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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
PAK2 ENST00000327134 3.36 13.75 5.82 3.84 2.06 3.30 0.30 0.59 0.28
FBXL16 ENST00000397621 3.37 13.07 5.55 3.84 2.06 3.39 0.30 0.59 0.26
USP9X ENST00000324545 3.37 0.10 0.47 3.84 4.12 4.74 0.30 0.28 0.17
NLGN2 ENST00000302926 3.38 2.08 1.01 3.84 3.70 4.47 0.30 0.29 0.21
CNIH2 ENST00000311445 3.38 13.90 5.90 3.84 2.05 3.30 0.30 0.59 0.29
TM9SF2 ENST00000376387 3.39 0.55 0.57 3.83 4.15 4.71 0.30 0.27 0.17
GLRA2 ENST00000218075 3.39 12.23 5.06 3.85 2.06 3.64 0.30 0.58 0.25
HYPK ENST00000406925 3.40 65.86 32.82 3.84 0.54 0.86 0.30 1.23 1.65
YBX1 ENST00000321358 3.40 16.46 7.30 3.84 1.78 2.81 0.30 0.69 0.34
PURA ENST00000331327 3.41 14.41 6.19 3.84 2.05 3.18 0.30 0.61 0.32
PRKCG ENST00000263431 3.41 5.60 2.19 3.84 3.00 4.05 0.30 0.33 0.23
ETV5 ENST00000306376 3.42 0.99 0.70 3.83 4.08 4.60 0.30 0.28 0.20
OSR1 ENST00000536433 3.42 22.28 10.46 3.83 1.53 2.19 0.30 0.83 0.43
RPL12 ENST00000361436 3.43 43.66 21.70 3.83 0.62 1.25 0.30 1.97 0.92
THRA ENST00000264637 3.43 22.94 10.78 3.83 1.47 2.19 0.30 0.90 0.43
SLC25A42 ENST00000318596 3.44 31.56 15.26 3.82 0.95 1.83 0.30 1.43 0.65
ING3 ENST00000315870 3.45 6.25 2.47 3.84 2.73 4.03 0.30 0.36 0.23
PDE2A ENST00000334456 3.45 14.74 6.41 3.83 1.96 3.06 0.30 0.62 0.32
CLK2 ENST00000361168 3.46 3.97 1.65 3.83 3.28 4.26 0.30 0.32 0.23
TAF1 ENST00000276072 3.46 0.05 0.49 3.83 4.11 4.73 0.30 0.27 0.17
DHX30 ENST00000445061 3.47 1.93 1.00 3.83 3.74 4.45 0.30 0.25 0.21
PRPF38B ENST00000370025 3.47 15.57 6.87 3.83 1.87 2.92 0.30 0.67 0.33
STT3B ENST00000295770 3.48 9.40 3.79 3.84 2.48 3.79 0.30 0.49 0.24
TFCP2 ENST00000257915 3.48 34.66 16.92 3.84 0.80 1.68 0.30 1.53 0.71
PIK3R1 ENST00000521381 3.49 7.70 3.02 3.83 2.53 3.96 0.30 0.42 0.24

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