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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
JAM3 ENST00000299106 50.58 45.82 46.94 0.59 0.73 0.70 1.81 2.02 1.87
GTF3C5 ENST00000372108 51.01 48.81 48.80 0.61 0.63 0.70 1.85 2.02 1.86
CCDC138 ENST00000295124 51.28 49.69 49.35 0.59 0.66 0.70 1.85 2.02 1.84
DUSP5 ENST00000369583 53.14 49.83 50.52 0.63 0.66 0.67 1.76 2.02 1.86
FOCAD ENST00000380249 53.48 45.92 48.60 0.62 0.76 0.67 1.77 2.02 1.85
CCKAR ENST00000295589 54.72 48.45 50.62 0.63 0.63 0.66 1.73 2.02 1.85
ABCC3 ENST00000285238 54.89 49.29 51.15 0.63 0.65 0.65 1.71 2.02 1.90
COL24A1 ENST00000370571 55.19 49.56 51.52 0.61 0.66 0.62 1.69 2.02 1.92
VIL1 ENST00000248444 56.19 47.55 50.92 0.58 0.61 0.66 1.62 2.02 1.85
CHML ENST00000366553 56.29 49.97 52.40 0.58 0.66 0.61 1.63 2.02 1.90
FBXL13 ENST00000313221 56.35 49.98 52.44 0.58 0.66 0.61 1.63 2.02 1.92
ELTD1 ENST00000370742 56.61 49.64 52.37 0.58 0.66 0.61 1.63 2.02 1.90
EMILIN3 ENST00000332312 57.41 46.44 50.98 0.57 0.73 0.66 1.55 2.02 1.85
RNASEH2A ENST00000221486 57.52 49.70 53.00 0.57 0.66 0.61 1.54 2.02 1.87
CYP11A1 ENST00000268053 59.07 49.63 53.78 0.56 0.66 0.62 1.48 2.02 1.80
CD9 ENST00000382518 59.20 45.76 51.63 0.54 0.75 0.62 1.46 2.02 1.92
IL1RN ENST00000259206 60.49 48.47 53.96 0.58 0.65 0.61 1.37 2.02 1.77
CERCAM ENST00000372838 61.00 45.92 52.77 0.58 0.76 0.61 1.34 2.02 1.89
DUS1L ENST00000354321 61.59 49.71 55.26 0.68 0.66 0.51 1.29 2.02 1.74
RBAK ENST00000396912 61.94 49.97 55.64 0.71 0.66 0.53 1.29 2.02 1.73
P2RY2 ENST00000311131 62.46 48.82 55.23 0.68 0.63 0.51 1.28 2.02 1.74
DPYSL4 ENST00000338492 63.41 49.96 56.48 0.59 0.66 0.52 1.24 2.02 1.70
ARMC3 ENST00000298032 63.97 49.66 56.61 0.58 0.66 0.52 1.21 2.02 1.71
KIF24 ENST00000379166 65.48 48.48 56.83 0.56 0.65 0.52 1.10 2.02 1.69
NADSYN1 ENST00000319023 66.98 49.26 58.20 0.61 0.66 0.48 1.03 2.02 1.65

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