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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
AL138764.1 ENST00000429930 93.94 99.78 96.30 0.11 0.17 0.07 0.13 0.11 0.09
ANKRD65 ENST00000537107 89.92 97.10 96.31 0.18 0.24 0.07 0.28 0.18 0.09
C21orf54 ENST00000451980 96.85 90.33 96.31 0.09 0.25 0.07 0.11 0.38 0.09
IFI27 ENST00000555744 98.89 88.29 96.32 0.10 0.23 0.07 0.11 0.37 0.09
COX8C ENST00000342144 94.91 92.28 96.32 0.10 0.25 0.07 0.12 0.30 0.09
HIST1H1T ENST00000338379 89.07 98.93 96.33 0.19 0.17 0.07 0.32 0.15 0.09
ADAMTSL4-AS1 ENST00000369035 89.64 97.53 96.33 0.16 0.22 0.07 0.29 0.19 0.09
RBMY1E ENST00000382659 93.62 93.47 96.34 0.13 0.28 0.07 0.13 0.28 0.09
MRGPRE ENST00000436689 88.26 99.31 96.34 0.20 0.16 0.07 0.35 0.12 0.09
GSC2 ENST00000086933 92.15 94.63 96.35 0.15 0.23 0.07 0.19 0.24 0.09
TMEM133 ENST00000303130 88.79 98.26 96.35 0.19 0.21 0.07 0.33 0.15 0.09
C10orf67 ENST00000323327 99.97 87.29 96.36 0.10 0.22 0.07 0.14 0.41 0.09
AC012215.1 ENST00000437887 89.67 97.54 96.36 0.16 0.22 0.07 0.29 0.19 0.09
FBXL8 ENST00000258200 92.02 94.81 96.37 0.15 0.23 0.07 0.20 0.24 0.09
FUT6 ENST00000318336 88.50 98.56 96.37 0.20 0.20 0.07 0.34 0.15 0.09
GPR32 ENST00000270590 89.19 97.98 96.38 0.18 0.20 0.07 0.32 0.17 0.09
LCN1 ENST00000263598 96.53 90.75 96.38 0.10 0.25 0.07 0.11 0.35 0.09
RP11-379H8.1 ENST00000568285 89.99 94.17 96.39 0.18 0.25 0.07 0.27 0.25 0.09
AL355390.1 ENST00000325811 93.11 93.92 96.39 0.15 0.25 0.07 0.16 0.26 0.09
KIR3DL2 ENST00000326321 95.13 92.20 96.40 0.10 0.25 0.07 0.12 0.31 0.09
OR4F4 ENST00000326183 94.67 92.66 96.41 0.10 0.29 0.07 0.11 0.31 0.09
AP000974.1 ENST00000544076 89.69 97.55 96.41 0.16 0.22 0.07 0.28 0.19 0.09
C9orf47 ENST00000334490 98.92 88.39 96.42 0.10 0.23 0.07 0.11 0.37 0.09
C11orf86 ENST00000308963 92.12 94.77 96.42 0.15 0.23 0.07 0.19 0.24 0.09
ZNF256 ENST00000282308 94.93 92.41 96.43 0.10 0.27 0.07 0.12 0.30 0.09

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