New Pan-cancer Cell Line Transcriptome Atlas provides access to 114 cancer types
Cancer researchers and clinicians now have access to an online dataset of extensive cancer cell lines developed by biochemistry and bioinformatics researchers at LSU Health Shreveport. The PCTA: PanCancer cell line Transcriptome Atlas launched on Jan. 14, 2024 and provides a user-friendly platform for visualizing gene expression across diverse samples. It was developed by Siyuan Cheng, PhD and Xiuping Yu, PhD of LSU Health Shreveport Department of Biochemistry and Molecular Biology. Both Drs. Cheng and Yu are members of the Louisiana Cancer Research Center.
PCTA is a valuable tool for cancer researchers, furnishing a robust quantification of gene expression data across a diverse spectrum of cancer types, surpassing other pan-cancer datasets in this aspect. “PCTA contains more than 80,000 gene expression profiles for a variety of cancer types, including rare cancers,” Dr. Cheng said.
PCTA contains RNAseq data of 84,385 samples derived from 5,677 studies. This comprehensive compilation spans 535 cell lines, representing a spectrum of 114 cancer types originating from 30 diverse tissue types.
Clinicians can utilize PCTA to verify a patient’s pathology immunohistochemistry, Dr. Yu explained. “They can utilize the dataset to visualize the expression status of their patient’s particular cancer driver gene and markers.”
“Congratulations to Drs. Yu and Cheng on development an interactive, user-friendly web application that allows researchers and clinicians to explore thousands of cancer cell lines. It is an example of the diligent work being done across Louisiana to further collaborative solutions to cancer,” said Joe W. Ramos, PhD, Director/CEO of the Louisiana Cancer Research Center and Director, LSU LCMC Health Cancer Center.
PCTA website: https://pcatools.shinyapps.io/PCTA_app/
PCTA manuscript: https://doi.org/10.1101/2024.01.10.575087
About the LCRC
Each year, more than 28,000 Louisianans receive a cancer diagnosis. The Louisiana Cancer Research Center serves as a collaborative hub that advances cancer research, improves prevention, and accelerates innovative treatments. LCRC brings together the collective talent of more than 200 researchers from across the state and four member institutions – LSU Health New Orleans, Tulane University School of Medicine, Xavier University of Louisiana, and Ochsner Health – to improve cancer outcomes for Louisianans and all those touched by the disease. https://www.louisianacancercenter.org/