Mr Vc v2

Mr Vc v2 provides a curated database of transcriptome datasets and experimentally validated interactions for Vibrio cholerae to support analysis of gene regulation and interaction networks.

Key Features:

• Curated Transcriptome Data: Contains 107 microarray experiments, 106 RNA-seq experiments, and 3 Tn-seq projects encompassing 56,839 differentially expressed genes (DEGs) from transcriptomes and 7,463 related genes from Tn-seq.
• Annotated Information: Includes manually curated annotations that document gene regulation mechanisms in Vibrio cholerae.
• Operon Identification: Identifies previously unknown operons through text-mining analysis to inform regulatory network structure.
• Gene Co-expression Analysis: Provides 270,129 gene co-expression entries for exploring expression-based gene relationships.
• Experiment-Experiment Correlation Analysis: Provides 11,990 experiment-experiment correlation entries for comparing experimental conditions.
• Functional Interactions Module: Compiles 1,316 experimentally validated interaction entries from public databases, MEDLINE documents, and life science journals, comprising 496 protein-chemical signaling interactions, 472 protein-protein interactions, 306 transcription factor–gene interactions, and 42 Vibrio cholerae–virus interactions.
• Text-Mining Coverage: Derives the majority of interactions via text-mining from 402 literature sources.

Scientific Applications:

• Gene Regulation Studies: Supports identification and characterization of regulatory mechanisms and operon structures in Vibrio cholerae.
• Interaction Network Analysis: Enables reconstruction and analysis of protein-protein, protein-chemical, transcription factor–gene, and pathogen-virus interaction networks.
• Comparative Transcriptomics: Facilitates comparative analysis across microarray, RNA-seq, and Tn-seq experiments and experimental conditions.

Methodology:

Data were compiled via manual curation and text-mining analysis of public databases, MEDLINE documents, and life science journals, organized in an experiment-centric manner.