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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
MAP2K1 ENST00000307102 1.99 16.93 6.80 4.25 1.66 2.97 0.23 0.71 0.32
ZNF536 ENST00000355537 1.58 7.12 2.08 4.25 2.58 4.09 0.20 0.37 0.23
PSMA5 ENST00000271308 1.99 5.43 1.65 4.26 3.02 4.27 0.23 0.33 0.23
SKP1 ENST00000353411 1.57 36.11 16.69 4.26 0.81 1.68 0.20 1.60 0.70
PA2G4 ENST00000303305 1.98 6.02 1.86 4.26 2.82 4.19 0.23 0.35 0.24
ACTG1 ENST00000575842 1.57 46.66 22.26 4.26 0.75 1.16 0.20 1.97 0.96
SF1 ENST00000377387 1.98 4.65 1.34 4.26 3.27 4.33 0.24 0.31 0.23
SAMD4B ENST00000314471 1.92 3.00 0.84 4.26 3.47 4.53 0.24 0.28 0.21
AP2B1 ENST00000312678 1.56 10.11 3.27 4.26 2.33 3.90 0.20 0.48 0.24
METTL14 ENST00000388822 1.97 32.99 15.25 4.27 0.84 1.83 0.24 1.49 0.65
TUBB3 ENST00000315491 1.59 14.13 5.10 4.27 2.05 3.63 0.20 0.59 0.25
RAD21 ENST00000297338 1.91 3.23 0.90 4.27 3.46 4.48 0.24 0.28 0.21
RRAGA ENST00000380527 1.79 39.12 18.39 4.27 0.70 1.64 0.22 1.62 0.81
SF3B5 ENST00000367569 1.55 59.77 28.79 4.27 0.52 0.80 0.20 1.37 1.32
KIF11 ENST00000260731 1.88 0.87 0.29 4.27 4.10 4.86 0.24 0.29 0.18
TSN ENST00000389682 1.97 24.02 10.58 4.27 1.38 2.16 0.24 0.96 0.44
RHOB ENST00000272233 1.94 64.21 31.31 4.27 0.49 0.87 0.24 1.20 1.55
YWHAE ENST00000264335 1.58 7.75 2.36 4.27 2.54 4.04 0.20 0.43 0.23
PQBP1 ENST00000218224 1.91 26.08 11.64 4.27 1.20 2.21 0.24 1.09 0.47
PSMC4 ENST00000157812 1.79 24.43 10.71 4.27 1.32 2.19 0.22 1.00 0.43
AGO3 ENST00000373191 1.55 5.45 1.49 4.27 3.04 4.35 0.20 0.33 0.22
HPRT1 ENST00000298556 1.87 14.80 5.61 4.27 1.94 3.40 0.24 0.62 0.27
PSME3 ENST00000293362 1.96 4.70 1.35 4.27 3.26 4.33 0.24 0.31 0.23
MYB ENST00000341911 1.84 13.92 5.14 4.27 2.04 3.59 0.22 0.60 0.25
G3BP2 ENST00000359707 1.93 4.50 1.28 4.27 3.26 4.38 0.24 0.32 0.21

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