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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
ACR ENST00000216139 81.15 40.35 61.44 0.33 0.61 0.44 0.59 1.75 1.47
ACRBP ENST00000229243 59.84 51.70 55.43 0.59 0.61 0.49 1.39 1.88 1.72
ACRC ENST00000373695 94.30 4.43 48.24 0.10 3.27 0.67 0.11 0.32 1.87
ACRV1 ENST00000533904 78.19 75.79 80.31 0.34 0.43 0.38 0.66 0.88 0.52
ACSBG1 ENST00000258873 34.37 31.55 31.16 0.97 0.95 0.85 1.80 1.43 1.54
ACSBG2 ENST00000586696 84.86 48.72 68.79 0.28 0.63 0.46 0.46 1.99 1.05
ACSF2 ENST00000300441 33.88 35.25 32.75 0.92 0.76 0.86 1.73 1.57 1.65
ACSF3 ENST00000317447 79.21 89.62 87.55 0.33 0.27 0.27 0.61 0.37 0.30
ACSL1 ENST00000515030 21.08 20.79 18.92 1.53 1.44 1.54 1.02 0.81 0.83
ACSL3 ENST00000357430 16.93 25.87 19.39 1.48 1.21 1.54 0.86 1.08 0.85
ACSL4 ENST00000340800 15.19 12.11 11.34 1.57 2.06 2.20 0.76 0.57 0.45
ACSL5 ENST00000356116 41.33 37.85 37.82 0.84 0.80 0.84 1.68 1.70 2.02
ACSL6 ENST00000379264 24.13 23.51 21.94 1.34 1.40 1.18 1.12 0.92 0.97
ACSM1 ENST00000307493 78.34 60.09 71.77 0.35 0.52 0.46 0.66 1.38 0.81
ACSM2A ENST00000573854 81.91 75.72 82.19 0.32 0.44 0.35 0.57 0.88 0.45
ACSM2B ENST00000329697 82.77 76.35 82.91 0.30 0.43 0.32 0.56 0.85 0.40
ACSM3 ENST00000289416 48.06 58.47 52.57 0.54 0.54 0.61 1.79 1.39 1.89
ACSM4 ENST00000399422 52.35 67.47 60.38 0.62 0.54 0.46 1.82 1.20 1.58
ACSM5 ENST00000331849 69.51 62.85 68.16 0.53 0.51 0.49 0.98 1.29 1.08
ACSS1 ENST00000323482 53.74 40.62 45.88 0.63 0.63 0.70 1.77 1.77 1.97
ACSS2 ENST00000253382 33.07 48.94 39.36 0.92 0.65 0.80 1.71 2.04 2.04
ACSS3 ENST00000548058 54.35 48.95 50.72 0.65 0.65 0.66 1.73 2.04 1.84
ACTA1 ENST00000366684 1.81 68.99 33.57 4.29 0.54 0.87 0.22 1.15 1.72
ACTA2 ENST00000458208 4.69 16.46 7.95 3.63 1.78 2.59 0.30 0.69 0.36
ACTB ENST00000331789 0.04 8.06 1.88 4.60 2.53 4.18 0.15 0.44 0.24

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