Hypergeometric Distribution Calculation
Summary
Compute expected value and variance of strain correlation scores under a hypergeometric null model to standardize raw scores across GCF–MF links of different sizes. This enables fair comparison of genomic–metabolomic associations independent of set cardinalities.
When to use
When you have raw strain correlation scores (or similar overlap-based metrics) computed across genomic cluster family (GCF) and molecular family (MF) pairs of varying sizes, and you need to make those scores comparable across links with different GCF sizes (#G), MF sizes (#m), and population sizes (#N). This is necessary when the raw score distribution is confounded by set size, making it difficult to distinguish true links from spurious high-scoring pairs that arise merely from large overlap counts.
When NOT to use
- Raw overlap counts are already normalized or size-adjusted by another method (e.g., Jaccard or hypergeometric p-values already computed).
- The GCF and MF assignments are not independent or do not follow a random sampling model (e.g., if overlap is structured by phylogeny or functional constraint rather than chance).
- Population size #N is not well-defined or strains are not uniformly sampled (violates hypergeometric model assumptions).
Inputs
- Raw strain correlation scores for all GCF–MF pairs
- GCF sizes (#G) for each pair
- MF sizes (#m) for each pair
- Observed overlap counts (#(G∩M)) for each pair
- Total population size (#N) — number of strains in the dataset
Outputs
- Standardized correlation scores (s*_corr) for all GCF–MF links
- Expected values E[σ_corr(M,G)] per link
- Variances Var[σ_corr(M,G)] per link
- Distribution statistics (mean, std) for validated vs. all links
How to apply
For each GCF–MF pair, compute the hypergeometric distribution over all possible overlap sizes k ∈ [0, min(#m, #G)], where p(overlap=k) follows hypergeometric(N, #m, #G). Calculate the expected value E[σ_corr(M,G)] and variance Var[σ_corr(M,G)] by marginalizing the raw correlation score σ_corr(M,G) over this distribution. Then standardize the observed raw score as s*_corr = (σ_corr(M,G) − E[σ_corr(M,G)]) / √Var[σ_corr(M,G)]. The hypergeometric model assumes a null hypothesis of random strain overlap: under this null, validated links should still cluster at high standardized scores (mean ≈ 3.67) while all links scatter near zero (mean ≈ −0.006), yielding large separation with p < 10^−60. This z-score transformation decouples the link score from the combinatorial bias inherent in comparing sets of different cardinalities.
Related tools
- antiSMASH (BGC detection from microbial genomes; produces GCF assignments used to define set membership (#G))
- BiG-SCAPE (BGC clustering into GCFs; establishes which strains contribute to each GCF cardinality (#G))
- GNPS (Metabolomics spectrum database; defines MF membership and sizes (#m) via spectral clustering)
- NPLinker (Framework for computing and standardizing strain correlation scores; implements hypergeometric expectation and variance calculation) — https://github.com/sdrogers/nplinker
- MIBiG (Reference BGC database; provides validated GCF–MF links for evaluation)
Evaluation signals
- Standardized scores for validated links have a significantly higher mean (target ≈ 3.67) and narrower range than all links (mean ≈ −0.006), with p-value < 10^−60 (e.g., t-test or Mann–Whitney U).
- Standardized scores have mean ≈ 0 and std ≈ 1 across all links (confirming z-score transformation).
- Raw and standardized score distributions show opposite trends: raw scores correlate with set size (larger #G and #m → higher raw scores); standardized scores are decoupled from cardinality.
- Validated links are significantly enriched (p < 10^−10) above the 90th percentile of standardized scores, whereas raw scores show no such enrichment.
- Histograms and boxplots comparing raw vs. standardized scores across multiple datasets (Crüsemann, Gross, Leão) show consistent separation patterns, confirming robustness of the hypergeometric model.
Limitations
- The hypergeometric model assumes strains are sampled uniformly and independently; violations (e.g., phylogenetic clustering, functional constraints on overlap) invalidate the null distribution.
- Requires well-defined population size (#N); incomplete or biased strain inventories will distort expected values and variance.
- High computational cost for large datasets: calculating E and Var over the full support of the hypergeometric distribution for every GCF–MF pair can be slow; optimization via lookup tables or caching is recommended.
