AlgaePath

'AlgaePath' is a web-based database designed to integrate gene information, biological pathways, and next-generation sequencing datasets for the green algae Chlamydomonas reinhardtii and Neodesmus sp. UTEX 2219-4. This resource makes it possible to retrieve transcript abundance profiles efficiently and accurately under various conditions in numerous metabolic pathways. In the past, gene expression profiles and biological pathways were displayed separately, making it impossible to search current databases effectively and identify the cellular response mechanisms. However, the increasing availability of next-generation sequencing data for algae genomes and transcriptomes has developed an integrated resource for retrieving gene expression data and metabolic pathways essential for functional analysis and systems biology. Users can search the AlgaePath database using five query pages: Gene Search, Pathway Search, Differentially Expressed Genes (DEGs) Search, Gene Group Analysis, and Co-expression Analysis. The transcript abundance data of 45 and four samples from C. reinhardtii and Neodesmus sp. UTEX 2219-4 can be obtained directly on pathway maps. Furthermore, users can identify genes that are differentially expressed between two conditions using Folds Search. The Gene Group Analysis page includes a pathway enrichment analysis, which can be used to compare the transcript abundance profiles of functionally related genes on a map easily. Finally, the Co-expression Analysis page can be used to search for co-expressed transcripts of a target gene. The results of the searches will provide a valuable reference for designing further experiments and elucidating critical mechanisms from high-throughput data.