title: Mass spectrometry based proteomics profiling of human monocytes.
abstract: Human monocyte is an important cell type which is involved in various complex human diseases. To better understand the biology of human monocytes and facilitate further studies, we developed the first comprehensive proteome knowledge base specifically for human monocytes by integrating both in vivo and in vitro datasets. The top 2000 expressed genes from in vitro datasets and 779 genes from in vivo experiments were integrated into this study. Altogether, a total of 2237 unique monocyte-expressed genes were cataloged. Biological functions of these monocyte-expressed genes were annotated and classified via Gene Ontology (GO) analysis. Furthermore, by extracting the overlapped genes from in vivo and in vitro datasets, a core gene list including 541 unique genes was generated. Based on the core gene list, further gene-disease associations, pathway and network analyses were performed. Data analyses based on multiple bioinformatics tools produced a large body of biologically meaningful information, and revealed a number of genes such as SAMHD1, G6PD, GPD2 and ENO1, which have been reported to be related to immune response, blood biology, bone remodeling, and cancer respectively. As a unique resource, this study can serve as a reference map for future in-depth research on monocytes biology and monocyte-involved human diseases.
authors.affiliation: College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.|Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zeng
authors.affiliation: Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.|Laboratory of Proteins and Proteomics, Department of Epidemiology, Soochow University School of Public Health, Suzhou, 205123, China.
authors.forename: Fei-Yan
authors.initials: FY
authors.lastname: Deng
authors.affiliation: Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.|College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zhu
authors.affiliation: Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.
authors.forename: Lan
authors.initials: L
authors.lastname: Zhang
authors.affiliation: Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: He
authors.affiliation: Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.
authors.forename: Chao
authors.initials: C
authors.lastname: Xu
authors.affiliation: Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.
authors.forename: Qing
authors.initials: Q
authors.lastname: Tian
authors.affiliation: Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.
authors.forename: Ji-Gang
authors.initials: JG
authors.lastname: Zhang
authors.affiliation: College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.
authors.forename: Li-Shu
authors.initials: LS
authors.lastname: Zhang
authors.affiliation: College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.
authors.forename: Hong-Gang
authors.initials: HG
authors.lastname: Hu
authors.affiliation: College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China. hdeng2@tulane.edu.|Center of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA. hdeng2@tulane.edu.
authors.forename: Hong-Wen
authors.initials: HW
authors.lastname: Deng
mesh_terms: D000368:Aged; D014408:Biomarkers, Tumor / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism; D005260:Female; D005954:Glucosephosphate Dehydrogenase / Q000378:metabolism; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D008875:Middle Aged; D009000:Monocytes / Q000378:metabolism*; D020559:Monomeric GTP-Binding Proteins / Q000378:metabolism; D010751:Phosphopyruvate Hydratase / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D000076106:SAM Domain and HD Domain-Containing Protein 1; D025521:Tumor Suppressor Proteins / Q000378:metabolism
chemical_list: D014408:Biomarkers, Tumor; D004268:DNA-Binding Proteins; D025521:Tumor Suppressor Proteins; D005954:Glucosephosphate Dehydrogenase; D000076106:SAM Domain and HD Domain-Containing Protein 1; C484280:SAMHD1 protein, human; D020559:Monomeric GTP-Binding Proteins; C095157:ENO1 protein, human; D010751:Phosphopyruvate Hydratase
keywords: gene ontology; gene-disease association; human monocytes; network analysis; proteomics knowledgebase