From: Information-based methods for predicting gene function from systematic gene knock-downs
Metric | Typea | Description |
---|---|---|
MatchPresent | P | Counts the number of matching present phenotypes. |
MatchAbsent | A | Counts the number of matching absent phenotypes. |
Match | P, A | Counts the number of matching present and absent phenotypes. |
Pearson Correlation Coefficient (PCC) | P, A | Vector correlation coefficient. |
Uncentered Pearson Correlation (UPC) | P, A | Same as PCC, with vector means set to 0. Used for network construction in [9]. |
UPC 2+ | P, A | Same as UPC, restricting to gene pairs sharing two or more phenotypes. |
Mutual Information (MI) | P, A | Measures the degree to which knowledge about one gene's phenotypes reduces the entropy of another's. |
Euclidean Distance | P, A | The "straight line" distance between two vectors. |
Jaccard Index | P, A | The number of matching present phenotypes divided by the number of phenotypes present in either gene. |
Frequency Dot Product (FDP) | P, F | Scales the number of matching present phenotypes by the frequency of each phenotype. |
Normalized FDP (nFDP) | P, F | Same as FDP, but normalized by the lengths of the phenotypic signature vectors. |
Residual FDP (rFDP) | P, F | Same as FDP, scaled by a score obtained by drawing random phenotypes from a Poisson distribution. |
Symmetric FDP (sFDP) | P, A, F | Same as FDP, but rewards for matching absent phenotypes as well as matching present phenotypes. |
The PhenoBlast Metric | P, A, F | Ranking system used by PhenoBlast (Gunsalus et al. 2004). First ranks gene pairs by MatchPresent, then by MatchAbsent, then by a metric similar to FDP. |
Agreement Score (AGREE) | P, A, F | Scales the number of matching present and absent phenotypes by their frequencies across all genes [8]. |
Weighted MatchPresent (wMatchPresent) | P, C | Same as MatchPresent, but incorporates weights. |
Pairwise FDP (pFDP) | P, F, C | Weights by present phenotype background pairwise co-occurences. |
Weighted FDP (wFDP) | P, F, C | Same as FDP, but incorporates weights. |
Weighted AGREE (wAGREE) | P, A, F, C | Same as AGREE, but incorporates weights. |