LACA Tutorial: 5 Core Workflows

See which species are covered and how each atlas is organized by system, tissue and cell type.

1. Open the Species Atlas from the top navigation “Longevity → Atlas”.
   URL: species.php
   You will see: The species overview: all atlas species with their scientific names and data status.
2. Click the demo species Mouse — SP121 (also reachable from the Demo menu).
   URL: content.php?SP_ID=SP121
   You will see: The SP121 atlas page with its UMAP embedding, cell-type legend and summary statistics read from the dataset config.
3. Switch hierarchy levels in the left panel — system, tissue, or cell atlas.
   URL: list.php?type=ct&SP_ID=SP121
   You will see: A browsable table of cell types with colors, counts and per-item atlas pages.
4. Open the atlas analysis view for the loaded context.
   URL: analysis.php?SP_ID=SP121&tisID=sys04tis01
   You will see: The analysis module for the selected tissue context: UMAP canvas plus result panels. A “How is this computed?” chip links to the matching Methods section.

Find a gene and inspect its expression across the atlas.

1. Open the gene search page.
   URL: gene.php
   You will see: A search box with a species selector (pre-selectable via ?SP_ID=).
2. Type a gene symbol — e.g. Mtor — and run the search.
   URL: gene.php?SP_ID=SP121
   You will see: Matching genes with their identifiers; pick one to open its detail page.
3. Open the gene detail page.
   URL: gene-detail.php?gene=Mtor
   You will see: Gene overview plus its per-species expression views rendered from the atlas gene vectors (genes/<GENE>.bin.gz).

Compare a gene or cell type across species.

1. Open the cross-species portal.
   URL: cross-species.php
   You will see: Entry points to all cross-species modules (gene/cell comparison and correlation, lifespan, animal models).
2. Open the gene comparison module and select a gene and the species to compare.
   URL: genecompare.php
   You will see: Side-by-side expression profiles of the chosen gene across species, restricted to one-to-one orthologs (see Methods).
3. Open the gene–longevity correlation view for the same comparison.
   URL: genecorrelation.php
   You will see: Correlation of the gene’s expression with longevity-related traits per species, with significance labeling.

Read correlation results correctly: effect direction, significance, and what is association vs. mechanism.

1. Open the longevity correlation module.
   URL: longevity-correlation.php
   You will see: Gene/trait correlation tables and plots. Effect sizes are ranked; color encodes direction and strength.
2. Open the cell-level correlation module.
   URL: cellcorrelation.php
   You will see: Cell-type level correlations for the selected context. SP121 also has a downloadable cell-level table (cell_level_celltype_correlation.csv, linked on the module page).
3. Before quoting any number, read the Methods section for this module.
   URL: methods.php#correlation
   You will see: Correlations use Spearman’s rank correlation by default; multiple-testing is controlled with Benjamini–Hochberg FDR; cell-level notes explain aggregation. Correlation here is association, not causation.

Download count matrices, atlas packages and cell-level metadata for offline analysis.

1. Open the Download Center (About → Download).
   URL: download.php
   You will see: Real, server-verified files: 173 CancerSCEM count matrices, bulk matrices, four curated h5ad datasets, and a filterable table of 141 species atlas packages.
2. In the species table, use “Atlas package” for the full bundle or “Cell-level metadata” for a per-cell CSV.
   URL: export.php?type=atlas&sp=SP013
   You will see: A generated download: the atlas package (tar.gz with embedding + legends + config) or cell_idx,x,y,cell_type CSV, generated on demand and cached.
3. To cite or reproduce a specific site state, check the archived snapshots.
   URL: versions.php
   You will see: Every site update is archived as a dated code snapshot with SHA-256 checksums.