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Genes Fold Enrichment Color Codes
  • Gene Name, Canonical Transcript - gene identifiers from gnomAD database (Build 37)
  • GeVIR % - gene rank measured in percentiles based on Gene Variation Intolerance Ranking (GeVIR) (low values indicate more variation intolerant genes, which is also true for "LOEUF %" and "VIRLoF %"). GeVIR is a method which we developed and applied on a list of 19,361 genes to sort them based on number, length and evolutionary conservation of regions without functional variants (i.e. between two missense, loss-of-function, insertion or delition variants) in gnomAD database (version 2.0.1). Only canonical transcripts were analysed.
  • LOEUF % - gene rank measured in percentiles based gnomAD loss-of-function observed/expected upper bound fraction (LOEUF) (see Figure 1). For more information about this metric, please read "Constraint" section of MacArthur Lab blog post. If you use this metric please cite gnomAD flagship paper and use most up-to-date values from gnomAD website.

    LoF observed/expected (o/e) upper Confidence Interval (CI)

    Figure 1. Screenshot of ELN gene constraint metrics from gnomAD browser

  • VIRLoF % - gene rank measured in percentiles based on both GeVIR and gnomAD LOEUF (shows the best overall performance, see Figure 2). If you use this metric please cite both GeVIR and gnomAD flagship paper.
  • GeVIR AD, LOEUF AD, VIRLoF AD, GeVIR AR, LOEUF AR, VIRLoF AR - to help users interpret gene ranks, we calculated fold enrichment of Autosomal Dominant (AD) and Autosomal Recessive (AR) genes with known molecular basis of disorder in OMIM in a range of +-5% of gene X (see Figure 2). Statistical significant fold enrichements (Fisher Exact Test p-value < 1e-5) are shown in bold in the table. For example CDK19 gene's GeVIR % is 2.37, so examined range is from 0 (2.37-5, rounded to minimal percentile) to 7.37% (2.37+5). Genes in this range are ~4 times more often (4.05 fold enrichement) associated with AD diseases and ~4 times less often (0.25 fold enrichement) associated with AR diseases. Both enrichment of AD genes and deficiency of AR genes is statistical significant. Thus GeVIR metric adds supportive evidence that CDK19 is more likely to be associated with AD than AR disease.

    Gene Percentiles AD AR Fold Enrichment

    Figure 2. Fold Enrichment of known Autosomal Dominant (AD) and Autosomal Recessive (AR) genes of each gene in the ranked lists (GeVIR, LOEUF, VIRLoF. AD genes are enriched among top ranked genes (lowest percentiles), whereas AR genes are enriched among middle ranked genes (approximetly 35-65 percentiles). Combined metric (VIRLoF, purple) shows the best perfornance, i.e. high ranked genes are more often associated with AD than AR diseases, low ranked genes are less often associated with both AD and AR diseases.
Gene Name Canonical Transcript GeVIR % LOEUF % VIRLoF % GeVIR AD LOEUF AD VIRLoF AD GeVIR AR LOEUF AR VIRLoF AR
AS3MT ENST00000369880 44.42 71.59 58.06 0.66 0.53 0.47 1.77 1.07 1.66
PODN ENST00000312553 44.43 55.62 48.91 0.66 0.53 0.71 1.77 1.60 1.84
RP11-20I23.1 ENST00000564543 44.43 82.43 64.83 0.65 0.34 0.51 1.77 0.52 1.33
ALG11 ENST00000521508 44.44 70.82 57.60 0.65 0.49 0.51 1.77 1.08 1.67
TAAR2 ENST00000367931 44.45 89.18 68.81 0.65 0.27 0.46 1.77 0.35 1.05
TMOD3 ENST00000308580 44.45 34.26 37.61 0.65 0.85 0.82 1.77 1.56 2.01
ITGB4 ENST00000200181 44.46 33.48 37.26 0.65 0.84 0.82 1.77 1.53 2.00
ADHFE1 ENST00000396623 44.46 54.02 48.10 0.65 0.65 0.66 1.77 1.69 1.88
DPH5 ENST00000370109 44.47 65.72 54.70 0.63 0.53 0.57 1.77 1.22 1.73
RTN2 ENST00000245923 44.47 20.08 30.49 0.63 1.44 0.80 1.78 0.74 1.46
PHAX ENST00000297540 44.48 50.82 46.34 0.65 0.63 0.67 1.78 1.93 1.90
CALB2 ENST00000302628 44.48 57.40 49.89 0.65 0.54 0.63 1.78 1.49 1.89
CENPE ENST00000265148 44.49 13.19 27.02 0.63 2.06 0.99 1.78 0.60 1.29
MYO1G ENST00000258787 44.49 33.27 37.12 0.63 0.84 0.81 1.78 1.50 1.95
CADPS2 ENST00000449022 44.50 13.65 27.21 0.63 2.05 0.99 1.78 0.59 1.25
ZC3H4 ENST00000253048 44.50 0.20 20.45 0.63 4.14 1.49 1.78 0.28 0.89
CD200 ENST00000473539 44.51 28.35 34.65 0.63 1.16 0.90 1.79 1.22 1.76
DTNBP1 ENST00000344537 44.51 56.58 49.46 0.63 0.53 0.70 1.80 1.55 1.83
OR4D1 ENST00000268912 44.52 83.04 65.24 0.65 0.32 0.53 1.80 0.49 1.31
DDIT4 ENST00000307365 44.52 69.72 56.98 0.65 0.53 0.49 1.80 1.13 1.70
NEUROG2 ENST00000313341 44.53 27.65 34.38 0.65 1.27 0.87 1.80 1.18 1.77
ELOVL7 ENST00000508821 44.53 36.96 39.09 0.65 0.75 0.77 1.80 1.70 2.06
ADAMTS5 ENST00000284987 44.54 36.72 38.96 0.65 0.76 0.80 1.80 1.66 2.06
NUDT2 ENST00000379158 44.54 77.59 61.82 0.65 0.42 0.47 1.80 0.79 1.46
REEP4 ENST00000306306 44.55 33.64 37.36 0.65 0.85 0.85 1.80 1.55 2.01

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