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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
AURKB ENST00000585124 36.81 39.25 36.15 0.95 0.68 0.87 1.75 1.64 1.80
MYO5B ENST00000285039 36.81 33.87 33.52 0.95 0.84 0.89 1.75 1.55 1.72
C3orf38 ENST00000318887 36.82 55.45 44.71 0.94 0.58 0.62 1.75 1.60 2.06
TMEM230 ENST00000342308 36.82 79.36 58.17 0.94 0.38 0.48 1.75 0.67 1.65
ZNF23 ENST00000393539 36.83 59.13 46.66 0.94 0.49 0.66 1.75 1.44 1.87
AMOTL1 ENST00000433060 36.83 23.41 28.28 0.92 1.42 0.80 1.75 0.93 1.29
ARSJ ENST00000315366 36.84 52.88 43.24 0.92 0.65 0.65 1.75 1.80 1.99
TBX1 ENST00000332710 36.84 20.82 26.98 0.92 1.43 1.00 1.75 0.82 1.28
SUSD1 ENST00000374270 36.85 49.49 41.40 0.92 0.65 0.73 1.75 2.02 2.02
MYO1D ENST00000318217 36.85 37.12 35.16 0.92 0.80 0.86 1.74 1.66 1.76
ZBTB46 ENST00000245663 36.86 18.30 25.66 0.92 1.51 1.05 1.74 0.74 1.21
FOXN4 ENST00000299162 36.86 18.96 26.08 0.92 1.52 0.99 1.74 0.76 1.25
CCDC22 ENST00000376227 36.87 1.91 17.23 0.92 3.76 1.64 1.74 0.26 0.74
PALLD ENST00000505667 36.87 25.26 29.21 0.92 1.29 0.82 1.74 1.02 1.33
TMPRSS11F ENST00000356291 36.88 55.58 44.87 0.92 0.53 0.68 1.75 1.60 2.04
ERGIC3 ENST00000357394 36.88 40.06 36.61 0.92 0.63 0.85 1.75 1.70 1.92
ADCK5 ENST00000308860 36.89 27.49 30.39 0.92 1.25 0.81 1.75 1.16 1.46
PDK1 ENST00000282077 36.89 42.90 38.19 0.92 0.62 0.85 1.75 1.91 2.04
SPG20 ENST00000451493 36.90 44.19 38.84 0.92 0.62 0.81 1.75 1.95 2.05
SLMO2 ENST00000355937 36.90 42.31 37.84 0.92 0.61 0.85 1.75 1.89 2.01
ALAD ENST00000409155 36.91 43.10 38.30 0.91 0.61 0.85 1.75 1.90 2.04
TMEM173 ENST00000330794 36.91 49.60 41.49 0.91 0.66 0.73 1.75 2.02 2.02
SPAG5 ENST00000321765 36.92 36.97 35.11 0.91 0.75 0.86 1.75 1.70 1.75
ZNF445 ENST00000425708 36.92 6.35 19.66 0.91 2.68 1.53 1.75 0.37 0.85
TICAM2 ENST00000408996 36.93 42.74 38.10 0.91 0.62 0.86 1.75 1.92 2.02

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