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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
HSPA5 ENST00000324460 3.23 19.09 8.51 3.86 1.51 2.51 0.30 0.76 0.37
CELF5 ENST00000292672 3.24 6.01 2.32 3.87 2.82 4.03 0.30 0.35 0.22
DHX8 ENST00000262415 3.24 25.10 11.77 3.88 1.32 2.20 0.30 1.03 0.46
KAT8 ENST00000448516 3.25 23.33 10.91 3.88 1.43 2.21 0.30 0.93 0.44
EEF1A1 ENST00000316292 3.25 11.84 4.82 3.88 2.09 3.66 0.30 0.58 0.24
ITPR1 ENST00000302640 3.26 2.11 0.96 3.88 3.69 4.46 0.30 0.28 0.21
FBXW7 ENST00000281708 3.26 8.12 3.13 3.88 2.53 3.92 0.30 0.44 0.24
HNRNPLL ENST00000409636 3.27 15.95 6.95 3.87 1.89 2.90 0.30 0.68 0.33
PPP2R5C ENST00000422945 3.27 13.81 5.81 3.87 2.06 3.31 0.30 0.60 0.28
MAST1 ENST00000251472 3.28 3.67 1.48 3.87 3.34 4.36 0.30 0.31 0.22
PHF6 ENST00000332070 3.28 4.21 1.66 3.87 3.26 4.26 0.30 0.32 0.23
SYT1 ENST00000261205 3.29 22.08 10.24 3.86 1.49 2.21 0.30 0.82 0.42
ZYG11B ENST00000294353 3.30 9.46 3.74 3.86 2.48 3.79 0.30 0.49 0.24
SSBP3 ENST00000371320 3.30 3.02 1.25 3.87 3.47 4.40 0.30 0.28 0.21
NALCN ENST00000251127 3.31 24.92 11.73 3.87 1.32 2.21 0.30 1.07 0.47
RPL39 ENST00000361575 3.31 58.79 29.17 3.87 0.54 0.84 0.30 1.42 1.32
RAC2 ENST00000249071 3.32 11.20 4.60 3.87 2.09 3.69 0.30 0.54 0.25
KIF1A ENST00000498729 3.32 1.47 0.80 3.86 3.91 4.54 0.30 0.26 0.21
AP1S2 ENST00000329235 3.33 21.56 10.06 3.86 1.43 2.26 0.30 0.81 0.42
MAPKAPK2 ENST00000367103 3.33 2.57 1.13 3.86 3.54 4.40 0.30 0.29 0.21
RPS8 ENST00000396651 3.34 6.63 2.56 3.86 2.64 4.00 0.30 0.36 0.23
RPS28 ENST00000600659 3.34 42.32 20.94 3.85 0.61 1.43 0.29 1.90 0.87
FMR1 ENST00000370475 3.35 19.17 8.59 3.85 1.49 2.53 0.29 0.76 0.36
YWHAH ENST00000248975 3.35 25.22 11.86 3.85 1.30 2.24 0.30 1.02 0.46
ACTR1A ENST00000369905 3.36 14.59 6.25 3.85 2.04 3.14 0.30 0.61 0.32

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