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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
ZBTB26 ENST00000373656 1.94 32.42 14.95 4.29 0.87 1.89 0.24 1.48 0.63
ARIH2 ENST00000356401 1.95 10.70 3.70 4.28 2.14 3.81 0.24 0.51 0.23
STAG1 ENST00000383202 1.95 1.79 0.53 4.28 3.80 4.69 0.24 0.26 0.17
KPNA3 ENST00000261667 1.96 14.27 5.43 4.28 2.06 3.44 0.24 0.61 0.26
PSME3 ENST00000293362 1.96 4.70 1.35 4.27 3.26 4.33 0.24 0.31 0.23
TSN ENST00000389682 1.97 24.02 10.58 4.27 1.38 2.16 0.24 0.96 0.44
METTL14 ENST00000388822 1.97 32.99 15.25 4.27 0.84 1.83 0.24 1.49 0.65
SF1 ENST00000377387 1.98 4.65 1.34 4.26 3.27 4.33 0.24 0.31 0.23
PA2G4 ENST00000303305 1.98 6.02 1.86 4.26 2.82 4.19 0.23 0.35 0.24
PSMA5 ENST00000271308 1.99 5.43 1.65 4.26 3.02 4.27 0.23 0.33 0.23
MAP2K1 ENST00000307102 1.99 16.93 6.80 4.25 1.66 2.97 0.23 0.71 0.32
SLC6A1 ENST00000287766 2.00 3.23 0.92 4.25 3.46 4.47 0.23 0.28 0.21
DPF2 ENST00000528416 2.00 3.84 1.10 4.25 3.31 4.42 0.23 0.31 0.21
TPM3 ENST00000368530 2.01 35.61 16.65 4.24 0.78 1.70 0.23 1.58 0.70
PARP6 ENST00000569795 2.01 5.11 1.57 4.24 3.20 4.30 0.24 0.33 0.23
FYN ENST00000354650 2.02 10.63 3.69 4.24 2.14 3.82 0.24 0.51 0.23
FBXO45 ENST00000311630 2.02 10.29 3.57 4.23 2.26 3.83 0.24 0.49 0.24
ATP6V0C ENST00000330398 2.03 34.38 16.03 4.23 0.82 1.71 0.24 1.56 0.66
SUZ12 ENST00000322652 2.04 2.38 0.71 4.23 3.62 4.59 0.24 0.29 0.20
KLHL7 ENST00000339077 2.04 32.88 15.22 4.23 0.82 1.83 0.24 1.45 0.65
VSNL1 ENST00000406397 2.05 31.84 14.69 4.24 0.94 1.96 0.24 1.48 0.61
GNB2L1 ENST00000512805 2.05 4.31 1.26 4.24 3.26 4.39 0.24 0.32 0.21
PRKACB ENST00000370685 2.06 24.11 10.68 4.23 1.35 2.18 0.24 0.98 0.42
NEK9 ENST00000238616 2.06 45.32 21.82 4.23 0.68 1.23 0.24 1.98 0.95
PPP2R1A ENST00000322088 2.07 12.41 4.56 4.23 2.06 3.70 0.24 0.59 0.25

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