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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
EPO ENST00000252723 57.47 47.91 51.85 0.58 0.59 0.62 1.54 1.99 1.92
LRRC61 ENST00000359623 57.47 76.66 69.15 0.58 0.40 0.44 1.54 0.83 0.99
DDX58 ENST00000379883 57.48 57.98 57.72 0.57 0.56 0.49 1.54 1.44 1.68
TXNDC11 ENST00000283033 57.48 43.93 49.64 0.57 0.61 0.66 1.54 1.97 1.84
MAP9 ENST00000311277 57.49 64.00 61.44 0.57 0.48 0.44 1.54 1.20 1.47
CCDC146 ENST00000285871 57.49 58.77 58.19 0.57 0.54 0.48 1.54 1.43 1.65
TGM6 ENST00000202625 57.50 73.47 67.27 0.57 0.53 0.52 1.54 1.03 1.15
SLFN14 ENST00000415846 57.50 50.08 53.22 0.57 0.67 0.61 1.54 1.99 1.88
RPP30 ENST00000413330 57.51 62.11 60.25 0.57 0.54 0.47 1.54 1.35 1.59
TPPP2 ENST00000321760 57.51 77.37 69.64 0.57 0.42 0.44 1.54 0.76 0.95
RNASEH2A ENST00000221486 57.52 49.70 53.00 0.57 0.66 0.61 1.54 2.02 1.87
PCK1 ENST00000319441 57.52 69.46 64.90 0.57 0.54 0.51 1.54 1.13 1.33
TMPRSS13 ENST00000524993 57.53 48.41 52.20 0.57 0.63 0.61 1.54 2.01 1.89
DDX60 ENST00000393743 57.53 29.66 41.82 0.57 1.10 0.71 1.54 1.39 2.01
RIOK1 ENST00000379834 57.54 60.08 58.91 0.57 0.52 0.49 1.54 1.38 1.65
PTF1A ENST00000376504 57.54 57.25 57.26 0.57 0.56 0.52 1.54 1.49 1.70
LRWD1 ENST00000292616 57.55 68.80 64.47 0.57 0.53 0.51 1.53 1.19 1.32
SLC35B3 ENST00000379660 57.55 74.51 67.96 0.57 0.53 0.51 1.53 1.00 1.10
GLIS1 ENST00000312233 57.56 31.45 42.82 0.57 0.96 0.68 1.53 1.42 2.01
COL10A1 ENST00000327673 57.56 50.98 53.67 0.57 0.65 0.62 1.53 1.92 1.80
PDLIM4 ENST00000253754 57.57 8.50 31.24 0.57 2.52 0.86 1.53 0.46 1.56
AIF1L ENST00000372309 57.57 62.81 60.78 0.57 0.51 0.44 1.53 1.29 1.61
TSPAN17 ENST00000310032 57.58 59.16 58.42 0.57 0.49 0.52 1.53 1.44 1.65
KRT3 ENST00000417996 57.58 65.65 62.48 0.57 0.53 0.48 1.53 1.22 1.40
NFATC2IP ENST00000320805 57.59 56.09 56.64 0.57 0.51 0.52 1.53 1.56 1.72

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