title: Systematic analysis of the gene expression in the livers of nonalcoholic steatohepatitis: implications on potential biomarkers and molecular pathological mechanism.
abstract: Non-alcoholic steatohepatitis (NASH) is a severe form of non-alcoholic fatty liver disease (NAFLD). The molecular pathological mechanism of NASH is poorly understood. Recently, high throughput data such as microarray data together with bioinformatics methods have become a powerful way to identify biomarkers and to investigate pathogenesis of diseases. Taking advantage of well characterized microarray datasets of NASH livers, we performed a systematic analysis of potential biomarkers and possible pathological mechanism of NASH from a bioinformatics perspective.CodeLink Human Whole Genome Bioarrays were analyzed to find differentially expressed genes (DEGs) between controls and NASH patients. Four methods were used to identify DEGs and the intersection of DEGs identified by these methods was subsequently used for both biomarker prediction and molecular pathological mechanism analysis. For biomarker prediction, rank aggregation was used to rank DEGs identified by all these methods according to their significance of different expression. Alcohol dehydrogenase 4 (ADH4) exhibited the highest rank suggesting the most significant differential expression between normal and disease condition. Together with the previous report demonstrating the association between ADH4 and the pathogenesis of NASH, our data suggest that ADH4 could be a potential biomarker for NASH. For molecular pathological mechanism analysis, two clusters of highly correlated annotation terms and genes in these terms were identified based on the intersection of DEGs. Then, pathways enriched with these genes were identified to construct the network. Using this network, both for the first time, amino acid catabolism is implicated to play a pivotal role and urea cycle is implicated to be involved in the development of NASH.The results of our study identified potential biomarkers and suggested possible molecular pathological mechanism of NASH. These findings provide a comprehensive and systematic understanding of the pathogenesis of NASH and may facilitate the diagnosis, prevention and treatment of NASH.
authors.affiliation: Department of Bioinformatics, Tongji University, Shanghai, PR China.
authors.forename: Yida
authors.initials: Y
authors.lastname: Zhang
authors.forename: Susan S
authors.initials: SS
authors.lastname: Baker
authors.forename: Robert D
authors.initials: RD
authors.lastname: Baker
authors.forename: Ruixin
authors.initials: R
authors.lastname: Zhu
authors.forename: Lixin
authors.initials: L
authors.lastname: Zhu
mesh_terms: D015415:Biomarkers / Q000378:metabolism*; D019295:Computational Biology; D005234:Fatty Liver / Q000235:genetics* / Q000473:pathology*; D020869:Gene Expression Profiling; D006801:Humans; D065626:Non-alcoholic Fatty Liver Disease; D020411:Oligonucleotide Array Sequence Analysis; D057089:Pathology, Molecular; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015398:Signal Transduction
chemical_list: D015415:Biomarkers; D012333:RNA, Messenger