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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
RAB11A ENST00000261890 0.91 6.15 1.53 4.35 2.75 4.32 0.18 0.35 0.22
HNRNPK ENST00000376263 0.91 0.96 0.13 4.35 4.08 4.86 0.18 0.29 0.18
PSMD14 ENST00000409682 0.92 12.36 3.96 4.34 2.06 3.76 0.18 0.59 0.23
MAPK14 ENST00000229795 0.92 19.11 7.39 4.34 1.49 2.80 0.18 0.76 0.34
ZBTB7A ENST00000322357 0.93 14.19 4.83 4.36 2.06 3.67 0.18 0.60 0.24
KCNMA1 ENST00000404857 0.93 9.09 2.59 4.37 2.45 4.00 0.18 0.47 0.23
NR2F2 ENST00000394166 0.94 6.70 1.71 4.39 2.66 4.24 0.18 0.37 0.23
GABRB2 ENST00000274547 0.95 17.56 6.62 4.39 1.58 3.00 0.18 0.72 0.32
SMARCA4 ENST00000429416 0.95 0.17 0.04 4.38 4.12 4.88 0.18 0.28 0.15
EIF5A ENST00000336452 0.96 27.13 11.66 4.38 1.23 2.21 0.18 1.14 0.47
ELAVL1 ENST00000407627 0.96 7.23 1.91 4.37 2.59 4.16 0.18 0.37 0.24
RPS15A ENST00000322989 0.97 27.98 12.05 4.37 1.20 2.29 0.18 1.19 0.48
SNAP25 ENST00000254976 0.97 7.64 2.04 4.37 2.49 4.12 0.18 0.42 0.23
RIMS4 ENST00000541604 0.98 36.21 16.39 4.36 0.82 1.71 0.18 1.61 0.68
ARF6 ENST00000298316 0.98 36.28 16.44 4.38 0.82 1.72 0.18 1.61 0.69
SMARCA5 ENST00000283131 0.99 0.46 0.08 4.38 4.10 4.88 0.18 0.28 0.15
FZD5 ENST00000295417 0.99 10.56 3.23 4.37 2.15 3.89 0.18 0.52 0.24
AP2S1 ENST00000263270 1.00 24.87 10.50 4.39 1.33 2.18 0.18 1.05 0.43
WDR82 ENST00000296490 1.00 19.26 7.49 4.39 1.47 2.77 0.18 0.76 0.33
NUTF2 ENST00000219169 1.01 18.03 6.86 4.38 1.52 2.94 0.18 0.74 0.33
ZNF629 ENST00000262525 1.01 3.96 0.86 4.38 3.28 4.52 0.18 0.32 0.20
NAA35 ENST00000361671 1.02 2.49 0.48 4.38 3.56 4.74 0.18 0.29 0.17
ACTR2 ENST00000377982 1.02 5.68 1.38 4.37 2.96 4.36 0.18 0.34 0.23
YPEL5 ENST00000379520 1.03 43.03 20.08 4.37 0.61 1.49 0.18 1.89 0.86
SMARCB1 ENST00000263121 1.03 7.06 1.87 4.36 2.57 4.18 0.18 0.37 0.24

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