atted_coexpression
Fetch co-expressed gene neighbors for a plant locus from ATTED-II. Returns top-ranked genes with z-scores to identify functional partners based on co-expression patterns.
Instructions
Fetch co-expressed gene neighbors from ATTED-II (atted.jp, API v5) for a plant locus. Returns top_n neighbors with target locus + NCBI Entrez gene ID + z-score (higher = stronger coexpression). The ATTED-II release (e.g. Ath-u.c4-0 for Arabidopsis, Osa-u.c1-0 for rice) is resolved per-organism; wheat, sorghum, barley, poplar, and brachypodium have no published release and raise OrganismNotSupported. Pairs with string_interactions to surface high-confidence functional partners (interactors that are also coexpressed).
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| locus | Yes | Plant locus, e.g. AT1G01010 (Arabidopsis) or Os01g0100100 (rice) | |
| organism | No | Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid | arabidopsis_thaliana |
| top_n | No |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| locus | Yes | ||
| atted_release | Yes | ATTED-II DB identifier, e.g. Ath-u.c4-0 (release version included) | |
| neighbors | Yes |