Mr.Vc v2: An updated version of database with increased data of transcriptome and experimental validated interactions

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Vibrio cholerae omics data is rapidly expanding, necessitating centralized, accessible resources.
• Existing data repositories may lack comprehensive annotation and integrated analysis.
• Facilitating data accessibility is crucial for understanding V. cholerae gene regulation and interactions.

Purpose of the Study:

• To develop and enhance Mr.Vc, a curated database for Vibrio cholerae transcriptome data.
• To improve the accessibility and reusability of V. cholerae omics data and annotations.
• To provide tools for analyzing gene regulation, co-expression, and interactions within V. cholerae.

Main Methods:

• Manual curation of transcriptome data from microarray, RNA-seq, and Tn-seq experiments.
• Text-mining analysis for annotating unknown operons and extracting interaction data.
• Gene co-expression and experiment-correlation analyses to reveal relationships.
• Integration of experimentally validated interactions from public databases and literature.

Main Results:

• Mr.Vc v2 contains 107 microarray, 106 RNA-seq, and 3 Tn-seq projects.
• Includes 56,839 Differentially Expressed Genes (DEGs) and 7,463 Tn-seq genes.
• Features 270,129 gene co-expression entries, 11,990 experiment correlations, and 1,316 interaction entries.
• Interaction data includes protein-chemical, protein-protein, TF-gene, and V. cholerae-virus interactions.

Conclusions:

• Mr.Vc v2 significantly expands curated Vibrio cholerae omics data and analysis capabilities.
• The database facilitates deeper understanding of V. cholerae gene regulation and molecular interactions.
• Mr.Vc v2 provides a valuable, accessible resource for the research community, available at http://mrvcv2.biownmc.info.