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
experiment
7,552 rows
| Column | Type | Description |
|---|---|---|
orgId |
string | FK -> `organism.orgId` |
expName |
string | **Primary Key** (with orgId). Experiment identifier |
expDesc |
string | Short condition description |
expDescLong |
string | Detailed condition description |
expGroup |
string | Experiment group (e.g., "stress", "carbon source", "lb") |
media |
string | Growth medium used |
mediaStrength |
string | Medium concentration |
temperature |
string | Growth temperature |
pH |
string | pH value |
vessel |
string | Growth vessel type |
aerobic |
string | Aerobic/Anaerobic |
liquid |
string | Liquid/Solid |
shaking |
string | Shaking method |
condition_1 |
string | Primary condition/compound |
units_1 |
string | Units for condition_1 |
concentration_1 |
string | Concentration of condition_1 |
condition_2..4 |
string | Additional conditions (up to 4) |
mutantLibrary |
string | Mutant library used |
person |
string | Experimenter |
dateStarted |
string | Experiment date |
pubId |
string | Publication reference |
nMapped |
string | Number of mapped reads |
nUsed |
string | Number of usable insertions |
gMed |
string | Median reads per gene |
cor12 |
string | Correlation between replicates |
mad12 |
string | Median absolute deviation |
maxFit |
string | Maximum fitness score |
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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