This work was funded by the USDA NIFA Award 2022-51181-38240, a USDA-ARS cooperative agreement (#58-2030-5-076), the E&J Gallo Winery, and the Ray Rossi Endowment in Viticulture and Enology.
Pick an organ (Berries, Leaves, Root, Stem, DormantBud, PreAnthesisFlowers, or the combined AllOrgans) from the dataset menu above, then use Search gene(s) in the sidebar. You can search by:
g012345Vitvi05_01chr01g00110kinaseMatching entries show both IDs, e.g. g000100 / Vitvi05_01chr01g00110 | [Protein-PII] uridylyltransferase.
Select one or more genes (each becomes a removable chip). To add many genes at once, click + Add
multiple genes below the search box to paste a list (Pixie or PN40024 v5.1 (T2T) IDs, separated by commas,
spaces, or one per line) or upload a .txt/.csv file. Use the tabs to inspect them: Cell Type
UMAP (cluster labels only), Gene Expression UMAP (expression of the first selected
gene), Expression Heatmap, and Expression Dot Plot. Use the Cell
types checkboxes to include/exclude clusters. For AllOrgans, the Heatmap and Dot Plot tabs each have
their own Order heatmap/dot plot by control (next to that tab's download button) to sort
columns by cell type or by organ, independently of one another.
Each organ opens with a curated set of marker genes (from the atlas paper's Figure 2) already selected, so the plots show something meaningful right away. They're also listed as clickable chips under Marker genes for <organ> in the sidebar — remove one from your selection and click its chip there to add it back, or use Reset to default markers to start over.
The Gene ID display control switches gene labels in the Heatmap, Dot Plot, and marker-gene chips between Pixie IDs (default) and PN40024 v5.1 (T2T) IDs — it's purely cosmetic and doesn't change your selection or the underlying data. Genes with no known PN40024 v5.1 (T2T) ortholog keep showing their Pixie ID even when switched.
Select Gene Expression Programs from the dataset menu to explore transcription-factor
regulons. Each regulon is named <Pixie TF gene>_<Organ>-<Cell type>-Cluster<N>,
e.g. g074540_Berry-Exocarp-Cluster1 — the transcription factor gene driving that regulon, the organ
it was found in, the cell type it was enriched in, and the cluster number that cell type came from (kept because
a handful of clusters within an organ share the same cell-type label, e.g. several Epidermis sub-clusters). Use
Search TF / Regulon to find regulons by the regulon name, the cell type, the Pixie TF ID, or its
PN40024 v5.1 (T2T) ortholog ID. Selected regulons can be viewed as a Regulon Heatmap (activity z-score
per cell type) or as a Target Genes table listing every gene the regulon regulates, downloadable
as CSV.
Downloads are temporarily disabled.