- Standardization by variance can be unstable or undefined for pairs with very small GCF or MF sizes, where variance is near zero; tail behavior may be unreliable.
Evidence
- [other] For each GCF-MF pair, compute expected value E[σ_corr(M,G)] and variance Var[σ_corr(M,G)] using hypergeometric distribution over all possible overlap sizes k, where p(o=k) follows hypergeometric with parameters N, m, g, and overlap.: "For each GCF-MF pair, compute expected value E[σ_corr(M,G)] and variance Var[σ_corr(M,G)] using hypergeometric distribution over all possible overlap sizes k, where p(o=k) follows hypergeometric with"
- [other] The standardised correlation score achieves a mean of -0.0060 for all links and 3.6717 for validated links (p=6.8302 × 10−64), compared to the raw score's means of 83.5144 and 14.6667 respectively, demonstrating that standardisation successfully enables comparison across links with different GCF and MF sizes.: "The standardised correlation score achieves a mean of -0.0060 for all links and 3.6717 for validated links (p=6.8302 × 10−64), compared to the raw score's means of 83.5144 and 14.6667 respectively,"
- [other] Calculate standardised correlation score s*_corr = (σ_corr(M,G) - E[σ_corr(M,G)]) / √Var[σ_corr(M,G)] for all links.: "Calculate standardised correlation score s*_corr = (σ_corr(M,G) - E[σ_corr(M,G)]) / √Var[σ_corr(M,G)] for all links."
- [abstract] Based on standardising a commonly used score, we introduce a new, more effective score: "Based on standardising a commonly used score, we introduce a new, more effective score"
- [results] we examine the distribution of scores for validated links in relation to the scores for all hypothetical links: "we examine the distribution of scores for validated links in relation to the scores for all hypothetical links"
1---2name: hypergeometric-distribution-calculation3description: Use when when you have raw strain correlation scores (or similar overlap-based metrics) computed across genomic cluster family (GCF) and molecular family (MF) pairs of varying sizes, and you need to make those scores comparable across links with different GCF sizes (#G), MF sizes (#m), and.4license: CC-BY-4.05---67# Hypergeometric Distribution Calculation89## Summary1011Compute expected value and variance of strain correlation scores under a hypergeometric null model to standardize raw scores across GCF–MF links of different sizes. This enables fair comparison of genomic–metabolomic associations independent of set cardinalities.1213## When to use1415When you have raw strain correlation scores (or similar overlap-based metrics) computed across genomic cluster family (GCF) and molecular family (MF) pairs of varying sizes, and you need to make those scores comparable across links with different GCF sizes (#G), MF sizes (#m), and population sizes (#N). This is necessary when the raw score distribution is confounded by set size, making it difficult to distinguish true links from spurious high-scoring pairs that arise merely from large overlap counts.1617## When NOT to use1819- Raw overlap counts are already normalized or size-adjusted by another method (e.g., Jaccard or hypergeometric p-values already computed).20- The GCF and MF assignments are not independent or do not follow a random sampling model (e.g., if overlap is structured by phylogeny or functional constraint rather than chance).21- Population size #N is not well-defined or strains are not uniformly sampled (violates hypergeometric model assumptions).2223## Inputs2425- Raw strain correlation scores for all GCF–MF pairs26- GCF sizes (#G) for each pair27- MF sizes (#m) for each pair28- Observed overlap counts (#(G∩M)) for each pair29- Total population size (#N) — number of strains in the dataset3031## Outputs3233- Standardized correlation scores (s*_corr) for all GCF–MF links34- Expected values E[σ_corr(M,G)] per link35- Variances Var[σ_corr(M,G)] per link36- Distribution statistics (mean, std) for validated vs. all links3738## How to apply3940For each GCF–MF pair, compute the hypergeometric distribution over all possible overlap sizes k ∈ [0, min(#m, #G)], where p(overlap=k) follows hypergeometric(N, #m, #G). Calculate the expected value E[σ_corr(M,G)] and variance Var[σ_corr(M,G)] by marginalizing the raw correlation score σ_corr(M,G) over this distribution. Then standardize the observed raw score as