TEx-MST: tissue expression profiles of MANE select transcripts.

Area of Science:

• Genomics
• Bioinformatics
• Gene Expression Analysis

Background:

• The Matched Annotation from the NCBI and EMBL-EBI (MANE) select project established unified representative transcripts for human protein-coding genes.
• However, explicit tissue expression data for these MANE select transcripts were lacking, hindering functional interpretation.

Purpose of the Study:

• To provide comprehensive tissue expression profiles for MANE select transcripts across various normal human tissues.
• To create a user-friendly web database (TEx-MST) for exploring these expression patterns and their functional significance.

Main Methods:

• Utilized the Genotype-Tissue Expression (GTEx) V9 dataset, based on long-read sequencing, for enhanced assessment of alternative splicing.
• Integrated MANE select transcript data with GTEx expression data, cross-referencing with GENCODE biotype information.
• Developed a web-based bioinformatics database (TEx-MST) with search and browsing functionalities.

Main Results:

• A total of 18,083 genes showed overlap between MANE and GTEx datasets.
• 13,245 MANE select transcripts were identified as top-ranked, highly expressed transcripts in the GTEx V9 dataset, confirming their dominant expression.
• The TEx-MST database offers a visualized interface for normal tissue expression patterns of MANE select transcripts.

Conclusions:

• The TEx-MST database successfully integrates MANE select transcript information with GTEx expression data, providing valuable insights into human gene expression.
• This resource facilitates the study of molecular modulations and functional significance of MANE select transcripts in normal human tissues.
• The database serves as a key resource for researchers investigating gene expression patterns and alternative splicing in human health and disease.