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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
FOXL2 ENST00000330315 21.31 21.06 19.16 1.53 1.44 1.53 1.06 0.83 0.85
SLAIN1 ENST00000488699 21.32 16.74 16.87 1.53 1.68 1.68 1.06 0.71 0.70
EXOC6 ENST00000260762 21.32 26.59 22.06 1.53 1.19 1.15 1.06 1.12 0.96
TNKS ENST00000310430 21.33 17.41 17.22 1.53 1.61 1.64 1.06 0.73 0.74
TMEM150C ENST00000515780 21.33 46.57 32.14 1.53 0.75 0.90 1.06 2.01 1.60
HPSE2 ENST00000370552 21.34 35.28 26.40 1.54 0.76 1.01 1.06 1.58 1.25
FBLN5 ENST00000342058 21.34 4.52 10.52 1.54 3.26 2.19 1.07 0.32 0.43
BRCC3 ENST00000369462 21.35 48.92 33.29 1.54 0.63 0.89 1.07 2.04 1.70
CCNA1 ENST00000255465 21.35 36.09 26.90 1.54 0.81 0.97 1.07 1.59 1.28
DHDDS ENST00000360009 21.36 25.19 21.40 1.54 1.32 1.33 1.07 1.02 0.91
PPARA ENST00000396000 21.36 31.77 24.62 1.54 0.94 1.06 1.07 1.48 1.10
INTS7 ENST00000366994 21.37 27.64 22.66 1.54 1.27 1.18 1.07 1.17 0.97
PGM3 ENST00000506587 21.37 35.55 26.59 1.54 0.77 0.97 1.07 1.58 1.25
BARX1 ENST00000253968 21.38 37.15 27.41 1.54 0.80 0.96 1.07 1.66 1.27
RPH3A ENST00000389385 21.38 20.94 19.15 1.54 1.43 1.53 1.07 0.83 0.85
GRHL3 ENST00000350501 21.39 10.92 13.82 1.54 2.11 2.09 1.07 0.51 0.57
MED7 ENST00000286317 21.39 58.42 38.21 1.54 0.54 0.85 1.06 1.39 2.04
NELFB ENST00000343053 21.40 30.85 24.15 1.54 1.08 1.11 1.06 1.36 1.05
HK2 ENST00000290573 21.40 21.33 19.36 1.54 1.43 1.54 1.06 0.80 0.85
NXN ENST00000336868 21.41 7.83 12.19 1.54 2.54 2.29 1.06 0.44 0.49
GNG4 ENST00000391854 21.41 85.98 53.12 1.54 0.27 0.61 1.07 0.43 1.87
GGPS1 ENST00000282841 21.42 33.10 25.36 1.56 0.84 1.05 1.07 1.49 1.17
SLC7A6 ENST00000566454 21.42 34.14 25.93 1.56 0.84 1.01 1.07 1.55 1.24
KLHL13 ENST00000539496 21.43 33.37 25.51 1.56 0.85 1.05 1.07 1.51 1.19
USP13 ENST00000263966 21.43 38.54 28.21 1.56 0.73 0.81 1.07 1.67 1.28

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