datasets obtained from the Gene Expression Omnibus (GEO) database were normalized and meta-analyzed for the LPAI and HPAI host response individually. Different undirected networks were constructed and their metrics determined e.g., degree centrality, closeness centrality, harmonic centrality, subgraph centrality and eigenvector centrality. The results showed that, based on criteria of centrality, the CMTR1, EPSTI1, RNF213, HERC4L, IFIT5 and LY96 genes were the most significant during HPAI challenge, with PARD6G, HMG20A, PEX14, RNF151 and TLK1L having the lowest values. However, for LPAI challenge, ZDHHC9, IMMP2L, COX7C, RBM18, DCTN3, and NDUFB1 genes had the largest values for aforementioned criteria, with GTF3C5, DROSHA, ATRX, RFWD2, MED23 and SEC23B genes having the lowest values. The results of this study can be used as a basis for future development of treatments/preventions of the effects of avian influenza in chicken.

【 授权许可】

Unknown