ArticleProceedings of the National Academy of Sciences of the United States of America2016
Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
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- Correlation of blood-based immune molecules with cardiac gene expression profiles reveals insights into Chagas cardiomyopathy pathogenesis.Frontiers in immunology · 2024Article
- FBXO11 constitutes a major negative regulator of MHC class II through ubiquitin-dependent proteasomal degradation of CIITA.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Steroid receptor coactivator 3 is a key modulator of regulatory T cell-mediated tumor evasion.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- RNA2Immune: A Database of Experimentally Supported Data Linking Non-coding RNA Regulation to The Immune System.Genomics, proteomics & bioinformatics · 2023Article
- COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations.Nucleic acids research · 2023Article
- Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization.Frontiers in immunology · 2023Article
- The NNature communications · 2022Article
- ATG101-related signature predicts prognosis and therapeutic option in hepatocellular carcinoma.Scientific reports · 2022Article
- Approaches in Gene Coexpression Analysis in Eukaryotes.Biology · 2022Review
- PARK7/DJ-1 promotes pyruvate dehydrogenase activity and maintains TNature metabolism · 2022Article
- Single-cell RNA sequencing coupled to TCR profiling of large granular lymphocyte leukemia T cells.Nature communications · 2022Article
- Evaluation of critical data processing steps for reliable prediction of gene co-expression from large collections of RNA-seq data.PloS one · 2022Article
- Sustained expression of inflammatory monocytes and activated T cells in COVID-19 patients and recovered convalescent plasma donors.Immunity, inflammation and disease · 2021Article
- Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review.Biomolecules · 2021Review
- Monocyte-driven atypical cytokine storm and aberrant neutrophil activation as key mediators of COVID-19 disease severity.Nature communications · 2021Article
- Brazilian green propolis promotes TNFR2 expression on regulatory T cells.Food science & nutrition · 2021Article
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
High-throughput gene expression data are one of the primary resources for exploring complex intracellular dynamics in modern biology. The integration of large amounts of public data may allow us to examine general dynamical relationships between regulators and target genes. However, obstacles for such analyses are study-specific biases or batch effects in the original data. Here we present Immuno-Navigator, a batch-corrected gene expression and coexpression database for 24 cell types of the mouse immune system. We systematically removed batch effects from the underlying gene expression data and showed that this removal considerably improved the consistency between inferred correlations and prior knowledge. The data revealed widespread cell type-specific correlation of expression. Integrated analysis tools allow users to use this correlation of expression for the generation of hypotheses about biological networks and candidate regulators in specific cell types. We show several applications of Immuno-Navigator as examples. In one application we successfully predicted known regulators of importance in naturally occurring Treg cells from their expression correlation with a set of Treg-specific genes. For one high-scoring gene, integrin β8 (Itgb8), we confirmed an association between Itgb8 expression in forkhead box P3 (Foxp3)-positive T cells and Treg-specific epigenetic remodeling. Our results also suggest that the regulation of Treg-specific genes within Treg cells is relatively independent of Foxp3 expression, supporting recent results pointing to a Foxp3-independent component in the development of Treg cells.
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