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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
MCAT ENST00000290429 74.77 66.19 73.24 0.38 0.53 0.43 0.78 1.21 0.79
PASK ENST00000358649 74.77 52.25 64.96 0.38 0.62 0.51 0.78 1.84 1.32
KCNU1 ENST00000399881 74.78 44.16 59.88 0.38 0.61 0.49 0.78 1.96 1.63
OR5AU1 ENST00000304418 74.78 93.03 87.09 0.38 0.28 0.28 0.78 0.30 0.30
TMPRSS5 ENST00000299882 74.79 52.62 65.14 0.38 0.68 0.52 0.78 1.81 1.31
ZNF613 ENST00000293471 74.79 37.78 55.98 0.38 0.80 0.49 0.78 1.70 1.76
CLEC6A ENST00000382073 74.80 75.96 78.64 0.38 0.44 0.38 0.78 0.86 0.55
CD96 ENST00000283285 74.81 52.60 65.14 0.38 0.67 0.52 0.78 1.82 1.31
GJB2 ENST00000382844 74.81 97.48 89.26 0.38 0.22 0.19 0.77 0.19 0.25
DNAJB7 ENST00000307221 74.82 92.48 86.81 0.38 0.27 0.29 0.77 0.30 0.32
ANGPT4 ENST00000381922 74.82 71.37 76.14 0.39 0.53 0.37 0.77 1.05 0.62
HLA-DOA ENST00000229829 74.83 88.76 85.15 0.38 0.25 0.33 0.77 0.36 0.37
SYT15 ENST00000374321 74.83 83.43 82.55 0.38 0.27 0.32 0.77 0.47 0.43
TRAT1 ENST00000295756 74.84 41.24 58.10 0.38 0.61 0.47 0.78 1.83 1.65
AHRR ENST00000316418 74.84 30.54 51.84 0.38 1.09 0.62 0.78 1.38 1.92
IFITM5 ENST00000382614 74.85 96.63 88.85 0.38 0.23 0.19 0.78 0.20 0.28
CES2 ENST00000317091 74.85 72.04 76.54 0.38 0.52 0.38 0.78 1.03 0.61
NMI ENST00000243346 74.86 61.89 70.71 0.38 0.57 0.43 0.78 1.35 0.87
SEPW1 ENST00000601048 74.86 75.77 78.55 0.38 0.43 0.38 0.78 0.88 0.55
ART1 ENST00000250693 74.87 85.95 83.80 0.38 0.28 0.34 0.78 0.43 0.42
SDE2 ENST00000272091 74.87 52.29 65.02 0.38 0.62 0.51 0.78 1.84 1.31
ADAM33 ENST00000356518 74.88 49.58 63.36 0.38 0.66 0.49 0.78 2.03 1.36
PLA2G4B ENST00000542534 74.88 71.82 76.47 0.38 0.51 0.38 0.78 1.07 0.61
JMJD7-PLA2G4B ENST00000382448 74.89 71.85 76.48 0.38 0.51 0.38 0.78 1.07 0.61
CLEC18C ENST00000569347 74.89 73.68 77.49 0.38 0.52 0.35 0.78 1.03 0.57

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