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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
ACTRT2 ENST00000378404 74.43 76.40 78.66 0.37 0.43 0.38 0.81 0.86 0.55
ACTRT3 ENST00000330368 59.90 85.54 75.72 0.63 0.27 0.38 1.38 0.44 0.64
ACVR1 ENST00000263640 6.66 21.63 11.76 2.99 1.44 2.21 0.37 0.81 0.46
ACVR1B ENST00000541224 5.35 5.01 2.69 3.37 3.25 4.00 0.32 0.32 0.23
ACVR1C ENST00000243349 30.31 32.61 29.64 1.01 0.85 0.85 1.61 1.47 1.40
ACVR2A ENST00000241416 3.12 3.82 1.47 3.87 3.31 4.34 0.30 0.31 0.22
ACVR2B ENST00000352511 14.35 17.65 13.67 1.56 1.58 2.02 0.73 0.73 0.58
ACVRL1 ENST00000388922 11.42 37.17 22.47 1.76 0.78 1.16 0.59 1.66 0.97
ACY1 ENST00000404366 53.40 60.99 57.08 0.62 0.54 0.52 1.76 1.41 1.71
ACY3 ENST00000255082 82.67 77.42 83.40 0.30 0.42 0.33 0.57 0.76 0.40
ACYP1 ENST00000238618 20.53 79.43 48.88 1.54 0.38 0.71 1.01 0.67 1.85
ACYP2 ENST00000394666 84.02 91.80 90.95 0.30 0.23 0.15 0.48 0.32 0.20
ADA ENST00000372874 49.37 69.41 59.74 0.57 0.56 0.49 1.81 1.13 1.66
ADAD1 ENST00000296513 28.32 24.28 24.38 1.18 1.30 1.08 1.49 0.99 1.07
ADAD2 ENST00000268624 81.94 63.83 75.90 0.32 0.49 0.38 0.57 1.21 0.62
ADAL ENST00000428046 52.53 66.95 60.19 0.67 0.53 0.48 1.80 1.25 1.61
ADAM10 ENST00000260408 2.49 1.59 0.62 4.09 3.86 4.66 0.27 0.26 0.19
ADAM11 ENST00000200557 10.65 27.25 16.80 1.99 1.25 1.70 0.57 1.15 0.70
ADAM12 ENST00000368679 54.10 29.99 40.31 0.63 1.09 0.80 1.73 1.41 2.00
ADAM15 ENST00000356955 54.39 46.64 49.43 0.65 0.75 0.70 1.72 1.99 1.84
ADAM17 ENST00000310823 14.45 9.01 9.17 1.56 2.44 2.33 0.73 0.47 0.38
ADAM18 ENST00000265707 80.38 82.49 84.79 0.33 0.34 0.34 0.58 0.52 0.40
ADAM19 ENST00000257527 27.64 23.59 23.71 1.24 1.39 1.15 1.43 0.93 1.02
ADAM2 ENST00000265708 98.61 64.03 84.67 0.10 0.49 0.34 0.11 1.20 0.40
ADAM20 ENST00000256389 96.83 99.85 99.63 0.09 0.17 0.12 0.11 0.11 0.04

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