ArticleNucleic acids research2022
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels.
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 26 papers.
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Who cites it
26 citing papers in PubMed.
- HuNT: A Reference Transcriptome Atlas for Human Normal Tissues.Phenomics (Cham, Switzerland) · 2026Article
- From Natural Discovery to AI-Guided Design: A Curated Collection of Compact Enhancers for Crop Engineering.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2026.Nucleic acids research · 2026Article
- Genome Variation Map: a platform for the analysis and integration of genomic variation.Nucleic acids research · 2026Article
- Computational methods and data resources for predicting tumor neoantigens.Briefings in bioinformatics · 2025Review
- Artificial Intelligence-Driven Drug Toxicity Prediction: Advances, Challenges, and Future Directions.Toxics · 2025Review
- Machine Learning-Enabled Drug-Induced Toxicity Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- Editome Disease Knowledgebase v2.0: an updated resource of editome-disease associations through literature curation and integrative analysis.Bioinformatics advances · 2025Article
- CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR.Database : the journal of biological databases and curation · 2024Article
- mosaicMPI: a framework for modular data integration across cohorts and -omics modalities.Nucleic acids research · 2024Article
- DeepFGRN: inference of gene regulatory network with regulation type based on directed graph embedding.Briefings in bioinformatics · 2024Article
- Global characterization of RNA editing in genetic regulation of multiple ovarian cancer subtypes.Molecular therapy. Nucleic acids · 2024Article
- Plant genomic resources at National Genomics Data Center: assisting in data-driven breeding applications.aBIOTECH · 2024Review
- Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024.Nucleic acids research · 2024Article
- TCOD: an integrated resource for tropical crops.Nucleic acids research · 2024Article
- BioKA: a curated and integrated biomarker knowledgebase for animals.Nucleic acids research · 2024Article
- From BIG Data Center to China National Center for Bioinformation.Genomics, proteomics & bioinformatics · 2023Article
- OrganoidDB: a comprehensive organoid database for the multi-perspective exploration of bulk and single-cell transcriptomic profiles of organoids.Nucleic acids research · 2023Article
- FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations.Nucleic acids research · 2023Article
- HGD: an integrated homologous gene database across multiple species.Nucleic acids research · 2023Article
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Authors and funding
20 authors.
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Abstract
Transcriptomic profiling is critical to uncovering functional elements from transcriptional and post-transcriptional aspects. Here, we present Gene Expression Nebulas (GEN, https://ngdc.cncb.ac.cn/gen/), an open-access data portal integrating transcriptomic profiles under various biological contexts. GEN features a curated collection of high-quality bulk and single-cell RNA sequencing datasets by using standardized data processing pipelines and a structured curation model. Currently, GEN houses a large number of gene expression profiles from 323 datasets (157 bulk and 166 single-cell), covering 50 500 samples and 15 540 169 cells across 30 species, which are further categorized into six biological contexts. Moreover, GEN integrates a full range of transcriptomic profiles on expression, RNA editing and alternative splicing for 10 bulk datasets, providing opportunities for users to conduct integrative analysis at both transcriptional and post-transcriptional levels. In addition, GEN provides abundant gene annotations based on value-added curation of transcriptomic profiles and delivers online services for data analysis and visualization. Collectively, GEN presents a comprehensive collection of transcriptomic profiles across multiple species, thus serving as a fundamental resource for better understanding genetic regulatory architecture and functional mechanisms from tissues to cells.
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