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Published on: December 26, 2013
Mass spectrometry based proteomics profiling of human monocytes
Yong Zeng1,2, Fei-Yan Deng2,3, Wei Zhu2,4
1College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.
Insights
Researchers created a comprehensive human monocyte proteome knowledge base by integrating in vivo and in vitro data. This resource catalogs 2237 genes, aiding future studies on monocyte biology and diseases.
Area of Science:
- Immunology
- Proteomics
- Genomics
Background:
- Human monocytes are crucial in various diseases.
- Understanding monocyte biology requires comprehensive data integration.
Purpose of the Study:
- To develop the first comprehensive proteome knowledge base for human monocytes.
- To integrate in vivo and in vitro datasets for a unified view of monocyte gene expression.
Main Methods:
- Integrated top 2000 expressed genes from in vitro and 779 genes from in vivo datasets.
- Cataloged 2237 unique monocyte-expressed genes.
- Performed Gene Ontology (GO) analysis for functional annotation.
Main Results:
- Generated a core gene list of 541 unique genes from overlapping in vivo and in vitro data.
- Identified key genes (e.g., SAMHD1, G6PD) linked to immune response, blood biology, bone remodeling, and cancer.
- Performed gene-disease, pathway, and network analyses on the core gene list.
Conclusions:
- The developed knowledge base serves as a unique reference map for monocyte research.
- Facilitates in-depth studies on monocyte biology and associated human diseases.
- Provides biologically meaningful information through integrated data analysis.
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.
