circExp database: an online transcriptome platform for human circRNA expressions in cancers

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Circular RNAs (circRNAs) are stable, non-coding RNA molecules with regulatory roles in gene expression.
• Their tissue-specific and developmental stage-specific expression patterns make them promising biomarkers for disease.
• Cancer diagnosis and prognosis can benefit from specific circRNA expression profiles.

Purpose of the Study:

• To establish a comprehensive, standardized human cancer circRNA expression profile.
• To identify circRNAs with significant differential expression between normal and cancerous tissues.
• To develop an accessible online resource for exploring circRNA expression data in cancer.

Main Methods:

• Curated circRNA expression data from 11 technical platforms, encompassing 48 datasets and over 860,000 expression records for 18 cancer types.
• Analyzed data to identify 189,193 differential expression signatures between normal and cancer samples.
• Developed the circExp online interface for data browsing, searching, and visualizing expression profiles via dynamic heatmaps.

Main Results:

• Identified 52 circRNAs consistently differentially expressed in 20 or more analyses.
• Mapped these key circRNAs to their parent genes, revealing potential profound impacts on patient survival in The Cancer Genome Atlas (TCGA) pan-cancer dataset.
• The circExp database provides pre-calculated expression data and analysis functions.

Conclusions:

• The circExp database and analysis provide a valuable resource for identifying circRNAs with diagnostic and prognostic significance in various cancers.
• This work facilitates the use of circRNAs as biomarkers for cancer detection and outcome prediction.
• The curated data and online tools support further research into the role of circRNAs in oncogenesis.