Fitness Browser
kescience_fitnessbrowser
Philosophy
Connect genotype to phenotype through systematic mutagenesis. Understand which genes are essential for growth, which provide advantages under specific conditions, and how genetic background affects fitness.
Citation & Attribution
Provider: Price Lab, LBNL
Cite as: Price MN et al. (2018) Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 557:503-509
DOI: 10.1038/s41586-018-0124-0
Website: https://fit.genomics.lbl.gov/
Scale
Schema Browser
Tables (9)
organism 48 gene 228,709 experiment 7,552 genefitness 27,410,721 cofit 13,656,145 ortholog genedomain specificphenotype 38,525 specog
specog
Specific phenotypes aggregated by ortholog group.
| Column | Type | Description |
|---|---|---|
ogId |
string | Ortholog group ID |
expGroup |
string | Experiment group |
condition |
string | Condition description |
orgId |
string | FK -> `organism.orgId` |
locusId |
string | FK -> `gene.locusId` |
minFit |
string | Minimum fitness in this condition |
maxFit |
string | Maximum fitness in this condition |
minT |
string | Minimum t-statistic |
maxT |
string | Maximum t-statistic |
nInOG |
string | Number of genes in ortholog group |
Sample Queries
Get organisms in the fitness browser
SELECT *
FROM kescience_fitnessbrowser.organism
LIMIT 20
Get fitness scores for a gene
SELECT
e.condition,
f.fitness,
f.t_score
FROM kescience_fitnessbrowser.fitness f
JOIN kescience_fitnessbrowser.experiment e
ON f.experiment_id = e.experiment_id
WHERE f.gene_id = 'YOUR_GENE_ID'
ORDER BY ABS(f.fitness) DESC
LIMIT 20
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