title: Gene expression profiling combined with bioinformatics analysis identify biomarkers for Parkinson disease.
abstract: Parkinson disease (PD) progresses relentlessly and affects approximately 4% of the population aged over 80 years old. It is difficult to diagnose in its early stages. The purpose of our study is to identify molecular biomarkers for PD initiation using a computational bioinformatics analysis of gene expression. We downloaded the gene expression profile of PD from Gene Expression Omnibus and identified differentially coexpressed genes (DCGs) and dysfunctional pathways in PD patients compared to controls. Besides, we built a regulatory network by mapping the DCGs to known regulatory data between transcription factors (TFs) and target genes and calculated the regulatory impact factor of each transcription factor. As the results, a total of 1004 genes associated with PD initiation were identified. Pathway enrichment of these genes suggests that biological processes of protein turnover were impaired in PD. In the regulatory network, HLF, E2F1 and STAT4 were found have altered expression levels in PD patients. The expression levels of other transcription factors, NKX3-1, TAL1, RFX1 and EGR3, were not found altered. However, they regulated differentially expressed genes. In conclusion, we suggest that HLF, E2F1 and STAT4 may be used as molecular biomarkers for PD; however, more work is needed to validate our result.
authors.affiliation: Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, China.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Diao
authors.forename: Xinxing
authors.initials: X
authors.lastname: Li
authors.forename: Sheng
authors.initials: S
authors.lastname: Hu
authors.forename: Yunhui
authors.initials: Y
authors.lastname: Liu
mesh_terms: D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D050976:Basic-Leucine Zipper Transcription Factors / Q000235:genetics; D015415:Biomarkers / Q000032:analysis* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D004268:DNA-Binding Proteins / Q000235:genetics; D050687:E2F1 Transcription Factor / Q000235:genetics; D051776:Early Growth Response Protein 3 / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D010300:Parkinson Disease / Q000235:genetics* / Q000378:metabolism*; D011518:Proto-Oncogene Proteins / Q000235:genetics; D000071701:Regulatory Factor X Transcription Factors; D000071716:Regulatory Factor X1; D050797:STAT4 Transcription Factor / Q000235:genetics; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; D014157:Transcription Factors / Q000235:genetics
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D050976:Basic-Leucine Zipper Transcription Factors; D015415:Biomarkers; D004268:DNA-Binding Proteins; D050687:E2F1 Transcription Factor; D051776:Early Growth Response Protein 3; D018398:Homeodomain Proteins; D011518:Proto-Oncogene Proteins; D000071701:Regulatory Factor X Transcription Factors; D000071716:Regulatory Factor X1; D050797:STAT4 Transcription Factor; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; D014157:Transcription Factors; C493753:E2F1 protein, human; C079945:EGR3 protein, human; C490671:HLF protein, human; C491178:NKX3-1 protein, human; C000605537:RFX1 protein, human; C494090:STAT4 protein, human; C067143:TAL1 protein, human