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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
FBXL13 ENST00000313221 56.35 49.98 52.44 0.58 0.66 0.61 1.63 2.02 1.92
ELTD1 ENST00000370742 56.61 49.64 52.37 0.58 0.66 0.61 1.63 2.02 1.90
EMILIN3 ENST00000332312 57.41 46.44 50.98 0.57 0.73 0.66 1.55 2.02 1.85
RNASEH2A ENST00000221486 57.52 49.70 53.00 0.57 0.66 0.61 1.54 2.02 1.87
CYP11A1 ENST00000268053 59.07 49.63 53.78 0.56 0.66 0.62 1.48 2.02 1.80
CD9 ENST00000382518 59.20 45.76 51.63 0.54 0.75 0.62 1.46 2.02 1.92
IL1RN ENST00000259206 60.49 48.47 53.96 0.58 0.65 0.61 1.37 2.02 1.77
CERCAM ENST00000372838 61.00 45.92 52.77 0.58 0.76 0.61 1.34 2.02 1.89
DUS1L ENST00000354321 61.59 49.71 55.26 0.68 0.66 0.51 1.29 2.02 1.74
RBAK ENST00000396912 61.94 49.97 55.64 0.71 0.66 0.53 1.29 2.02 1.73
P2RY2 ENST00000311131 62.46 48.82 55.23 0.68 0.63 0.51 1.28 2.02 1.74
DPYSL4 ENST00000338492 63.41 49.96 56.48 0.59 0.66 0.52 1.24 2.02 1.70
ARMC3 ENST00000298032 63.97 49.66 56.61 0.58 0.66 0.52 1.21 2.02 1.71
KIF24 ENST00000379166 65.48 48.48 56.83 0.56 0.65 0.52 1.10 2.02 1.69
NADSYN1 ENST00000319023 66.98 49.26 58.20 0.61 0.66 0.48 1.03 2.02 1.65
GPR179 ENST00000342292 68.03 45.98 56.86 0.58 0.77 0.52 1.03 2.02 1.70
SH2B2 ENST00000536178 68.65 49.22 59.11 0.56 0.66 0.49 0.94 2.02 1.68
ZNF772 ENST00000343280 69.24 49.23 59.54 0.56 0.66 0.49 0.97 2.02 1.69
MEIS3 ENST00000561293 69.26 49.64 59.84 0.54 0.66 0.49 0.98 2.02 1.63
ADCK2 ENST00000072869 69.61 49.74 60.11 0.54 0.66 0.48 0.97 2.02 1.61
IAH1 ENST00000497473 70.22 49.74 60.51 0.49 0.66 0.44 0.91 2.02 1.58
CD69 ENST00000228434 70.26 48.42 59.67 0.49 0.63 0.49 0.92 2.02 1.67
RPLP2 ENST00000321153 70.63 49.70 60.74 0.49 0.66 0.44 0.91 2.02 1.61
FAM71F2 ENST00000480462 70.87 48.81 60.30 0.47 0.63 0.47 0.87 2.02 1.59
COQ2 ENST00000311469 72.01 48.45 60.81 0.34 0.63 0.43 0.81 2.02 1.60

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