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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
ABCB8 ENST00000358849 60.60 61.05 61.48 0.58 0.54 0.44 1.34 1.39 1.48
ABCB9 ENST00000542678 58.78 33.43 44.68 0.56 0.84 0.62 1.48 1.52 2.06
ABCC1 ENST00000399410 43.10 17.53 28.49 0.82 1.58 0.78 1.78 0.73 1.29
ABCC10 ENST00000372530 46.13 54.13 49.00 0.58 0.63 0.72 1.81 1.68 1.84
ABCC11 ENST00000394747 78.95 67.32 76.21 0.32 0.56 0.37 0.64 1.21 0.62
ABCC12 ENST00000311303 57.69 70.38 65.59 0.57 0.52 0.51 1.53 1.09 1.29
ABCC2 ENST00000370449 56.58 63.74 60.70 0.58 0.49 0.44 1.63 1.22 1.61
ABCC3 ENST00000285238 54.89 49.29 51.15 0.63 0.65 0.65 1.71 2.02 1.90
ABCC4 ENST00000376887 34.27 24.90 27.74 0.96 1.32 0.91 1.78 1.07 1.27
ABCC5 ENST00000334444 12.42 17.15 12.38 1.64 1.61 2.23 0.63 0.75 0.50
ABCC6 ENST00000205557 69.25 56.54 64.17 0.54 0.52 0.51 0.98 1.54 1.36
ABCC8 ENST00000389817 19.17 40.54 28.04 1.58 0.63 0.82 0.94 1.77 1.28
ABCC9 ENST00000261200 2.36 23.54 10.53 4.09 1.39 2.19 0.27 0.93 0.43
ABCD1 ENST00000218104 21.15 3.09 9.58 1.53 3.46 2.28 1.02 0.28 0.40
ABCD2 ENST00000308666 9.08 37.26 21.26 2.30 0.76 1.39 0.46 1.66 0.90
ABCD3 ENST00000370214 10.70 19.95 12.89 1.95 1.47 2.10 0.57 0.73 0.53
ABCD4 ENST00000356924 48.16 49.57 47.70 0.56 0.66 0.65 1.78 2.03 1.89
ABCE1 ENST00000296577 2.29 13.31 5.03 4.13 2.05 3.67 0.28 0.60 0.25
ABCF1 ENST00000326195 16.39 29.38 21.02 1.47 1.10 1.43 0.82 1.36 0.88
ABCF2 ENST00000222388 16.12 23.13 17.52 1.51 1.46 1.63 0.80 0.90 0.75
ABCF3 ENST00000429586 38.13 28.56 31.55 0.91 1.16 0.86 1.73 1.27 1.57
ABCG1 ENST00000361802 18.82 22.33 18.53 1.56 1.51 1.62 0.91 0.82 0.81
ABCG2 ENST00000237612 71.32 81.87 79.92 0.39 0.35 0.37 0.84 0.51 0.52
ABCG4 ENST00000307417 27.81 42.19 33.19 1.19 0.61 0.87 1.45 1.87 1.69
ABCG5 ENST00000260645 58.31 75.01 68.68 0.56 0.53 0.47 1.52 0.93 1.05

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