ArticleCell systems2017
Comprehensive Analysis of Tissue-wide Gene Expression and Phenotype Data Reveals Tissues Affected in Rare Genetic Disorders.
Article in Cell systems, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 22 citations in OpenAlex.
- Tissue-specific expression and regulation of congenital disorders of glycosylation genes: A GTEx-based in silico study.Molecular genetics and metabolism reports · 2026Article
- Exploring cell-type associations of rare disease phenotypes using non-diseased cell atlases.Briefings in bioinformatics · 2026Article
- Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes.Bioinformatics (Oxford, England) · 2024Article
- STIGMA: Single-cell tissue-specific gene prioritization using machine learning.American journal of human genetics · 2024Article
- Identification of genetic mechanisms for tissue-specific genetic effects based on CRISPR screens.Genetics · 2022Article
- scMAPA: Identification of cell-type-specific alternative polyadenylation in complex tissues.GigaScience · 2022Article
- Profiling the Genome-Wide Landscape of Short Tandem Repeats by Long-Read Sequencing.Frontiers in genetics · 2022Article
- Prioritizing and characterizing functionally relevant genes across human tissues.PLoS computational biology · 2021Article
- PathExt: a general framework for path-based mining of omics-integrated biological networks.Bioinformatics (Oxford, England) · 2021Article
- An analytical method for the identification of cell type-specific disease gene modules.Journal of translational medicine · 2021Article
- Pheno-RNA, a method to associate genes with a specific phenotype, identifies genes linked to cellular transformation.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Article
- Improving the diagnostic yield of exome- sequencing by predicting gene-phenotype associations using large-scale gene expression analysis.Nature communications · 2019Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Linking putatively pathogenic variants to the tissues they affect is necessary for determining the correct diagnostic workup and therapeutic regime in undiagnosed patients. Here, we explored how gene expression across healthy tissues can be used to infer this link. We integrated 6,665 tissue-wide transcriptomes with genetic disorder knowledge bases covering 3,397 diseases. Receiver-operating characteristics (ROC) analysis using expression levels in each tissue and across tissues indicated significant but modest associations between elevated expression and phenotype for most tissues (maximum area under ROC curve = 0.69). At extreme elevation, associations were marked. Upregulation of disease genes in affected tissues was pronounced for genes associated with autosomal dominant over recessive disorders. Pathways enriched for genes expressed and associated with phenotypes highlighted tissue functionality, including lipid metabolism in spleen and DNA repair in adipose tissue. These results suggest features useful for evaluating the likelihood of particular tissue manifestations in genetic disorders. The web address of an interactive platform integrating these data is provided.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.