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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
CELA1 ENST00000293636 63.53 50.32 56.75 0.59 0.66 0.52 1.24 1.96 1.70
RELT ENST00000064780 63.54 51.37 57.38 0.59 0.63 0.51 1.24 1.89 1.68
TMEM201 ENST00000340381 63.55 11.24 35.54 0.59 2.11 0.85 1.24 0.55 1.78
TMEM211 ENST00000407886 63.55 91.87 81.07 0.59 0.23 0.39 1.24 0.32 0.49
NAAA ENST00000286733 63.56 68.75 68.14 0.59 0.53 0.49 1.24 1.17 1.08
CYP20A1 ENST00000356079 63.56 74.93 71.81 0.59 0.53 0.44 1.24 0.94 0.82
POMC ENST00000405623 63.57 77.37 73.21 0.59 0.42 0.43 1.24 0.76 0.79
OR5AR1 ENST00000302969 63.57 96.34 83.30 0.59 0.22 0.32 1.24 0.19 0.40
MRGPRF ENST00000309099 63.58 51.57 57.54 0.59 0.62 0.52 1.24 1.87 1.66
SLC28A1 ENST00000394573 63.58 68.27 67.81 0.59 0.52 0.51 1.24 1.20 1.12
ART5 ENST00000397068 63.59 53.15 58.42 0.59 0.66 0.52 1.24 1.77 1.65
CAND2 ENST00000456430 63.59 48.34 55.66 0.59 0.63 0.53 1.24 2.00 1.73
GLIS3 ENST00000381971 63.60 36.36 48.89 0.59 0.82 0.71 1.23 1.63 1.85
ANKRD32 ENST00000265140 63.60 38.59 50.11 0.59 0.72 0.62 1.23 1.66 1.90
CYP1B1 ENST00000260630 63.61 64.82 65.81 0.59 0.48 0.51 1.22 1.24 1.25
LYPD3 ENST00000244333 63.61 93.61 81.99 0.61 0.28 0.37 1.22 0.28 0.47
CAPN9 ENST00000271971 63.62 64.36 65.52 0.61 0.49 0.53 1.22 1.22 1.28
OR56A3 ENST00000329564 63.62 95.54 82.92 0.61 0.23 0.32 1.22 0.21 0.40
F10 ENST00000375559 63.63 52.31 58.04 0.61 0.62 0.47 1.22 1.83 1.66
FKRP ENST00000318584 63.63 67.69 67.46 0.61 0.53 0.52 1.22 1.19 1.14
LEFTY2 ENST00000366820 63.64 51.51 57.52 0.61 0.63 0.52 1.22 1.87 1.66
LGALS1 ENST00000215909 63.64 85.03 77.56 0.61 0.25 0.37 1.22 0.45 0.57
IL1F10 ENST00000393197 63.65 91.48 80.90 0.61 0.23 0.39 1.22 0.32 0.51
FAM155B ENST00000252338 63.65 24.47 42.33 0.61 1.32 0.70 1.22 1.01 2.01
PLCZ1 ENST00000266505 63.66 55.25 59.83 0.61 0.57 0.49 1.22 1.62 1.62

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