s*_corr = (σ_corr(M,G) − E[σ_corr(M,G)]) / √Var[σ_corr(M,G)]. The hypergeometric model assumes a null hypothesis of random strain overlap: under this null, validated links should still cluster at high standardized scores (mean ≈ 3.67) while all links scatter near zero (mean ≈ −0.006), yielding large separation with p < 10^−60. This z-score transformation decouples the link score from the combinatorial bias inherent in comparing sets of different cardinalities.4142## Related tools4344- **antiSMASH** (BGC detection from microbial genomes; produces GCF assignments used to define set membership (#G))45- **BiG-SCAPE** (BGC clustering into GCFs; establishes which strains contribute to each GCF cardinality (#G))46- **GNPS** (Metabolomics spectrum database; defines MF membership and sizes (#m) via spectral clustering)47- **NPLinker** (Framework for computing and standardizing strain correlation scores; implements hypergeometric expectation and variance calculation) — https://github.com/sdrogers/nplinker48- **MIBiG** (Reference BGC database; provides validated GCF–MF links for evaluation)4950## Evaluation signals5152- Standardized scores for validated links have a significantly higher mean (target ≈ 3.67) and narrower range than all links (mean ≈ −0.006), with p-value < 10^−60 (e.g., t-test or Mann–Whitney U).53- Standardized scores have mean ≈ 0 and std ≈ 1 across all links (confirming z-score transformation).54- Raw and standardized score distributions show opposite trends: raw scores correlate with set size (larger #G and #m → higher raw scores); standardized scores are decoupled from cardinality.55- Validated links are significantly enriched (p < 10^−10) above the 90th percentile of standardized scores, whereas raw scores show no such enrichment.56- Histograms and boxplots comparing raw vs. standardized scores across multiple datasets (Crüsemann, Gross, Leão) show consistent separation patterns, confirming robustness of the hypergeometric model.5758## Limitations5960- The hypergeometric model assumes strains are sampled uniformly and independently; violations (e.g., phylogenetic clustering, functional constraints on overlap) invalidate the null distribution.61- Requires well-defined population size (#N); incomplete or biased strain inventories will distort expected values and variance.62- High computational cost for large datasets: calculating E and Var over the full support of the hypergeometric distribution for every GCF–MF pair can be slow; optimization via lookup tables or caching is recommended.63- Standardization by variance can be unstable or undefined for pairs with very small GCF or MF sizes, where variance is near zero; tail behavior may be unreliable.6465## Evidence6667- [other] For each GCF-MF pair, compute expected value E[σ_corr(M,G)] and variance Var[σ_corr(M,G)] using hypergeometric distribution over all possible overlap sizes k, where p(o=k) follows hypergeometric with parameters N, m, g, and overlap.: "For each GCF-MF pair, compute expected value E[σ_corr(M,G)] and variance Var[σ_corr(M,G)] using hypergeometric distribution over all possible overlap sizes k, where p(o=k) follows hypergeometric with"68- [other] The standardised correlation score achieves a mean of -0.0060 for all links and 3.6717 for validated links (p=6.8302 × 10−64), compared to the raw score's means of 83.5144 and 14.6667 respectively, demonstrating that standardisation successfully enables comparison across links with different GCF and MF sizes.: "The standardised correlation score achieves a mean of -0.0060 for all links and 3.6717 for validated links (p=6.8302 × 10−64), compared to the raw score's means of 83.5144 and 14.6667 respectively,"69- [other] Calculate standardised correlation score s*_corr = (σ_corr(M,G) - E[σ_corr(M,G)]) / √Var[σ_corr(M,G)] for all links.: "Calculate standardised correlation score s*_corr = (σ_corr(M,G) - E[σ_corr(M,G)]) / √Var[σ_corr(M,G)] for all links."70- [abstract] Based on standardising a commonly used score, we introduce a new, more effective score: "Based on standardising a commonly used score, we introduce a new, more effective score"71- [results] we examine the distribution of scores for validated links in relation to the scores for all hypothetical links: "we examine the distribution of scores for validated links in relation to the scores for all hypothetical links"
HolobiomicsLab