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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
RBM17 ENST00000446108 0.74 1.85 0.26 4.35 3.77 4.83 0.19 0.26 0.18
ANKRD17 ENST00000358602 2.31 0.29 0.27 4.12 4.12 4.83 0.28 0.29 0.18
U2AF2 ENST00000308924 0.21 2.47 0.27 4.50 3.57 4.85 0.16 0.29 0.18
SPOP ENST00000393331 0.11 2.61 0.28 4.55 3.54 4.87 0.15 0.29 0.18
PSMC1 ENST00000261303 0.31 2.44 0.28 4.43 3.59 4.86 0.17 0.29 0.18
KIF11 ENST00000260731 1.88 0.87 0.29 4.27 4.10 4.86 0.24 0.29 0.18
RBM25 ENST00000261973 2.29 0.47 0.29 4.13 4.10 4.85 0.28 0.28 0.18
TNPO1 ENST00000337273 2.61 0.19 0.30 4.03 4.15 4.85 0.28 0.28 0.18
PPP1CB ENST00000395366 0.08 2.75 0.30 4.58 3.53 4.84 0.15 0.29 0.18
KCNB1 ENST00000371741 0.51 2.33 0.31 4.39 3.63 4.84 0.18 0.29 0.18
VCP ENST00000358901 0.74 2.10 0.32 4.36 3.69 4.83 0.19 0.28 0.18
WHSC1 ENST00000382895 1.78 1.05 0.32 4.27 4.06 4.83 0.22 0.28 0.18
SMU1 ENST00000397149 1.49 1.36 0.33 4.31 3.96 4.83 0.20 0.27 0.18
CAND1 ENST00000545606 1.67 1.18 0.33 4.31 4.01 4.82 0.22 0.28 0.18
PRKCB ENST00000303531 2.32 0.60 0.34 4.12 4.16 4.82 0.28 0.28 0.18
TBL1XR1 ENST00000430069 1.50 1.41 0.34 4.31 3.95 4.81 0.20 0.27 0.18
MAP3K12 ENST00000547035 2.55 0.44 0.35 4.06 4.12 4.81 0.28 0.28 0.18
NIPBL ENST00000282516 2.97 0.03 0.35 3.91 4.11 4.80 0.30 0.26 0.18
ATP1A1 ENST00000537345 1.08 1.92 0.36 4.39 3.75 4.80 0.18 0.26 0.18
WDR5 ENST00000358625 1.10 1.95 0.36 4.40 3.75 4.79 0.18 0.25 0.18
SF3A3 ENST00000373019 1.29 1.72 0.37 4.39 3.84 4.79 0.17 0.26 0.18
PHF21A ENST00000418153 2.46 0.55 0.37 4.10 4.17 4.78 0.27 0.27 0.18
PPP3CB ENST00000394829 1.92 1.12 0.38 4.28 4.01 4.78 0.24 0.28 0.18
WDR26 ENST00000414423 2.34 0.69 0.38 4.10 4.09 4.77 0.27 0.28 0.18
STXBP1 ENST00000373302 2.39 0.68 0.39 4.11 4.10 4.77 0.27 0.28 0.18

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