IMP: Bridging the Gap for Medicinal Plant Genomics
2024-01-10
Overview of IMP
Figure 0.1: The basic structure of IMP construction.
Synthetic biology medicine is built on the molecular metabolic pathways of medicinal plants. Finding functional genes and assembling the metabolic pathways requires a number of critical steps, one of which is the comparative genome and transcriptome analysis. We developed IMP as an integrated toolset for organizing, analyzing, and sharing omics data of molecular pharmacognosy with 10 computation modules to deal with the volume of omics data and the complexity of analysis operations. Typing in either IDs, function descriptions, or pathway annotations would generate a list of matched genes. Users could choose several genes and send them to various programs, including (1) Gene expression profile module to compare their transcriptome profiles across various organs or treatment conditions to screen key functional genes, (2) Gene fishing to look for additional genes with similar expression profiles that may work together, (3) Gene map viewer to see if these genes could form gene clusters to be involved in one metabolite pathway, (4) Multiple sequence alignments to locate conserved catalytic sites for metabolite synthesis, (5) Sequences fetch to download related sequences, (6) Primer design to produce primers for experimental verification, and (7) BLAST to compare their hits across species. Users might also create an in-silico project to resolve the medicinal component synthetic pathways utilizing (8) DE gene analysis model to perform cross-organ comparison or along-inducing comparison. The identified differentially expressed genes could be used for function discovery in (9) GO/KEGG enrichment analysis and (10) Gene set enrichment analysis.
Figure 0.2: The basic structure of IMP construction.
How to cite?
Tong Chen, Mei Yang, Guanghong Cui, Jinfu Tang, Ye Shen, Juan Liu, Yuan Yuan, Juan Guo, Luqi Huang, IMP: bridging the gap for medicinal plant genomics, Nucleic Acids Research, 2023;, gkad898, https://doi.org/10.1093/nar/gkad898
Down citation in RIS format.