xCell: digitally portraying the tissue cellular heterogeneity landscape
TLDR
This work presents xCell, a novel gene signature-based method, and uses it to infer 64 immune and stromal cell types and shows that xCell outperforms other methods.Abstract:
Tissues are complex milieus consisting of numerous cell types. Several recent methods have attempted to enumerate cell subsets from transcriptomes. However, the available methods have used limited sources for training and give only a partial portrayal of the full cellular landscape. Here we present xCell, a novel gene signature-based method, and use it to infer 64 immune and stromal cell types. We harmonized 1822 pure human cell type transcriptomes from various sources and employed a curve fitting approach for linear comparison of cell types and introduced a novel spillover compensation technique for separating them. Using extensive in silico analyses and comparison to cytometry immunophenotyping, we show that xCell outperforms other methods. xCell is available at http://xCell.ucsf.edu/ .read more
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The GTEx Consortium atlas of genetic regulatory effects across human tissues
François Aguet,Alvaro N. Barbeira,Rodrigo Bonazzola,Andrew A. Brown,SE Castel,Brian Jo,Silva Kasela,Sarah Kim-Hellmuth,Yanyu Liang,Meritxell Oliva,Elise D. Flynn,Princy Parsana,Laure Fresard,Eric R. Gamazon,Andrew R. Hamel,Yuan He,Farhad Hormozdiari,Pejman Mohammadi,Manuel Muñoz-Aguirre,YoSon Park,Ashis Saha,Ayellet V. Segrè,Benjamin J. Strober,Xiaoquan Wen,Wucher,Kristin G. Ardlie,Alexis Battle,Christopher D. Brown,Nancy J. Cox,Souvik Das,Emmanouil T. Dermitzakis,Barbara E. Engelhardt,D Garrido-Martin,Gad Getz,Roderic Guigó,Robert E. Handsaker,Paul J. Hoffman,Hae Kyung Im,Seva Kashin,Alan Kwong,Lappalainen T,Xiao Li,Daniel G. MacArthur,Stephen B. Montgomery,John M. Rouhana,Matthew Stephens,Barbara E. Stranger,Ellen Todres,Ana Viñuela,Gao Wang,Yuxin Zou,Shankara Anand,S. Gabriel,Aaron Graubert,Kane Hadley,Katherine H. Huang,Meier,Jared L. Nedzel,Duyen T. Nguyen,Brunilda Balliu,Donald F. Conrad,Daniel J. Cotter,OM deGoede,Jonah Einson,Eskin E,Tiffany Eulalio,Nicole M. Ferraro,Michael J. Gloudemans,Lei Hou,Serghei Mangul,Daniel Nachun,Andrew B. Nobel,Abhiram Rao,Ferran Reverter,Chiara Sabatti,Andrew D Skol,Nicole A. Teran,Fred A. Wright,Pedro G. Ferreira,Gen Li,Marta Melé,Esti Yeger-Lotem,Mary Barcus,Debra Bradbury,T Krubit,Jeffrey McLean,Liqun Qi,Karna Robinson,Nancy Roche,Anna M. Smith,David E. Tabor,Anita H. Undale,Jason Bridge,Lori E. Brigham,Barbara A. Foster,Bryan Gillard,Rick Hasz,Marcus Hunter,Christopher Johns,Mark H. Johnson,Ellen Karasik,Gene Kopen,William F. Leinweber,Alisa McDonald,Mike Moser,Kevin Myer,Kimberly Ramsey,Bruce A. Roe,Saboor Shad,Jeffrey A. Thomas,Gary Walters,Michael Washington,Jessica Wheeler,Scott D. Jewell,Daniel C. Rohrer,David A. Davis,Deborah C. Mash,Leslie H. Sobin,Laura Barker,HM Gardiner,Maghboeba Mosavel,Laura A. Siminoff,Paul Flicek,Maximilian Haeussler,Thomas Juettemann,W. J. Kent,Christopher Lee,CC Powell,Kate R. Rosenbloom,Magali Ruffier,Dan Sheppard,Kieron Taylor,Stephen J. Trevanion,Zerbino,Nathan S. Abell,Joshua M. Akey,Lin Chen,Kathryn Demanelis,Jennifer A. Doherty,Andrew P. Feinberg,Kasper D. Hansen,Peter Hickey,Farzana Jasmine,Lihua Jiang,Rajinder Kaul,Manolis Kellis,Muhammad G. Kibriya,Jin Billy Li,Qin Li,Shin Lin,Sandra Linder,Brandon L. Pierce,Lindsay F. Rizzardi,Kevin S. Smith,Michael Snyder,John A. Stamatoyannopoulos,Hua Tang,Meng Wang,Phillip Branton,Latarsha J. Carithers,Ping Guan,Susan E. Koester,AR Little,Helen M. Moore,Concepcion R. Nierras,Abhi Rao,Jimmie B. Vaught,Simona Volpi +167 more
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