The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment
Open accessAbstract
Cancer immunotherapy targeting co-inhibitory pathways by checkpoint blockade shows remarkable efficacy in a variety of cancer types. However, only a minority of patients respond to treatment due to the stochastic heterogeneity of tumor microenvironment (TME). Recent advances in single-cell RNA-seq technologies enabled comprehensive characterization of the immune system heterogeneity in tumors but posed computational challenges on integrating and utilizing the massive published datasets to inform immunotherapy. Here, we present Tumor Immune Single Cell Hub (TISCH, http://tisch.comp-genomics.org), a large-scale curated database that integrates single-cell transcriptomic profiles of nearly 2 million cells from 76 high-quality tumor datasets across 27 cancer types. All the data were uniformly processed with a standardized workflow, including quality control, batch effect removal, clustering, cell-type annotation, malignant cell classification, differential expression analysis and functional enrichment analysis. TISCH provides interactive gene expression visualization across multiple datasets at the single-cell level or cluster level, allowing systematic comparison between different cell-types, patients, tissue origins, treatment and response groups, and even different cancer-types. In summary, TISCH provides a user-friendly interface for systematically visualizing, searching and downloading gene expression atlas in the TME from multiple cancer types, enabling fast, flexible and comprehensive exploration of the TME.
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Cites
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PD-1 and PD-L1 Immune Checkpoint Blockade to Treat Breast Cancer
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Comprehensive Integration of Single-Cell Data
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Cited by
Han, Y., Wang, Y., Dong, X., Sun, D., Liu, Z., Yue, J., Wang, H., Li, T., & Wang, C. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac959 · Cited by 630
Self-citationTherapeutically Increasing MHC-I Expression Potentiates Immune Checkpoint Blockade
Gu, S. S., Zhang, W., Wang, X., Jiang, P., Traugh, N., Li, Z., Meyer, C., Stewig, B., Xie, Y., Bu, X., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-20-0812 · Cited by 273
Self-citationBig data in basic and translational cancer research
Jiang, P., Sinha, S., Aldape, K., Hannenhalli, S., Sahinalp, C., & Ruppin, E. (2022) · Nature Reviews Cancer · doi:10.1038/s41568-022-00502-0 · Cited by 254
DISCO: A database of Deeply Integrated human Single-Cell Omics data
Li, M., Zhang, X., Ang, K. S., Ling, J., Sethi, R., Lee, N. Y. S., Ginhoux, F., & Chen, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab1020 · Cited by 205
Statistical and machine learning methods for spatially resolved transcriptomics data analysis
Zeng, Z., Li, Y., Li, Y., & Luo, Y. (2022) · Genome Biology · doi:10.1186/s13059-022-02653-7 · Cited by 186
Metadata
- Authors
- Sun, D., Wang, J., Han, Y., Dong, X., Ge, J., Zheng, R., Shi, X., Wang, B., Li, Z., Ren, P., Sun, L., Yan, Y., Zhang, P., Zhang, F., Li, T., & Wang, C.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-11-12
- Volume
- 49
- Issue
- D1
- Pages
- D1420-D1430
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W3103119004
- Cited by
- 1,082
- References
- 45
- FWCI
- 34.23
- Type
- journal article
- Language
- en
- Open access
- gold
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- Sun, D., Wang, J., Han, Y., Dong, X., Ge, J., Zheng, R., Shi, X., Wang, B., Li, Z., Ren, P., Sun, L., Yan, Y., Zhang, P., Zhang, F., Li, T., & Wang, C. (2021). TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa1020
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