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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
SLC10A3 ENST00000263512 54.37 29.24 40.09 0.65 1.14 0.82 1.73 1.36 1.99
PDE6H ENST00000266395 54.37 89.58 74.88 0.65 0.27 0.39 1.73 0.37 0.64
GKN1 ENST00000377938 54.38 86.38 73.11 0.65 0.25 0.42 1.73 0.42 0.79
OPRM1 ENST00000434900 54.38 73.99 65.78 0.65 0.53 0.51 1.72 1.02 1.26
TCEAL4 ENST00000472745 54.39 33.45 42.17 0.65 0.84 0.68 1.72 1.52 2.01
ADAM15 ENST00000356955 54.39 46.64 49.43 0.65 0.75 0.70 1.72 1.99 1.84
OR6C1 ENST00000379668 54.40 41.60 46.69 0.65 0.63 0.66 1.72 1.80 1.86
CEP120 ENST00000306467 54.40 41.59 46.68 0.65 0.63 0.66 1.72 1.80 1.87
DYRK4 ENST00000540757 54.41 79.75 69.16 0.65 0.37 0.44 1.72 0.64 0.99
ACOXL ENST00000439055 54.41 61.54 58.05 0.65 0.54 0.47 1.71 1.41 1.66
SEC13 ENST00000350697 54.42 30.39 40.59 0.65 1.08 0.81 1.70 1.39 2.04
XDH ENST00000379416 54.42 44.98 48.57 0.65 0.68 0.67 1.70 1.97 1.85
DIDO1 ENST00000266070 54.43 4.68 27.71 0.65 3.27 0.92 1.70 0.31 1.27
TMPRSS11E ENST00000305363 54.43 51.19 52.03 0.65 0.66 0.62 1.70 1.91 1.94
GAN ENST00000568107 54.44 25.23 38.11 0.65 1.30 0.86 1.70 1.02 2.02
TRAPPC2P1 ENST00000543226 54.44 90.71 75.53 0.65 0.25 0.37 1.71 0.35 0.66
BEND6 ENST00000370746 54.45 53.05 53.17 0.65 0.66 0.61 1.72 1.77 1.87
CENPJ ENST00000381884 54.45 52.35 52.73 0.65 0.62 0.61 1.71 1.82 1.88
ITGA11 ENST00000315757 54.46 28.58 39.88 0.65 1.16 0.78 1.71 1.27 2.02
COX10 ENST00000261643 54.47 33.46 42.21 0.65 0.84 0.68 1.72 1.52 2.02
C10orf32 ENST00000339834 54.47 92.70 76.67 0.65 0.29 0.35 1.72 0.30 0.61
CASP7 ENST00000369321 54.48 48.03 50.29 0.65 0.63 0.65 1.71 2.00 1.92
TSPYL5 ENST00000322128 54.48 23.18 37.07 0.63 1.46 0.80 1.71 0.91 1.95
FMO2 ENST00000441535 54.49 59.18 56.63 0.63 0.49 0.52 1.72 1.44 1.72
ZNF628 ENST00000598519 54.49 16.40 33.61 0.63 1.81 0.90 1.72 0.69 1.72

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