ArticleNucleic acids research2022
TissueNexus: a database of human tissue functional gene networks built with a large compendium of curated RNA-seq data.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
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- Oculocutaneous albinism variants in 28 consanguineous families and functional classification of a pathogenic deep intron variant in TYR.European journal of human genetics : EJHG · 2026Article
- Identification and validation of key biomarkers of the glycolysis-ketone body metabolism in heart failure based on multi-omics and machine learning.Frontiers in cardiovascular medicine · 2025Article
- Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata.Briefings in bioinformatics · 2024Article
- LIMO-GCN: a linear model-integrated graph convolutional network for predicting Alzheimer disease genes.Briefings in bioinformatics · 2024Article
- Zinc Transporters Serve as Prognostic Predictors and their Expression Correlates with Immune Cell Infiltration in Specific Cancer: A Pan-cancer Analysis.Journal of Cancer · 2024Article
- Identification and characterization of bone/cartilage-associated signatures in common fibrotic skin diseases.Frontiers in genetics · 2023Article
- Article
- In vivo tumor immune microenvironment phenotypes correlate with inflammation and vasculature to predict immunotherapy response.Nature communications · 2022Article
- An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease.Briefings in bioinformatics · 2022Article
- Using genome-wide expression compendia to study microorganisms.Computational and structural biotechnology journal · 2022Review
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5 authors.
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Abstract
Mapping gene interactions within tissues/cell types plays a crucial role in understanding the genetic basis of human physiology and disease. Tissue functional gene networks (FGNs) are essential models for mapping complex gene interactions. We present TissueNexus, a database of 49 human tissue/cell line FGNs constructed by integrating heterogeneous genomic data. We adopted an advanced machine learning approach for data integration because Bayesian classifiers, which is the main approach used for constructing existing tissue gene networks, cannot capture the interaction and nonlinearity of genomic features well. A total of 1,341 RNA-seq datasets containing 52,087 samples were integrated for all of these networks. Because the tissue label for RNA-seq data may be annotated with different names or be missing, we performed intensive hand-curation to improve quality. We further developed a user-friendly database for network search, visualization, and functional analysis. We illustrate the application of TissueNexus in prioritizing disease genes. The database is publicly available at https://www.diseaselinks.com/TissueNexus/.
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