ArticleBMC bioinformatics2016
Tissue enrichment analysis for C. elegans genomics.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers.
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Who cites it
127 citing papers in PubMed.
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- tRNA-derived RNA processing in sperm transmits non-genetically inherited phenotypes to offspring in C. elegans.Nature communications · 2026Article
- Transcriptome- and phenotype-based epistasis analysis in Caenorhabditis elegans reveals daf-16/FoxO-dependent and independent effects of daf-2/InsR in L1 starvation and recovery.G3 (Bethesda, Md.) · 2026Article
- Increased FICD-mediated protein AMPylation triggers conserved endoplasmic reticulum stress signaling across species.Cell stress & chaperones · 2026Article
- Widespread intron retention and exon skipping characterise alternative splicing changes in a C. elegans model of spinal muscular atrophy.Human molecular genetics · 2026Article
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- The GPCR NMUR-1 mediates neural regulation of energy homeostasis in response to pathogen infection.Infection and immunity · 2025Article
- Cohesin forms fountains at active enhancers in C. elegans.Nature communications · 2025Article
- AMPK modulates a DEAH box RNA-helicase to attenuate TOR signaling and establish developmental quiescence in Caenorhabditis elegans.PLoS biology · 2025Article
- Different gametogenesis states uniquely impact longevity in Caenorhabditis elegans.Nature communications · 2025Article
- The chromatin remodeler LET-418/Mi-2 regulates the intracellular pathogen response in the C. elegans intestine.BMC genomics · 2025Article
- Article
67 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
backgroundOver the last ten years, there has been explosive development in methods for measuring gene expression. These methods can identify thousands of genes altered between conditions, but understanding these datasets and forming hypotheses based on them remains challenging. One way to analyze these datasets is to associate ontologies (hierarchical, descriptive vocabularies with controlled relations between terms) with genes and to look for enrichment of specific terms. Although Gene Ontology (GO) is available for Caenorhabditis elegans, it does not include anatomical information.
resultsWe have developed a tool for identifying enrichment of C. elegans tissues among gene sets and generated a website GUI where users can access this tool. Since a common drawback to ontology enrichment analyses is its verbosity, we developed a very simple filtering algorithm to reduce the ontology size by an order of magnitude. We adjusted these filters and validated our tool using a set of 30 gold standards from Expression Cluster data in WormBase. We show our tool can even discriminate between embryonic and larval tissues and can even identify tissues down to the single-cell level. We used our tool to identify multiple neuronal tissues that are down-regulated due to pathogen infection in C. elegans.
conclusionsOur Tissue Enrichment Analysis (TEA) can be found within WormBase, and can be downloaded using Python's standard pip installer. It tests a slimmed-down C. elegans tissue ontology for enrichment of specific terms and provides users with a text and graphic representation of the results.
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