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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
SOWAHB ENST00000334306 71.80 34.33 52.33 0.34 0.82 0.61 0.82 1.56 1.91
ADAM28 ENST00000265769 71.80 64.79 70.60 0.34 0.49 0.43 0.82 1.24 0.90
PSD4 ENST00000245796 71.81 16.44 42.38 0.34 1.78 0.68 0.82 0.69 2.02
RAD9A ENST00000307980 71.81 53.91 64.13 0.34 0.65 0.52 0.82 1.70 1.37
CORO7-PAM16 ENST00000572467 71.82 47.98 60.37 0.34 0.61 0.46 0.82 2.00 1.58
MYL10 ENST00000223167 71.82 56.72 65.90 0.34 0.53 0.51 0.82 1.56 1.24
IFT140 ENST00000426508 71.83 43.12 57.40 0.34 0.61 0.51 0.81 1.90 1.67
CCDC68 ENST00000591504 71.84 74.90 76.49 0.34 0.53 0.38 0.81 0.95 0.61
ABLIM2 ENST00000447017 71.84 23.82 46.50 0.34 1.38 0.66 0.82 0.93 1.91
RSAD2 ENST00000382040 71.85 89.79 84.08 0.34 0.27 0.35 0.83 0.37 0.42
ZNF793 ENST00000445217 71.85 74.10 75.98 0.34 0.53 0.38 0.83 1.03 0.62
AIMP2 ENST00000223029 71.86 54.82 64.72 0.34 0.57 0.49 0.83 1.63 1.33
DOC2B ENST00000343572 71.86 59.28 67.36 0.34 0.49 0.52 0.83 1.42 1.15
LCE1B ENST00000360090 71.87 91.41 84.99 0.34 0.23 0.33 0.83 0.33 0.39
SLC11A1 ENST00000233202 71.87 75.83 76.97 0.34 0.43 0.37 0.82 0.88 0.61
ELN ENST00000252034 71.88 46.83 59.69 0.34 0.71 0.49 0.82 1.97 1.67
GAPDHS ENST00000222286 71.88 41.91 56.72 0.33 0.61 0.52 0.82 1.83 1.71
SLC17A4 ENST00000377905 71.89 60.92 68.37 0.33 0.56 0.49 0.82 1.40 1.05
TAS1R1 ENST00000333172 71.89 61.46 68.68 0.33 0.54 0.47 0.82 1.40 1.05
SLC41A3 ENST00000315891 71.90 70.52 74.01 0.33 0.52 0.39 0.82 1.08 0.69
CDH16 ENST00000299752 71.90 74.26 76.11 0.33 0.53 0.38 0.81 1.01 0.62
DCXR ENST00000306869 71.91 78.41 78.39 0.33 0.43 0.38 0.81 0.73 0.54
GPRC5A ENST00000014914 71.91 84.52 81.59 0.33 0.29 0.37 0.81 0.43 0.47
OR10P1 ENST00000309675 71.92 67.58 72.45 0.33 0.53 0.44 0.81 1.19 0.83
SNCG ENST00000372017 71.92 83.61 81.11 0.33 0.27 0.39 0.81 0.47 0.49

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