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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
TPRX1 ENST00000322175 95.83 89.38 95.32 0.11 0.27 0.08 0.11 0.37 0.10
PP13439 ENST00000331659 90.21 97.80 96.94 0.16 0.21 0.08 0.25 0.18 0.07
SLC22A18AS ENST00000533594 97.63 87.58 95.33 0.10 0.23 0.08 0.11 0.37 0.10
OR2L3 ENST00000359959 89.07 99.12 96.94 0.19 0.15 0.08 0.32 0.14 0.07
RP11-210M15.2 ENST00000559008 91.31 93.46 95.33 0.15 0.28 0.08 0.20 0.28 0.10
EME2 ENST00000568449 88.67 96.54 95.34 0.19 0.22 0.08 0.34 0.19 0.10
CSAG1 ENST00000370287 97.55 90.79 96.95 0.10 0.25 0.08 0.11 0.35 0.07
C10orf91 ENST00000392630 94.74 90.48 95.34 0.10 0.25 0.08 0.11 0.37 0.10
DHRS4-AS1 ENST00000354854 91.16 98.26 96.95 0.15 0.21 0.08 0.21 0.15 0.07
TCEAL2 ENST00000372780 95.59 89.63 95.35 0.11 0.27 0.08 0.11 0.36 0.10
RP11-247C2.2 ENST00000514871 92.75 96.72 96.96 0.15 0.23 0.08 0.17 0.19 0.07
CCL23 ENST00000293280 99.23 86.00 95.35 0.11 0.27 0.08 0.12 0.43 0.10
BX088651.1 ENST00000540551 89.52 98.61 96.96 0.16 0.20 0.08 0.30 0.15 0.07
RBMY1A1 ENST00000382707 91.18 93.58 95.36 0.15 0.28 0.08 0.21 0.28 0.10
WFDC10B ENST00000335769 99.68 88.71 96.97 0.12 0.25 0.08 0.13 0.35 0.07
DEFB107A ENST00000335021 93.64 91.47 95.36 0.13 0.23 0.08 0.13 0.32 0.10
AC006132.1 ENST00000593161 92.71 96.85 96.97 0.15 0.23 0.08 0.17 0.19 0.07
C8orf86 ENST00000358138 98.31 86.94 95.37 0.09 0.22 0.08 0.10 0.40 0.10
CCRL2 ENST00000357392 96.40 88.86 95.37 0.10 0.25 0.08 0.11 0.35 0.10
AL033381.1 ENST00000314040 91.20 96.19 96.98 0.15 0.22 0.08 0.21 0.20 0.07
RNF222 ENST00000399398 92.40 92.47 95.38 0.15 0.27 0.08 0.18 0.30 0.10
TAS2R16 ENST00000249284 88.84 99.52 96.98 0.19 0.16 0.08 0.32 0.13 0.07
IFI27L2 ENST00000238609 89.29 95.97 95.38 0.18 0.22 0.08 0.32 0.20 0.10
ZNF665 ENST00000396424 98.44 90.02 96.99 0.10 0.25 0.08 0.11 0.37 0.07
C1orf147 ENST00000367119 93.08 95.26 95.39 0.15 0.23 0.08 0.15 0.21 0.10

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