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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
CDR1 ENST00000370532 96.99 97.74 99.17 0.09 0.21 0.11 0.11 0.17 0.04
FAM47A ENST00000346193 96.07 97.90 99.18 0.11 0.20 0.11 0.11 0.17 0.04
USP17L2 ENST00000333796 95.80 98.83 99.18 0.11 0.16 0.11 0.11 0.14 0.04
MAGEA4 ENST00000360243 96.63 99.03 99.19 0.11 0.15 0.11 0.11 0.15 0.04
OR2T12 ENST00000317996 95.69 98.98 99.19 0.11 0.17 0.11 0.12 0.15 0.04
IFNA10 ENST00000357374 95.83 98.81 99.20 0.11 0.16 0.11 0.11 0.14 0.04
SBP1 ENST00000594414 96.41 99.60 99.20 0.10 0.16 0.11 0.11 0.12 0.04
FLG ENST00000368799 97.90 97.00 99.21 0.11 0.24 0.11 0.11 0.19 0.04
ZNF645 ENST00000323684 97.05 98.53 99.21 0.10 0.20 0.11 0.11 0.15 0.04
OR1N1 ENST00000304880 95.53 99.22 99.22 0.11 0.15 0.11 0.11 0.13 0.04
FAM24A ENST00000368894 99.26 95.67 99.23 0.11 0.23 0.11 0.12 0.20 0.04
KRTAP9-8 ENST00000254072 96.08 98.60 99.23 0.11 0.20 0.11 0.11 0.15 0.04
ANP32D ENST00000266594 96.26 98.46 99.24 0.12 0.21 0.11 0.11 0.14 0.04
ARMS2 ENST00000528446 98.33 96.64 99.24 0.09 0.23 0.11 0.10 0.20 0.04
C22orf29 ENST00000405640 95.55 99.32 99.25 0.11 0.16 0.11 0.11 0.12 0.04
C15orf37 ENST00000560255 95.17 99.78 99.25 0.10 0.17 0.11 0.12 0.11 0.04
IFNA16 ENST00000380216 95.63 98.74 99.26 0.11 0.16 0.11 0.11 0.14 0.04
DEFB125 ENST00000382410 99.24 95.82 99.26 0.11 0.22 0.11 0.12 0.20 0.04
DPRX ENST00000376650 98.80 96.33 99.27 0.10 0.22 0.11 0.11 0.19 0.04
OR2M3 ENST00000456743 97.30 97.77 99.27 0.10 0.21 0.11 0.11 0.17 0.04
FAM220A ENST00000313324 95.87 99.14 99.28 0.11 0.15 0.11 0.11 0.14 0.04
MRGPRD ENST00000309106 97.55 97.59 99.28 0.10 0.22 0.11 0.11 0.20 0.04
KRTAP13-1 ENST00000355459 96.13 98.88 99.29 0.11 0.17 0.11 0.11 0.14 0.04
C4orf6 ENST00000195455 97.79 97.44 99.29 0.11 0.22 0.11 0.11 0.19 0.04
EDDM3B ENST00000326783 95.96 99.15 99.30 0.11 0.15 0.11 0.11 0.14 0.04

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