An Integrated Bioinformatics Approach to Identify Network-Derived Hub Genes in Starving Zebrafish
Amin Mortazavi,
Mostafa Ghaderi-Zefrehei,
Mustafa Muhaghegh Dolatabady,
Mahdi Golshan,
Sajad Nazari,
Ayeh Sadat Sadr,
Saeid Kadkhodaei,
Ikhide G. Imumorin,
Sunday O. Peters,
Jacqueline Smith
Affiliations
Amin Mortazavi
Cold-Water Fishes Genetic and Breeding Research Center, Iranian Fisheries Research Institute, Agriculture Research Education and Extension Organization (AREEO), Yasouj 74394-75918, Iran
Mostafa Ghaderi-Zefrehei
Department of Animal Science, Faculty of Agriculture, Yasouj University, Yasouj 74394-75918, Iran
Mustafa Muhaghegh Dolatabady
Department of Animal Science, Faculty of Agriculture, Yasouj University, Yasouj 74394-75918, Iran
Mahdi Golshan
Iranian Fisheries Research Institute, Agriculture Research Education and Extension Organization (AREEO), Tehran 14968-13151, Iran
Sajad Nazari
Cold-Water Fishes Genetic and Breeding Research Center, Iranian Fisheries Research Institute, Agriculture Research Education and Extension Organization (AREEO), Yasouj 74394-75918, Iran
Ayeh Sadat Sadr
South of Iran Aquaculture Research Institute, Iranian Fisheries Science Research Institute (IFSRI), Agricultural Research Education and Extension Organization (AREEO), Ahvaz 19395-1113, Iran
Saeid Kadkhodaei
Agricultural Biotechnology Research Institute of Iran (ABRII), Center of Iran, Isfahan 14968-13151, Iran
Ikhide G. Imumorin
School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
Sunday O. Peters
Department of Animal Science, Berry College, Mount Berry, GA 30149, USA
Jacqueline Smith
The Roslin Institute and Royal (Dick), School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
The present study was aimed at identifying causative hub genes within modules formed by co-expression and protein–protein interaction (PPI) networks, followed by Bayesian network (BN) construction in the liver transcriptome of starved zebrafish. To this end, the GSE11107 and GSE112272 datasets from the GEO databases were downloaded and meta-analyzed using the MetaDE package, an add-on R package. Differentially expressed genes (DEGs) were identified based upon expression intensity N(µ = 0.2, σ2 = 0.4). Reconstruction of BNs was performed by the bnlearn R package on genes within modules using STRINGdb and CEMiTool. ndufs5 (shared among PPI, BN and COEX), rps26, rpl10, sdhc (shared between PPI and BN), ndufa6, ndufa10, ndufb8 (shared between PPI and COEX), skp1, atp5h, ndufb10, rpl5b, zgc:193613, zgc:123327, zgc:123178, wu:fc58f10, zgc:111986, wu:fc37b12, taldo1, wu:fb62f08, zgc:64133 and acp5a (shared between COEX and BN) were identified as causative hub genes affecting gene expression in the liver of starving zebrafish. Future work will shed light on using integrative analyses of miRNA and DNA microarrays simultaneously, and performing in silico and experimental validation of these hub-causative (CST) genes affecting starvation in zebrafish.
