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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
AC093157.1 ENST00000593496 60.03 87.51 76.92 0.63 0.23 0.35 1.39 0.38 0.60
AC093802.1 ENST00000407524 93.02 89.47 94.13 0.16 0.27 0.09 0.15 0.36 0.12
AC097381.1 ENST00000429019 91.53 98.47 97.60 0.15 0.21 0.09 0.20 0.14 0.06
AC099552.4 ENST00000404289 92.75 77.83 88.48 0.15 0.42 0.22 0.17 0.79 0.29
AC103809.2 ENST00000599136 83.60 89.16 89.51 0.29 0.27 0.18 0.52 0.35 0.23
AC104057.1 ENST00000593865 92.61 92.77 94.40 0.15 0.29 0.10 0.18 0.30 0.12
AC104472.1 ENST00000399242 90.14 97.79 96.90 0.16 0.21 0.08 0.25 0.17 0.07
AC105020.1 ENST00000435356 90.75 98.10 96.93 0.16 0.20 0.08 0.23 0.16 0.07
AC106873.4 ENST00000420664 90.36 89.70 94.57 0.15 0.27 0.09 0.25 0.37 0.11
AC106876.2 ENST00000409905 99.77 87.30 96.28 0.12 0.22 0.07 0.13 0.41 0.09
AC107021.1 ENST00000422482 92.09 98.79 98.14 0.15 0.16 0.09 0.20 0.14 0.05
AC110615.1 ENST00000599764 59.40 91.09 78.49 0.57 0.25 0.38 1.44 0.35 0.54
AC110619.2 ENST00000404327 90.64 78.57 88.06 0.16 0.40 0.23 0.24 0.74 0.30
AC110781.3 ENST00000402221 97.21 92.30 97.38 0.10 0.25 0.08 0.11 0.30 0.07
AC112693.2 ENST00000599897 92.66 99.13 97.72 0.15 0.15 0.09 0.17 0.14 0.05
AC112715.2 ENST00000445534 93.99 83.92 91.78 0.10 0.28 0.14 0.13 0.47 0.18
AC112721.1 ENST00000409162 90.71 98.07 97.05 0.16 0.20 0.08 0.23 0.16 0.07
AC114494.1 ENST00000596131 67.12 94.29 83.99 0.61 0.24 0.35 1.04 0.25 0.42
AC114546.1 ENST00000391457 92.73 99.17 98.45 0.15 0.15 0.10 0.17 0.14 0.05
AC114783.1 ENST00000450035 89.88 85.55 90.87 0.16 0.27 0.15 0.28 0.44 0.20
AC115618.1 ENST00000376775 91.96 98.72 98.08 0.15 0.16 0.09 0.20 0.15 0.05
AC117834.1 ENST00000391681 94.19 72.83 86.67 0.10 0.49 0.30 0.13 1.04 0.33
AC120194.1 ENST00000391684 90.13 91.98 93.92 0.16 0.23 0.09 0.25 0.33 0.11
AC124890.1 ENST00000399333 91.88 98.66 98.03 0.14 0.20 0.09 0.20 0.15 0.05
AC127496.1 ENST00000321930 91.64 98.52 97.92 0.14 0.21 0.09 0.20 0.15 0.04

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