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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
KISS1 ENST00000367194 40.29 75.30 57.79 0.86 0.49 0.51 1.73 0.90 1.67
SRD5A3 ENST00000264228 40.30 58.17 48.10 0.86 0.54 0.66 1.73 1.45 1.89
SIPA1L3 ENST00000222345 40.30 6.02 21.23 0.86 2.82 1.40 1.73 0.35 0.90
HMX3 ENST00000357878 40.31 16.62 26.62 0.86 1.72 0.97 1.73 0.71 1.25
LRIG2 ENST00000361127 40.31 48.31 42.59 0.86 0.63 0.67 1.73 2.00 2.02
TSC22D4 ENST00000300181 40.32 12.14 24.25 0.86 2.07 1.10 1.73 0.57 1.05
COLEC10 ENST00000332843 40.32 52.71 45.19 0.86 0.67 0.70 1.73 1.80 2.00
SPRTN ENST00000295050 40.33 13.59 25.00 0.86 2.05 1.04 1.73 0.59 1.14
POFUT1 ENST00000375749 40.33 14.98 25.77 0.86 1.92 1.04 1.73 0.64 1.23
TCAIM ENST00000342649 40.34 39.87 38.40 0.86 0.65 0.84 1.73 1.69 2.04
NAA16 ENST00000379406 40.34 52.94 45.31 0.85 0.63 0.70 1.73 1.78 2.01
MTAP ENST00000380172 40.35 76.15 58.29 0.85 0.43 0.48 1.73 0.87 1.65
HMGB3 ENST00000325307 40.35 30.34 33.51 0.85 1.08 0.89 1.73 1.41 1.72
POSTN ENST00000379747 40.36 37.78 37.35 0.85 0.80 0.84 1.72 1.70 2.01
CXCL9 ENST00000264888 40.36 87.31 65.37 0.85 0.22 0.53 1.72 0.41 1.31
TMEM98 ENST00000579849 40.37 47.71 42.36 0.85 0.61 0.68 1.72 1.99 2.02
TMEM5 ENST00000261234 40.37 50.99 44.12 0.85 0.65 0.61 1.72 1.92 2.03
SAV1 ENST00000324679 40.38 36.47 36.54 0.85 0.82 0.85 1.73 1.64 1.90
GABRR2 ENST00000402938 40.39 49.61 43.36 0.85 0.66 0.63 1.73 2.02 2.00
DKK3 ENST00000396505 40.39 57.53 47.80 0.85 0.56 0.65 1.73 1.48 1.89
POLR3C ENST00000334163 40.40 55.64 46.72 0.85 0.53 0.66 1.73 1.60 1.86
CHST15 ENST00000346248 40.40 39.85 38.42 0.86 0.65 0.84 1.73 1.69 2.04
MUT ENST00000274813 40.41 65.50 52.18 0.86 0.54 0.61 1.73 1.23 1.89
TTR ENST00000237014 40.41 38.76 37.81 0.86 0.70 0.84 1.73 1.67 2.01
TRIP11 ENST00000267622 40.42 25.05 30.93 0.86 1.33 0.80 1.74 1.03 1.51

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