Dongqing Sun; Jin Wang; Ya Han; Xin Dong; Jun Ge; Rongbin Zheng; Xiaoying Shi; Binbin Wang; Ziyi Li; Pengfei Ren; Liangdong Sun; Yilv Yan; Peng Zhang; Fan Zhang; Taiwen Li; Chenfei Wang · 2020 · Nucleic Acids Research
Paper
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.
Analysis
TISCH is a curated database integrating single-cell transcriptomic profiles from numerous tumor datasets to facilitate the exploration and visualization of the tumor microenvironment (TME) for immunotherapy research.
Discovery
Ruby Srivastava
Karthick Vasudevan; T Dhanushkumar; Sripad Rama Hebbar; Prasanna Kumar Selvam; Majji Rambabu; K. Anbarasu; Rohini Karunakaran
Dariush Haghmorad; Majid Eslami; Niloufar Orooji; Iryna Halabitska; Iryna Kamyshna; Oleksandr Kamyshnyi; Valentyn Oksenych
Zachary Sethna; Pablo Guasp; Charlotte Reiche; Martina Milighetti; Nicholas Ceglia; Erin Patterson; Jayon Lihm; George C. Payne; Olga Lyudovyk; Luis A. Rojas; Nan Pang; Akihiro Ohmoto; Masataka Amisaki; Abderezak Zebboudj; Zagaa Odgerel; Emmanuel M. Bruno; Siqi Linsey Zhang; C. K. Cheng; Yuval Elhanati; Evelyna Derhovanessian; Luisa Manning; Felicitas Müller; Ina Rhee; Mahesh Yadav; Taha Merghoub; Jedd D. Wolchok; Olca Baştürk; Mithat Gönen; Andrew S. Epstein; Parisa Momtaz; Wungki Park; Ryan Sugarman; Anna M. Varghese; Elizabeth Won; Avni M. Desai; Alice C. Wei; Michael I. D’Angelica; T. Peter Kingham; Kevin C. Soares; William R. Jarnagin; Jeffrey A. Drebin; Eileen M. O’Reilly; Ira Mellman; Uğur Şahin; Özlem Türeci; Benjamin D. Greenbaum; Vinod P. Balachandran
David A. Braun; Giorgia Moranzoni; Vipheaviny Chea; Bradley A. McGregor; Eryn Blass; Chloe Ran Tu; Allison P. Vanasse; Cleo Forman; Juliet Forman; Alexander B. Afeyan; Nicholas Schindler; Yiwen Liu; Shuqiang Li; Jackson Southard; Steven L. Chang; Michelle S. Hirsch; Nicole R. LeBoeuf; Oriol Olive; Ambica Mehndiratta; Haley Greenslade; Keerthi Shetty; Susan Klaeger; Siranush Sarkizova; Christina B. Pedersen; Matthew Mossanen; Isabel Carulli; Anna Tarren; Joseph Duke-Cohan; Alexis A. Howard; J. Bryan Iorgulescu; Bohoon Shim; Jeremy M. Simon; Sabina Signoretti; Jon C. Aster; Liudmila Elagina; Steven A. Carr; Ignaty Leshchiner; Gad Getz; Stacey Gabriel; Nir Hacohen; Lars Rønn Olsen; Giacomo Oliveira; Donna Neuberg; Kenneth J. Livak; Sachet A. Shukla; Edward F. Fritsch; Catherine J. Wu; Derin B. Keskin; Patrick A. Ott; Toni K. Choueiri
Ting Fan; Congcong Xu; Jichuan Wu; Yihua Cai; WuQiang Cao; Haifa Shen; Mingna Zhang; Hanfei Zhu; Jingxian Yang; Zhounan Zhu; Xiaopin Ma; Jiale Ren; Lei Huang; Qianyun Li; Yuying Tang; Bo Yu; Chunxiu Chen; Mingcheng Xu; Qiuhe Wang; Zhuya Xu; Fengjia Chen; Shujing Liang; Zhixian Zhong; Anmbreen Jamroze; Dean G. Tang; Hangwen Li; Chunyan Dong
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