title: Common Marker Genes Identified from Various Sample Types for Systemic Lupus Erythematosus.
abstract: OBJECTIVE
  Systemic lupus erythematosus (SLE) is a complex auto-immune disease. Gene expression studies have been conducted to identify SLE-related genes in various types of samples. It is unknown whether there are common marker genes significant for SLE but independent of sample types, which may have potentials for follow-up translational research. The aim of this study is to identify common marker genes across various sample types for SLE.
  
  
  METHODS
  Based on four public microarray gene expression datasets for SLE covering three representative types of blood-born samples (monocyte; peripheral blood mononuclear cell, PBMC; whole blood), we utilized three statistics (fold-change, FC; t-test p value; false discovery rate adjusted p value) to scrutinize genes simultaneously regulated with SLE across various sample types. For common marker genes, we conducted the Gene Ontology enrichment analysis and Protein-Protein Interaction analysis to gain insights into their functions.
  
  
  RESULTS
  We identified 10 common marker genes associated with SLE (IFI6, IFI27, IFI44L, OAS1, OAS2, EIF2AK2, PLSCR1, STAT1, RNASE2, and GSTO1). Significant up-regulation of IFI6, IFI27, and IFI44L with SLE was observed in all the studied sample types, though the FC was most striking in monocyte, compared with PBMC and whole blood (8.82-251.66 vs. 3.73-74.05 vs. 1.19-1.87). Eight of the above 10 genes, except RNASE2 and GSTO1, interact with each other and with known SLE susceptibility genes, participate in immune response, RNA and protein catabolism, and cell death.
  
  
  CONCLUSIONS
  Our data suggest that there exist common marker genes across various sample types for SLE. The 10 common marker genes, identified herein, deserve follow-up studies to dissert their potentials as diagnostic or therapeutic markers to predict SLE or treatment response.
authors.affiliation: Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu 215123, P. R. China.|Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu 215123, P. R. China.
authors.forename: Peng-Fei
authors.initials: PF
authors.lastname: Bing
authors.affiliation: Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu 215123, P. R. China.|Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu 215123, P. R. China.
authors.forename: Wei
authors.initials: W
authors.lastname: Xia
authors.affiliation: Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu 215123, P. R. China.|Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu 215123, P. R. China.
authors.forename: Lan
authors.initials: L
authors.lastname: Wang
authors.affiliation: Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu 215123, P. R. China.
authors.forename: Yong-Hong
authors.initials: YH
authors.lastname: Zhang
authors.affiliation: Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu 215123, P. R. China.|Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu 215123, P. R. China.
authors.forename: Shu-Feng
authors.initials: SF
authors.lastname: Lei
authors.affiliation: Center for Genetic Epidemiology and Genomics, School of Public Health, Soochow University, Suzhou, Jiangsu 215123, P. R. China.|Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, School of Public Health, Soochow University, Suzhou, Jiangsu 215123, P. R. China.
authors.forename: Fei-Yan
authors.initials: FY
authors.lastname: Deng
mesh_terms: D015088:2',5'-Oligoadenylate Synthetase / Q000235:genetics; D000293:Adolescent; D000328:Adult; D000368:Aged; D047208:Eosinophil-Derived Neurotoxin / Q000235:genetics; D005260:Female; D015870:Gene Expression / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D055106:Genome-Wide Association Study; D005982:Glutathione Transferase / Q000235:genetics; D006801:Humans; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D008180:Lupus Erythematosus, Systemic / Q000235:genetics*; D008297:Male; D008565:Membrane Proteins / Q000235:genetics; D008875:Middle Aged; D024101:Mitochondrial Proteins / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D011485:Protein Binding / Q000235:genetics; D050794:STAT1 Transcription Factor / Q000235:genetics; D055815:Young Adult; D019892:eIF-2 Kinase / Q000235:genetics
chemical_list: D005819:Genetic Markers; C406887:IFI27 protein, human; C468762:IFI6 protein, human; D008565:Membrane Proteins; D024101:Mitochondrial Proteins; D050794:STAT1 Transcription Factor; C494079:STAT1 protein, human; C490476:GSTO1 protein, human; D005982:Glutathione Transferase; C000602769:EIF2AK2 protein, human; D019892:eIF-2 Kinase; C475085:OAS1 protein, human; C000607948:OAS2 protein, human; D015088:2',5'-Oligoadenylate Synthetase; D047208:Eosinophil-Derived Neurotoxin; C479221:RNASE2 protein, human