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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
DPYSL4 ENST00000338492 63.41 49.96 56.48 0.59 0.66 0.52 1.24 2.02 1.70
ZNF181 ENST00000492450 63.41 75.63 72.16 0.59 0.44 0.43 1.24 0.91 0.82
MMP20 ENST00000260228 63.42 75.13 71.86 0.59 0.51 0.44 1.24 0.91 0.83
TNK2 ENST00000381916 63.42 37.32 49.26 0.59 0.76 0.71 1.24 1.66 1.85
SERPINB12 ENST00000269491 63.43 96.90 83.53 0.59 0.23 0.33 1.24 0.19 0.40
FLT3LG ENST00000594009 63.43 15.77 37.83 0.59 1.89 0.84 1.24 0.69 2.01
MGP ENST00000228938 63.44 80.64 74.97 0.59 0.37 0.40 1.23 0.57 0.66
OXNAD1 ENST00000285083 63.44 77.80 73.42 0.59 0.42 0.42 1.23 0.79 0.76
RDH8 ENST00000591589 63.45 61.67 63.82 0.59 0.56 0.49 1.23 1.39 1.38
GMNC ENST00000442080 63.45 28.11 44.26 0.59 1.19 0.61 1.24 1.20 2.05
CPXM2 ENST00000241305 63.46 49.51 56.25 0.59 0.65 0.49 1.24 2.03 1.76
NT5C3B ENST00000435506 63.46 78.18 73.60 0.59 0.43 0.40 1.24 0.73 0.74
DIABLO ENST00000443649 63.47 70.33 68.96 0.59 0.52 0.46 1.23 1.10 1.04
CYB5A ENST00000340533 63.47 76.75 72.85 0.59 0.40 0.40 1.22 0.83 0.81
TCTEX1D2 ENST00000325318 63.48 76.94 72.97 0.59 0.43 0.40 1.23 0.79 0.81
KLHL33 ENST00000344581 63.48 54.94 59.48 0.59 0.57 0.49 1.24 1.63 1.70
FUT11 ENST00000372841 63.49 63.78 65.07 0.59 0.49 0.51 1.24 1.22 1.31
DCTPP1 ENST00000319285 63.49 45.17 53.75 0.59 0.70 0.62 1.24 1.98 1.80
OTOGL ENST00000458043 63.50 47.33 55.00 0.59 0.66 0.51 1.24 2.01 1.74
KRT33A ENST00000007735 63.50 86.86 78.43 0.59 0.22 0.38 1.24 0.40 0.54
THYN1 ENST00000341541 63.51 93.57 81.93 0.59 0.28 0.37 1.24 0.28 0.46
SDR39U1 ENST00000399395 63.51 82.19 75.87 0.59 0.34 0.38 1.24 0.52 0.63
LRRC31 ENST00000316428 63.52 42.84 52.50 0.59 0.62 0.61 1.24 1.91 1.91
CNPY1 ENST00000321736 63.52 95.87 83.03 0.59 0.22 0.30 1.24 0.20 0.40
MRO ENST00000436348 63.53 65.62 66.25 0.59 0.53 0.52 1.24 1.21 1.20

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