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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
NOTCH1 ENST00000277541 21.18 0.65 8.26 1.53 4.13 2.57 1.03 0.28 0.37
DES ENST00000373960 21.19 31.29 24.28 1.53 0.99 1.10 1.03 1.38 1.06
NFATC2 ENST00000396009 21.19 5.02 10.73 1.53 3.25 2.20 1.03 0.32 0.43
UBTD2 ENST00000393792 21.20 51.09 34.40 1.52 0.66 0.90 1.03 1.92 1.77
CRY1 ENST00000008527 21.20 43.13 30.36 1.52 0.62 0.81 1.03 1.89 1.45
RUNDC3B ENST00000338056 21.21 29.64 23.52 1.52 1.10 1.18 1.03 1.39 1.01
IREB2 ENST00000258886 21.21 7.44 11.94 1.52 2.54 2.28 1.04 0.39 0.46
RAPGEF5 ENST00000344041 21.22 11.59 14.13 1.52 2.10 2.00 1.04 0.57 0.59
PREP ENST00000369110 21.22 18.79 17.92 1.52 1.53 1.68 1.04 0.74 0.77
RPS7 ENST00000304921 21.23 12.73 14.76 1.52 2.10 1.96 1.04 0.59 0.62
PRKD3 ENST00000379066 21.23 21.07 19.14 1.52 1.44 1.53 1.04 0.83 0.85
PPP2R1B ENST00000311129 21.24 58.71 38.24 1.52 0.54 0.85 1.05 1.44 2.04
EPHA5 ENST00000273854 21.24 28.06 22.79 1.53 1.19 1.19 1.05 1.20 0.98
GALNT10 ENST00000297107 21.25 33.33 25.38 1.53 0.85 1.04 1.05 1.51 1.17
ANKRD40 ENST00000285243 21.25 23.53 20.49 1.53 1.39 1.49 1.05 0.92 0.89
TECR ENST00000215567 21.26 27.22 22.43 1.53 1.24 1.15 1.05 1.15 0.97
CERS6 ENST00000392687 21.26 25.38 21.45 1.53 1.27 1.30 1.05 1.04 0.91
LARP4 ENST00000398473 21.27 14.88 15.88 1.53 1.92 1.76 1.06 0.62 0.66
RAPGEF4 ENST00000397081 21.27 11.99 14.34 1.53 2.07 2.00 1.06 0.57 0.59
FASN ENST00000306749 21.28 2.50 9.34 1.53 3.56 2.32 1.06 0.29 0.39
RALGDS ENST00000372050 21.29 14.76 15.85 1.53 1.96 1.77 1.06 0.62 0.66
VPS13D ENST00000358136 21.29 14.20 15.57 1.53 2.06 1.77 1.06 0.60 0.67
PSMB6 ENST00000270586 21.30 44.50 31.09 1.53 0.63 0.84 1.06 1.97 1.52
HSD17B11 ENST00000358290 21.30 77.58 48.31 1.53 0.42 0.67 1.06 0.79 1.89
GART ENST00000381831 21.31 25.25 21.40 1.53 1.29 1.33 1.06 1.02 0.91

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