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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
C2orf42 ENST00000264434 17.44 28.77 21.21 1.46 1.15 1.40 0.87 1.29 0.90
ZNF827 ENST00000379448 17.44 8.08 10.33 1.46 2.52 2.19 0.87 0.44 0.43
MBD5 ENST00000407073 17.45 2.49 7.35 1.46 3.57 2.80 0.87 0.29 0.34
DUSP6 ENST00000279488 17.45 9.23 10.97 1.46 2.47 2.21 0.87 0.47 0.44
DCLK2 ENST00000302176 17.46 14.00 13.34 1.46 2.06 2.05 0.87 0.59 0.55
MAPRE1 ENST00000375571 17.46 6.96 9.69 1.46 2.58 2.26 0.87 0.37 0.40
ZDHHC21 ENST00000380916 17.47 39.81 26.81 1.46 0.65 0.96 0.87 1.68 1.28
CDH7 ENST00000397968 17.47 18.06 15.58 1.46 1.53 1.77 0.87 0.74 0.66
LBH ENST00000395323 17.48 83.98 49.66 1.46 0.28 0.66 0.87 0.46 1.84
OLFM2 ENST00000264833 17.48 27.32 20.51 1.46 1.27 1.49 0.87 1.15 0.89
RPS19 ENST00000598742 17.49 27.12 20.37 1.46 1.23 1.49 0.87 1.13 0.88
KCNAB1 ENST00000490337 17.49 17.56 15.29 1.46 1.58 1.83 0.88 0.72 0.66
SPSB1 ENST00000328089 17.50 31.87 22.83 1.46 0.94 1.19 0.88 1.48 0.97
C15orf57 ENST00000558750 17.50 35.74 24.68 1.46 0.78 1.05 0.88 1.58 1.10
SSR1 ENST00000244763 17.51 25.50 19.50 1.47 1.25 1.54 0.88 1.06 0.83
TMEM41B ENST00000528080 17.51 33.00 23.36 1.47 0.85 1.20 0.88 1.49 0.99
TMEM39A ENST00000319172 17.52 15.35 14.13 1.47 1.89 2.00 0.88 0.68 0.59
STRADB ENST00000194530 17.52 35.45 24.56 1.47 0.77 1.06 0.88 1.56 1.09
BRE ENST00000344773 17.53 24.03 18.79 1.47 1.38 1.57 0.88 0.96 0.83
SYVN1 ENST00000377190 17.54 4.53 8.41 1.46 3.25 2.53 0.88 0.32 0.38
USP1 ENST00000339950 17.54 9.52 11.19 1.46 2.51 2.16 0.88 0.49 0.45
TTL ENST00000233336 17.55 26.72 20.20 1.46 1.20 1.48 0.88 1.12 0.88
DUSP10 ENST00000366899 17.55 22.19 17.79 1.46 1.53 1.66 0.88 0.81 0.78
MTMR2 ENST00000346299 17.56 32.73 23.23 1.46 0.84 1.19 0.88 1.44 1.01
HTRA1 ENST00000368984 17.56 39.16 26.47 1.46 0.70 1.00 0.88 1.62 1.25

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