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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
HDC ENST00000267845 25.96 26.83 24.45 1.37 1.23 1.08 1.22 1.12 1.08
RNF150 ENST00000515673 25.96 44.64 33.42 1.37 0.66 0.87 1.22 1.97 1.71
GAREM ENST00000269209 25.97 18.24 20.17 1.37 1.49 1.48 1.22 0.74 0.87
DOK6 ENST00000382713 25.97 29.30 25.76 1.37 1.14 1.04 1.22 1.36 1.22
GDF5 ENST00000374372 25.98 22.71 22.52 1.35 1.47 1.16 1.22 0.88 0.97
GPC3 ENST00000394299 25.99 3.28 12.22 1.35 3.44 2.26 1.22 0.27 0.50
RAI14 ENST00000515799 25.99 10.61 16.11 1.35 2.14 1.71 1.22 0.51 0.66
FASTK ENST00000297532 26.00 31.37 26.85 1.35 0.97 0.97 1.22 1.41 1.27
OSTF1 ENST00000346234 26.00 36.68 29.49 1.35 0.78 0.84 1.22 1.66 1.38
MAP1LC3B ENST00000268607 26.01 74.99 49.37 1.35 0.53 0.70 1.22 0.93 1.84
EGFR ENST00000275493 26.01 15.12 18.51 1.35 1.91 1.62 1.22 0.66 0.81
PLCH1 ENST00000340059 26.02 15.71 18.89 1.35 1.87 1.54 1.23 0.69 0.83
ERO1L ENST00000395686 26.02 16.89 19.46 1.35 1.66 1.53 1.23 0.71 0.84
KIAA0226 ENST00000296343 26.03 40.63 31.56 1.35 0.63 0.87 1.24 1.77 1.56
KIAA1958 ENST00000337530 26.03 32.22 27.27 1.35 0.86 0.97 1.24 1.46 1.25
FAM134B ENST00000306320 26.04 44.54 33.43 1.35 0.65 0.87 1.24 1.97 1.71
SPTLC3 ENST00000399002 26.04 46.78 34.63 1.35 0.72 0.90 1.23 1.97 1.76
TJP1 ENST00000346128 26.05 0.40 10.84 1.35 4.13 2.19 1.22 0.28 0.44
ZNF398 ENST00000475153 26.05 24.74 23.50 1.35 1.32 1.18 1.23 1.05 1.01
TGFB1 ENST00000221930 26.06 27.83 25.00 1.35 1.23 1.04 1.24 1.18 1.14
KBTBD8 ENST00000417314 26.06 43.40 32.93 1.35 0.61 0.86 1.24 1.95 1.67
EDEM3 ENST00000318130 26.07 22.63 22.53 1.35 1.47 1.16 1.24 0.86 0.97
ESF1 ENST00000202816 26.07 22.53 22.48 1.35 1.48 1.16 1.24 0.84 0.97
HYOU1 ENST00000404233 26.08 14.24 18.12 1.35 2.05 1.67 1.24 0.61 0.78
ARMCX1 ENST00000372829 26.08 57.84 40.24 1.35 0.57 0.81 1.24 1.47 2.00

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