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
genefitness
27,410,721 rows
Gene fitness scores per experiment.
| Column | Type | Description |
|---|---|---|
orgId |
string | FK -> `organism.orgId` |
locusId |
string | FK -> `gene.locusId` |
expName |
string | FK -> `experiment.expName` |
fit |
string | Fitness score (log2 ratio) |
t |
string | T-statistic for 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
Related Collections
Projects Using This Collection
Carbon Source Utilization Predicts Ecology and Lifestyle in Pseudomonas
Among free-living *Pseudomonas* clades, does the carbon source utilization profile predict the soil ecosystem type from ...
CF Protective Microbiome Formulation Design
Can we build a multi-criterion framework that explains measured *P. aeruginosa* PA14 inhibition from metabolic competiti...
AMR Co-Fitness Support Networks
What genes are co-regulated with antimicrobial resistance (AMR) genes across growth conditions, and do these "support ne...
Metabolic Consistency of Pseudomonas FW300-N2E3
For *Pseudomonas fluorescens* FW300-N2E3 (ENIGMA groundwater isolate), how consistent are exometabolomic outputs (Web of...
Pan-Bacterial Metal Fitness Atlas
Across diverse bacteria subjected to genome-wide fitness profiling under metal stress, what is the genetic architecture ...
Field vs Lab Gene Importance in *Desulfovibrio vulgaris* Hildenborough
Which genes matter for survival under environmentally-realistic conditions but appear dispensable in the lab, and vice v...
Fitness Effects vs Conservation -- Quantitative Analysis
Is there a continuous gradient from essential genes (core) to dispensable genes (accessory) across the full fitness spec...
Web of Microbes Data Explorer
What does the `kescience_webofmicrobes` exometabolomics collection contain, which organisms overlap with the Fitness Bro...
Co-fitness Predicts Co-inheritance in Bacterial Pangenomes
Do genes with correlated fitness profiles (co-fit) tend to co-occur in the same genomes across a species' pangenome? Doe...
Counter Ion Effects on Metal Fitness Measurements
When bacteria are exposed to metal salts (CoCl₂, NiCl₂, CuCl₂), how much of the observed fitness effect is caused by the...
Conservation vs Fitness -- Linking FB Genes to Pangenome Clusters
Are essential genes preferentially conserved in the core genome, and what functional categories distinguish essential-co...
BacDive Phenotype Signatures of Metal Tolerance
Can BacDive-measured bacterial phenotypes (Gram stain, oxygen tolerance, metabolite utilization, enzyme activities) pred...
The 5,526 Costly + Dispensable Genes
What characterizes genes that are simultaneously burdensome (fitness improves when deleted) and not conserved in the pan...
Pan-bacterial Fitness Modules via Independent Component Analysis
Can we decompose RB-TnSeq fitness compendia into latent functional modules via robust ICA, align them across organisms u...
Pan-Bacterial AMR Gene Landscape
What is the distribution, conservation, phylogenetic structure, functional context, and environmental association of ant...
PaperBLAST Data Explorer
What does the `kescience_paperblast` collection contain, how current is it, and what are its coverage patterns across or...
Acinetobacter baylyi ADP1 Data Explorer
What is the scope and structure of a comprehensive ADP1 database, and how do its annotations, metabolic models, and phen...
Aromatic Catabolism Support Network in ADP1
Why does aromatic catabolism in *Acinetobacter baylyi* ADP1 require Complex I (NADH dehydrogenase), iron acquisition, an...
Metabolic Capability vs Metabolic Dependency
Just because a bacterium's genome encodes a complete metabolic pathway (metabolic *capability*), does the organism actua...
Metabolic Capability vs Dependency
When a bacterium's genome encodes a complete biosynthetic or catabolic pathway, does the organism actually depend on it?...
The Pan-Bacterial Essential Genome
Which essential genes are conserved across bacteria, which are context-dependent, and can we predict function for unchar...
Condition-Specific Respiratory Chain Wiring in ADP1
How is *Acinetobacter baylyi* ADP1's branched respiratory chain wired across carbon sources — which NADH dehydrogenases ...
Fitness Cost of Antimicrobial Resistance Genes
Do antimicrobial resistance (AMR) genes impose a fitness cost in the absence of antibiotic selection pressure? Using gen...
Truly Dark Genes — What Remains Unknown After Modern Annotation?
Among the ~6,400 Fitness Browser genes that remain functionally unannotated even after bakta v1.12.0 reannotation, what ...
Functional Dark Matter — Experimentally Prioritized Novel Genetic Systems
Which genes of unknown function across 48 bacteria have strong fitness phenotypes, and can biogeographic patterns, pathw...
SNIPE Defense System: Prevalence and Taxonomic Distribution in the BERDL Pangenome
How prevalent are SNIPE (Surface-associated Nuclease Inhibiting Phage Entry) homologues across the 293K-genome BERDL pan...
Antibiotic Resistance Hotspots in Microbial Pangenomes
Which microbial species and ecological environments show the highest concentration of antibiotic resistance genes, and c...