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About CSEA-DB (Cell-type-Specific Enrichment Analysis DataBase)
- CSEA-DB is an omnibus for systematic exploration of human complex trait and cell type associations. Previously, we developed an algorithm, deTS (R package) to decode tissue specificity and built the Tissue-Specific Enrichment Analysis DataBase (TSEA-DB). In this work, we leveraged the fast-growing single-cell transcriptome profiling for human tissues generated by multiple international consortiums (e.g. Human Cell Landscape, The Human Lung Cell Atlas) and literature resources to conduct the cell type-specific enrichment analysis (CSEA) modified from deTS. Currently, CSEA-DB maintained the CSEA results for 13,756 sets of trait-associated gene (TAG) sets specifically-expressed cell types among 752 tissue-cell types. Overall, we identified a total of 598 (11.68 % of 5120) GWAS traits with at least one Bonferroni corrected significant association with at least one tissue-cell type (TC) and a total of 460 (61.17 % of the 752) TCs have at least one Bonferroni corrected significant association with at least one GWAS disease or trait. Interestingly, we identified multiple traits that are associated with the same tissue cell type, indicating the potential comorbidity and shared genetic basis of these traits. On the other hand, multiple cells in one tissue could be found associated with the same phenotype, indicating that these cells in the same tissue will work collaboratively to contribute to the phenotype. Users can browse and search the traits and single-cell tissue panel information. Users could also filter, prioritize, and compare the CSEA results from cell types from one or multiple tissues. CSEA-DB could also serve as a respiratory of human complex diseases and traits information and human sinlge-cell transcriptome data sources. Overall, CSEA-DB finemaps the genetic signals at cellular resolution and sheds light on the underlying mechanism of human complex traits and diseases. For detail of usage of this database please see the documentation.
Dataset panels
- Multi-Trait Collection (MTC): 432 GWAS summary statistics datasets for more than 200 human complex traits and diseases adapted from other curators. (Data source) More...
- UK Biobank (UKBB): 4372 GWAS summary statistics adapted from Ben Neale’s lab . (Data source) More..
- Expanded Trait Collection (ETC): 316 GWAS summary statistics curated from GWAS catalog and literature. More...
- Single-cell Transcriptome Panel: 71 human tissues datasets across all 11 organ systems adapted from Human Cell Landscape, Human cell atlas , Single Cell Expression Atlas , and literature, with unique annotated ~100 cell types and overall 752 tissue-cell types. Tissues and cell types are further annotated with the Uberon and Cell Ontology. More...
Developer
- Ruifeng Hu (Author, Website maintainer)
- Yulin Dai (Author, Data source maintainer)
- Astrid Manuel (Author, GWAS Data source curator)
- Andi Liu (Author, single-cell expression Data source curator)
- Peilin Jia (Author, Website maintainer)
- Zhongming Zhao (Author, Website maintainer)
Citation:
- Yulin Dai†, Ruifeng Hu†, Astrid M. Manual, Andi Liu, Peilin Jia*, Zhongming Zhao*, CSEA-DB: An omnibus for human complex trait and cell type associations,Nucleic Acids Research, gkaa1064, https://doi.org/10.1093/nar/gkaa1064.
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News
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October 15, 2020
Minor update to documents
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August 13, 2020
CSEA-DB V1.0 release!
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July 26, 2020
Cell Ontology annotation finish.
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July 15, 2020
Collected more human tissue single-cell data from Single Cell Expression Atlas.
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July 5, 2020
Uberon annotation finish.
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June 29, 2020
More advanced functions were under construction, including the comparison of enriched cell types between multiple traits.
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June 28, 2020
Essential functions have been deployed on the website for testing.
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June 15, 2020
CSEA for > 5000 traits among 534 tissue-cell types was conducted.
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May 20, 2020
Tissue single-cell transcriptome panel was curated and preprocessed.
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May 18, 2020
GWAS summary statistics update was frozen and start preprocessing.
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Feb 03, 2020
GWAS summary statistics update was started.
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Nov 25, 2019
Traits-associated genes sets were calculated by an updated pipeline using Magma.