ArticleBMC bioinformatics2023
Empowering biologists to decode omics data: the Genekitr R package and web server.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
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- Surface CD81 supports leukemia stem cell function and reveals a therapeutic vulnerability in acute myeloid leukemia.Signal transduction and targeted therapy · 2026Article
- Evolutionarily informed gene sets reveal conserved and lineage-modified transcriptional programs during vertebrate forebrain evolution.bioRxiv : the preprint server for biology · 2026Article
- Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.iScience · 2026Article
- Cardiometabolic adaptations in the cave nectar bat Eonycteris spelaea.Communications biology · 2026Article
- Characterization of resistance to bacterial panicle blight in rice revealed by transcriptome and QTL mapping analyses.Frontiers in plant science · 2026Article
- LECT2 promotes liver regeneration across developmental stages by activating the ADAM10-NOTCH signaling pathway.Hepatology communications · 2025Article
- Transcriptomics-based analysis of acetate and propionate transport and metabolism in Yarrowia lipolytica.Biotechnology for biofuels and bioproducts · 2025Article
- Escherichia coli gene expression is influenced more by gut environmental changes from inflammation and microbiota modulation than by colitis severity.Scientific reports · 2025Article
- Mitochondrial ABHD11 inhibition drives sterol metabolism to modulate T-cell effector function.Nature communications · 2025Article
- Article
- Type I interferon protects against bone loss in periodontitis by mitigating an interleukin (IL)-17-neutrophil axis.Life sciences · 2025Article
- Dipeptidase-1-knockout mice develop invasive tumors with features of microsatellite-unstable colorectal cancer.JCI insight · 2025Article
- Altered huntingtin-chromatin interactions predict transcriptional and epigenetic changes in Huntington's disease.Disease models & mechanisms · 2025Article
- X-Linked Gene Dosage and SOX2 Act as Key Roadblocks for Human Germ Cell Specification in Klinefelter Syndrome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
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Authors and funding
2 authors.
Funding
Abstract
backgroundA variety of high-throughput analyses, such as transcriptome, proteome, and metabolome analysis, have been developed, producing unprecedented amounts of omics data. These studies generate large gene lists, of which the biological significance shall be deeply understood. However, manually interpreting these lists is difficult, especially for non-bioinformatics-savvy scientists.
resultsWe developed an R package and a corresponding web server-Genekitr, to assist biologists in exploring large gene sets. Genekitr comprises four modules: gene information retrieval, ID (identifier) conversion, enrichment analysis and publication-ready plotting. Currently, the information retrieval module can retrieve information on up to 23 attributes for genes of 317 organisms. The ID conversion module assists in ID-mapping of genes, probes, proteins, and aliases. The enrichment analysis module organizes 315 gene set libraries in different biological contexts by over-representation analysis and gene set enrichment analysis. The plotting module performs customizable and high-quality illustrations that can be used directly in presentations or publications.
conclusionsThis web server tool will make bioinformatics more accessible to scientists who might not have programming expertise, allowing them to perform bioinformatics tasks without coding.
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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 OpenQuestion graph.