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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
GDF11 ENST00000257868 2.85 11.68 4.59 3.95 2.10 3.70 0.28 0.57 0.25
ZBTB34 ENST00000373452 2.85 11.91 4.72 3.95 2.10 3.69 0.29 0.59 0.25
ATF2 ENST00000264110 2.86 11.09 4.26 3.95 2.09 3.75 0.30 0.53 0.24
WAPAL ENST00000298767 2.86 1.56 0.72 3.95 3.88 4.58 0.30 0.26 0.20
KCNC2 ENST00000549446 2.87 28.27 13.17 3.94 1.19 2.10 0.30 1.22 0.52
CSNK2A2 ENST00000262506 2.87 5.67 2.02 3.94 2.96 4.11 0.30 0.34 0.23
PSMA4 ENST00000044462 2.88 24.71 11.47 3.94 1.30 2.21 0.30 1.05 0.45
GJB1 ENST00000374022 2.88 25.56 11.83 3.93 1.25 2.21 0.30 1.05 0.46
EIF1B ENST00000232905 2.89 40.39 19.64 3.93 0.61 1.53 0.30 1.76 0.85
RAB7A ENST00000265062 2.89 10.59 4.05 3.93 2.15 3.75 0.30 0.51 0.23
KCNQ5 ENST00000342056 2.90 13.14 5.27 3.93 2.07 3.54 0.30 0.60 0.25
SOX2 ENST00000325404 2.90 28.09 13.08 3.92 1.19 2.10 0.30 1.20 0.52
SUV420H1 ENST00000304363 2.91 0.52 0.45 3.92 4.15 4.73 0.30 0.27 0.17
PCNA ENST00000379160 2.91 9.39 3.56 3.92 2.49 3.81 0.30 0.49 0.24
ARNTL ENST00000389707 2.92 11.82 4.71 3.92 2.09 3.69 0.30 0.57 0.25
GRIA3 ENST00000264357 2.92 5.30 1.94 3.91 3.11 4.14 0.30 0.32 0.24
FZD8 ENST00000374694 2.93 19.49 8.54 3.91 1.46 2.51 0.30 0.74 0.37
EZH2 ENST00000320356 2.93 1.44 0.69 3.91 3.93 4.60 0.30 0.26 0.20
NONO ENST00000276079 2.94 8.47 3.15 3.91 2.52 3.92 0.30 0.46 0.24
CHRM1 ENST00000306960 2.94 6.48 2.40 3.90 2.63 4.04 0.30 0.37 0.23
ARF4 ENST00000303436 2.95 11.59 4.61 3.90 2.10 3.69 0.30 0.57 0.25
NTRK2 ENST00000376214 2.95 1.35 0.66 3.90 3.97 4.63 0.30 0.27 0.20
CSNK2B-LY6G5B-1181 ENST00000375880 2.96 40.37 19.69 3.91 0.61 1.53 0.30 1.76 0.85
CAPZB ENST00000375142 2.96 16.67 7.16 3.91 1.72 2.86 0.30 0.71 0.33
NIPBL ENST00000282516 2.97 0.03 0.35 3.91 4.11 4.80 0.30 0.26 0.18

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