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A compendium of monocyte transcriptome datasets to foster biomedical knowledge discovery
Darawan Rinchai1, Sabri Boughorbel2, Scott Presnell3
1Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar.
F1000Research
|May 10, 2016
Summary
Researchers can now explore a vast collection of human monocyte transcriptome data. The Gene Expression Browser (GXB) provides an interactive platform for analyzing immunological studies and discovering new insights from complex datasets.
Area of Science:
- Immunology
- Bioinformatics
- Genomics
Background:
- Systems-scale profiling generates large biomedical datasets.
- Public repositories store vast, heterogeneous data.
- Accessible interfaces are needed for data exploration.
Purpose of the Study:
- To describe a curated compendium of human monocyte immunological datasets.
- To introduce the Gene Expression Browser (GXB) as an interactive data analysis tool.
- To facilitate knowledge discovery from transcriptome profiles.
Main Methods:
- Compiled 93 public datasets (4,516 transcriptome profiles) from human monocyte studies.
- Uploaded data to a Gene Expression Browser (GXB) instance.
- Integrated study descriptions, sample annotations, and clinical/immunological data.
Main Results:
- Created a browsable compendium of human monocyte transcriptomics data.
- Enabled overlay of molecular data with rich contextual information.
- Generated ranked gene lists based on group comparisons within GXB.
Conclusions:
- The Gene Expression Browser (GXB) provides a valuable interface for exploring complex immunological datasets.
- This resource enhances the potential for insight and knowledge discovery in monocyte research.
- The curated compendium and GXB are publicly available for scientific use.
