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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
CPQ ENST00000220763 47.39 78.54 64.26 0.56 0.40 0.51 1.82 0.73 1.35
URI1 ENST00000542441 47.40 35.83 39.95 0.56 0.80 0.81 1.82 1.59 2.00
TIGD2 ENST00000317005 47.40 46.67 45.74 0.56 0.75 0.67 1.82 1.97 1.98
GNL3L ENST00000336470 47.41 7.91 25.78 0.56 2.53 1.04 1.81 0.44 1.23
SCNN1B ENST00000343070 47.41 43.22 43.67 0.56 0.62 0.61 1.81 1.91 2.02
KIF20B ENST00000260753 47.42 33.60 38.79 0.56 0.85 0.82 1.81 1.55 2.03
AMPD1 ENST00000520113 47.43 65.20 56.03 0.56 0.51 0.49 1.81 1.23 1.76
GALM ENST00000272252 47.43 81.56 66.16 0.56 0.33 0.52 1.81 0.52 1.20
EFTUD1 ENST00000268206 47.44 28.37 36.01 0.56 1.16 0.87 1.80 1.22 1.79
TTLL13 ENST00000339615 47.44 64.67 55.75 0.56 0.48 0.53 1.80 1.24 1.74
HOXC5 ENST00000312492 47.45 80.73 65.71 0.56 0.37 0.51 1.81 0.57 1.27
TOM1 ENST00000411850 47.45 55.38 50.43 0.56 0.58 0.67 1.81 1.61 1.89
C1orf145 ENST00000295012 47.46 90.90 71.75 0.56 0.25 0.46 1.81 0.35 0.81
WDHD1 ENST00000360586 47.46 43.50 43.85 0.56 0.61 0.62 1.81 1.97 2.02
PRTFDC1 ENST00000320152 47.47 85.33 68.40 0.56 0.25 0.47 1.81 0.45 1.05
NT5C1A ENST00000235628 47.47 56.77 51.20 0.57 0.53 0.63 1.81 1.55 1.92
STYK1 ENST00000075503 47.48 64.59 55.68 0.57 0.48 0.53 1.80 1.22 1.73
CSRP3 ENST00000533783 47.48 70.46 59.14 0.57 0.52 0.51 1.80 1.08 1.68
DONSON ENST00000303071 47.49 49.38 47.19 0.57 0.65 0.67 1.80 2.02 1.89
DUOX2 ENST00000603300 47.49 70.30 59.05 0.57 0.52 0.49 1.80 1.10 1.66
NSUN4 ENST00000474844 47.50 49.82 47.42 0.57 0.66 0.65 1.80 2.02 1.87
HIF3A ENST00000377670 47.50 31.04 37.52 0.57 1.04 0.84 1.79 1.36 2.01
AC010336.1 ENST00000539278 47.51 90.11 71.26 0.57 0.25 0.44 1.79 0.38 0.87
GXYLT1 ENST00000398675 47.51 22.47 33.15 0.56 1.52 0.87 1.79 0.83 1.69
FLII ENST00000327031 47.52 31.95 38.01 0.56 0.92 0.85 1.79 1.48 2.02

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