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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
TLE3 ENST00000558939 6.74 0.52 1.60 2.97 4.15 4.28 0.37 0.27 0.23
PPP1R9B ENST00000316878 3.16 4.18 1.62 3.85 3.25 4.28 0.30 0.32 0.23
ZNF131 ENST00000509634 3.79 3.45 1.59 3.77 3.40 4.28 0.30 0.29 0.23
ATRX ENST00000373344 6.51 0.80 1.62 3.02 4.10 4.29 0.37 0.27 0.23
U2AF1 ENST00000291552 0.82 6.44 1.59 4.35 2.63 4.29 0.18 0.37 0.23
MARCH6 ENST00000274140 4.16 3.04 1.58 3.72 3.47 4.29 0.30 0.28 0.23
GATA6 ENST00000269216 2.43 4.72 1.58 4.10 3.27 4.29 0.27 0.31 0.23
EFTUD2 ENST00000426333 6.17 0.97 1.57 3.05 4.10 4.30 0.35 0.29 0.23
PARP6 ENST00000569795 2.01 5.11 1.57 4.24 3.20 4.30 0.24 0.33 0.23
PCSK2 ENST00000262545 1.15 5.93 1.56 4.39 2.83 4.30 0.17 0.35 0.23
PPM1A ENST00000325642 3.55 3.54 1.55 3.82 3.38 4.31 0.30 0.30 0.23
CHD3 ENST00000380358 3.99 3.08 1.55 3.77 3.46 4.31 0.29 0.28 0.22
CSNK1A1 ENST00000515768 0.41 6.67 1.54 4.38 2.67 4.31 0.18 0.37 0.22
ADNP ENST00000396029 5.00 1.89 1.45 3.56 3.75 4.32 0.30 0.26 0.22
CREBBP ENST00000262367 6.74 0.34 1.54 2.99 4.15 4.32 0.37 0.28 0.22
TBR1 ENST00000389554 0.32 6.34 1.36 4.43 2.69 4.32 0.17 0.37 0.23
RBM5 ENST00000347869 4.63 2.26 1.45 3.66 3.65 4.32 0.29 0.30 0.23
RAB11A ENST00000261890 0.91 6.15 1.53 4.35 2.75 4.32 0.18 0.35 0.22
CSTF2 ENST00000372972 4.03 2.62 1.35 3.76 3.55 4.32 0.29 0.29 0.23
AGPS ENST00000264167 5.24 1.62 1.44 3.42 3.86 4.32 0.32 0.26 0.23
CSNK1E ENST00000396832 4.24 2.81 1.53 3.71 3.51 4.32 0.30 0.28 0.22
ZBTB18 ENST00000358704 2.52 4.38 1.47 4.07 3.27 4.33 0.28 0.32 0.22
RPTOR ENST00000306801 5.88 1.14 1.52 3.15 4.00 4.33 0.33 0.28 0.22
ARHGAP35 ENST00000404338 6.63 0.22 1.44 2.97 4.13 4.33 0.37 0.28 0.23
PSME3 ENST00000293362 1.96 4.70 1.35 4.27 3.26 4.33 0.24 0.31 0.23

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