Hello,
I am trying to perform Joint Pathway Analysis for Arabidopsis thaliana (ath) using metabolomics + transcriptomics data.
My transcriptomics input uses Arabidopsis AT locus IDs with fold-change values, for example:
AT4G31310 -1.0561
AT4G00165 -1.6076
AT1G53580 1.7824
The same type of input was previously recognized in the MetaboAnalyst web version. However, when I repeat the analysis now, the web version does not seem to recognize the transcriptomic gene list properly.
I also tested the issue in MetaboAnalystR. After installing MetaboAnalystR from GitHub on Windows with R 4.4.1, gene mapping failed because the required SQLite database file could not be downloaded:
genes_entries_130_species.sqlite
When I tried to download it through R, the download failed and the resulting file size was 0 bytes. This caused errors such as:
- no such table: entrez
- file is not a database
The input file can be parsed normally in R as a two-column gene/value table. Therefore, the issue may be related to the official MetaboAnalyst / MetaboAnalystR gene-entry mapping database or its download path, rather than the basic file structure.
Could you please check whether the Arabidopsis gene-entry mapping database used for Joint Pathway Analysis is currently available, and whether AT locus IDs such as AT4G31310 are still supported?