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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
CD160 ENST00000235933 73.09 78.37 79.02 0.33 0.43 0.39 0.78 0.74 0.54
CCDC115 ENST00000259229 73.10 88.64 84.13 0.33 0.24 0.34 0.79 0.35 0.42
NME4 ENST00000219479 73.10 79.88 79.80 0.33 0.37 0.38 0.79 0.61 0.52
FCGR2B ENST00000358671 73.11 24.05 47.33 0.33 1.37 0.66 0.78 0.96 1.87
OR52A1 ENST00000380367 73.11 80.63 80.20 0.33 0.37 0.35 0.78 0.57 0.52
PAWR ENST00000328827 73.12 37.20 54.74 0.33 0.78 0.56 0.78 1.66 1.73
CES4A ENST00000540947 73.12 48.85 61.71 0.33 0.63 0.46 0.78 2.03 1.46
SNX8 ENST00000222990 73.13 29.01 50.05 0.33 1.15 0.62 0.78 1.31 1.92
HSPA1B ENST00000375650 73.13 79.58 79.60 0.33 0.38 0.38 0.78 0.66 0.52
KIAA1522 ENST00000401073 73.14 28.55 49.80 0.33 1.16 0.65 0.78 1.27 1.89
ZNF471 ENST00000308031 73.14 48.17 61.33 0.33 0.63 0.44 0.78 1.97 1.48
OR2A25 ENST00000408898 73.15 80.96 80.37 0.33 0.35 0.38 0.78 0.57 0.50
OR8S1 ENST00000310194 73.15 92.84 86.23 0.33 0.29 0.33 0.78 0.30 0.33
OR6K2 ENST00000359610 73.16 92.83 86.24 0.33 0.29 0.33 0.78 0.30 0.33
THEM5 ENST00000368817 73.16 91.42 85.64 0.33 0.23 0.32 0.78 0.33 0.35
DYTN ENST00000452335 73.17 69.87 74.42 0.33 0.54 0.40 0.79 1.15 0.70
CC2D1B ENST00000371586 73.17 48.63 61.63 0.33 0.63 0.46 0.79 2.00 1.47
SRGN ENST00000242465 73.18 42.28 57.74 0.34 0.61 0.49 0.79 1.89 1.68
TNXB ENST00000451343 73.18 27.58 49.27 0.34 1.25 0.70 0.79 1.17 1.85
TUBA3E ENST00000312988 73.19 73.01 76.15 0.34 0.51 0.37 0.79 1.03 0.62
PMF1-BGLAP ENST00000368276 73.19 76.98 78.35 0.34 0.43 0.38 0.79 0.79 0.54
PMF1 ENST00000567140 73.20 77.00 78.33 0.34 0.43 0.38 0.79 0.78 0.54
TMEM184A ENST00000297477 73.20 73.44 76.43 0.34 0.53 0.38 0.79 1.03 0.62
CELA3A ENST00000290122 73.21 74.34 76.91 0.34 0.53 0.35 0.79 1.01 0.60
SPRR1A ENST00000307122 73.21 92.37 86.03 0.34 0.25 0.33 0.79 0.30 0.33

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