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PCTA, A PAN-CANCER CELL LINE TRANSCRIPTOME ATLAS
Siyuan Cheng1,2, Lin Li1,2, Xiuping Yu1,2,3
1Department of Biochemistry & Molecular Biology, LSU Health Shreveport.
Biorxiv : the Preprint Server for Biology
|January 23, 2024
Summary
The Pan-cancer Cell Line Transcriptome Atlas (PCTA) provides accessible gene expression data for 535 cancer cell lines. This resource empowers researchers to explore molecular signatures and potential therapeutic targets without extensive bioinformatics skills.
Area of Science:
- * Cancer Genomics
- * Transcriptomics
- * Bioinformatics
Background:
- * Large volumes of RNA sequencing data from cancer cell lines exist but are difficult to access for non-bioinformaticians.
- * Existing pan-cancer datasets lack sufficient sample numbers per cell line for robust analysis.
- * A need exists for a user-friendly resource to explore cancer cell line gene expression.
Approach:
- * Integrated and curated data from CCLE, SRA, and ARCHS4 databases.
- * Utilized R programming for data retrieval, normalization, and visualization.
- * Focused analysis on protein-coding genes and long non-coding RNAs (LncRNAs).
Key Points:
- * The Pan-cancer Cell Line Transcriptome Atlas (PCTA) dataset includes 24,965 genes from 84,385 samples across 535 cell lines and 114 cancer types.
- * Cell lines cluster by tissue type on UMAP plots, indicating captured biological relationships.
- * An interactive web application allows exploration of gene expression patterns and identification of marker genes.
Conclusions:
- * PCTA offers a comprehensive resource for exploring gene expression in cancer cell lines.
- * Facilitates the discovery of molecular signatures and potential therapeutic targets.
- * Empowers researchers without bioinformatics expertise to leverage valuable transcriptomic data.
