title: Microarray gene expression profiling and bioinformatics analysis of premature ovarian failure in a rat model.
abstract: Premature ovarian failure (POF) remains one of the major gynecological problems worldwide which affected 1% of women. Even though tremendous achievements had been acquired as opposed to years past, molecular pathogenesis associated with POF is still unclear and needs to be well-defined. The aim of this study was to analyze the gene expression profiles in the POF rat model. To predict potential regulating factors, we firstly treated female Sprague Dawley (SD) rat with 4-vinylcyclohexene diepoxide (VCD). Total RNA from ovarian tissue was converted to cDNA and hybridized to mRNA Chip array. The differentially expressed genes (DEGs) were identified by two-sample t test and assessed using hierarchical clustering and Principal Component Analysis methods. Potential regulatory targets associated with these DEGs were constructed using BisoGenet in Cytoscape. Gene Ontology (GO) and functional enrichment analysis were performed using BiNGO and DAVID, respectively. As the results, 25 DEGs were found to be closely associated with POF initiation. Hierarchical clustering and Principal Component Analysis on the transcriptional profiles revealed an excellent separation of the vehicle and POF compartments. Pathway enrichment analysis based on the disease-gene interaction network analysis led to the identification of two core signaling pathways that were strongly affected during POF initiation and progression: immune response and cardiovascular disorders. In conclusion, we constructed a gene regulatory network associated with POF using the microarray gene expression profiling, and screened out some genes or transcription factors that may be used as potential molecular therapeutic targets for POF.
authors.affiliation: Key Laboratory of State Administration of Traditional Chinese Medicine of the People's Republic of China, Department of Formulas of Traditional Chinese Medicine, School of Basic Medical Sciences, Heilongjinag University of Chinese Medicine, Harbin 150040, China. Electronic address: liji@hljucm.net.
authors.forename: Ji
authors.initials: J
authors.lastname: Li
authors.affiliation: State Key Laboratory of Natural and Biomimetic Drugs, Department of Pharmacology, School of Basic Medical Sciences, Peking University Health Science Center and Beijing Key Laboratory of Tumor Systems Biology, Peking University, Beijing 100191, China. Electronic address: herryvan@sohu.com.
authors.forename: Shengjun
authors.initials: S
authors.lastname: Fan
authors.affiliation: Department of Pharmacology, School of Basic Medical Sciences, Heilongjinag University of Chinese Medicine, Harbin 150040, China. Electronic address: hdw516@gmail.com.
authors.forename: Dongwei
authors.initials: D
authors.lastname: Han
authors.affiliation: Department of Pharmacology, School of Basic Medical Sciences, Heilongjinag University of Chinese Medicine, Harbin 150040, China. Electronic address: jiaming7xie@163.com.
authors.forename: Jiaming
authors.initials: J
authors.lastname: Xie
authors.affiliation: Key Laboratory of Ministry of Education, Department of Pharmacology, Heilongjiang University of Chinese Medicine, Harbin 150040, China. Electronic address: kuanghaixue@hljucm.net.
authors.forename: Haixue
authors.initials: H
authors.lastname: Kuang
authors.affiliation: Department of Pharmacology, School of Basic Medical Sciences, Heilongjinag University of Chinese Medicine, Harbin 150040, China; The Key Laboratory of Myocardial Ischemia (Harbin Medical University) of Chinese Ministry of Education, Harbin 150086, China. Electronic address: penglingge@126.com.
authors.forename: Pengling
authors.initials: P
authors.lastname: Ge
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D004195:Disease Models, Animal; D004797:Enzyme-Linked Immunosorbent Assay; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D016649:Primary Ovarian Insufficiency / Q000235:genetics*; D025341:Principal Component Analysis; D012333:RNA, Messenger / Q000032:analysis; D051381:Rats; D017207:Rats, Sprague-Dawley
chemical_list: D012333:RNA, Messenger
keywords: Bioinformatics analysis; Expression profiling; Premature ovarian failure