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...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2016-11-01
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| Series: | Protein & Cell |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1007/s13238-016-0342-x |
| _version_ | 1797714685645029376 |
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| author | Yong Zeng Fei-Yan Deng Wei Zhu Lan Zhang Hao He Chao Xu Qing Tian Ji-Gang Zhang Li-Shu Zhang Hong-Gang Hu Hong-Wen Deng |
| author_facet | Yong Zeng Fei-Yan Deng Wei Zhu Lan Zhang Hao He Chao Xu Qing Tian Ji-Gang Zhang Li-Shu Zhang Hong-Gang Hu Hong-Wen Deng |
| author_sort | Yong Zeng |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-12T07:55:37Z |
| format | Article |
| id | doaj.art-2e015b28117d43a2808187439172f9e5 |
| institution | Directory Open Access Journal |
| issn | 1674-800X 1674-8018 |
| language | English |
| last_indexed | 2024-03-12T07:55:37Z |
| publishDate | 2016-11-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | Protein & Cell |
| spelling | doaj.art-2e015b28117d43a2808187439172f9e52023-09-02T20:14:01ZengOxford University PressProtein & Cell1674-800X1674-80182016-11-018212313310.1007/s13238-016-0342-xMass spectrometry based proteomics profiling of human monocytesYong Zeng0Fei-Yan Deng1Wei Zhu2Lan Zhang3Hao He4Chao Xu5Qing Tian6Ji-Gang Zhang7Li-Shu Zhang8Hong-Gang Hu9Hong-Wen Deng10College of Life Sciences and Bioengineering, Beijing Jiaotong UniversityCenter of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical MedicineCenter of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical MedicineCenter of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical MedicineCenter of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical MedicineCenter of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical MedicineCenter of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical MedicineCenter of Bioinformatics and Genomics, Tulane University School of Public Health and Tropical MedicineCollege of Life Sciences and Bioengineering, Beijing Jiaotong UniversityCollege of Life Sciences and Bioengineering, Beijing Jiaotong UniversityCollege of Life Sciences and Bioengineering, Beijing Jiaotong UniversityAbstract 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.http://link.springer.com/article/10.1007/s13238-016-0342-xhuman monocytesproteomics knowledgebasegene ontologygene-disease associationnetwork analysis |
| spellingShingle | Yong Zeng Fei-Yan Deng Wei Zhu Lan Zhang Hao He Chao Xu Qing Tian Ji-Gang Zhang Li-Shu Zhang Hong-Gang Hu Hong-Wen Deng Mass spectrometry based proteomics profiling of human monocytes Protein & Cell human monocytes proteomics knowledgebase gene ontology gene-disease association network analysis |
| title | Mass spectrometry based proteomics profiling of human monocytes |
| title_full | Mass spectrometry based proteomics profiling of human monocytes |
| title_fullStr | Mass spectrometry based proteomics profiling of human monocytes |
| title_full_unstemmed | Mass spectrometry based proteomics profiling of human monocytes |
| title_short | Mass spectrometry based proteomics profiling of human monocytes |
| title_sort | mass spectrometry based proteomics profiling of human monocytes |
| topic | human monocytes proteomics knowledgebase gene ontology gene-disease association network analysis |
| url | http://link.springer.com/article/10.1007/s13238-016-0342-x |
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