Overview of VPI-MD

VPI-MD is a comprehensive database closely related to verticillium wilt, integrating data collection, analysis, and visualization. The data includes both that of fungi and plants, comes from NCBI and self-generated data. It encompass genome, transcriptome, proteome, variome, and epigenome among >100 specials and >3000 samples.

Typing in either IDs or function descriptions would generate a list of matched genes and their annotation infomations. 
Users can choose several genes and send them to various programs, including (1) Gene expression profile module to compare their expression profiles under different treatments, (2) Gene fishing to look for additional genes with similar expression profiles that may work together, (3) Gene map viewer to see the distribution of these genes on the genome, (4) Multiple sequence alignments to locate conserved domain or motif, (5) Primer design to produce primers for experimental verification and (6) BLAST to compare their hits across species. 
Users can create an in-silico project using the data in the database or their own data, utilizing (7) DE gene analysis model to identify which genes show significant expression differences under different conditions. The identified genes could be used for function discovery in (8) GO/KEGG enrichment analysis and interaction predict in (9) Protein-Protein Interaction.
Users also can view the epigenetic modifications, variations, and more for a specific gene or within a certain region, utilizing (10) Methyl View and (11) IGV Browser.

How to cite?

Shi S, Wang F, Cai Y, Tang R, Zhou X, Long M, Jiang C, Chen K, Xie Q, Xie S, Meng Z, Ismayil A, Jin X, Li H. VPI-MD: a multi-omics database for Verticillium-plant interaction. Plant Biotechnol J. 2025 Jan 7. doi: 10.1111/pbi.14555. Epub ahead of print. PMID: 39776224.