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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
CDC25B ENST00000245960 32.16 21.88 25.10 0.96 1.46 1.05 1.72 0.81 1.17
EPB41L4B ENST00000374566 32.16 8.49 18.26 0.96 2.52 1.66 1.73 0.46 0.79
BIVM ENST00000257336 32.17 34.93 31.72 0.96 0.76 0.89 1.73 1.54 1.58
UVRAG ENST00000356136 32.17 11.95 20.12 0.96 2.07 1.49 1.73 0.59 0.85
MED17 ENST00000251871 32.18 41.79 35.15 0.96 0.61 0.86 1.73 1.78 1.76
SHANK1 ENST00000293441 32.18 4.99 16.39 0.96 3.26 1.71 1.73 0.32 0.68
TM6SF1 ENST00000322019 32.19 59.30 44.22 0.96 0.51 0.62 1.73 1.41 2.04
TGIF2-C20orf24 ENST00000558530 32.19 21.76 25.03 0.96 1.46 1.04 1.73 0.81 1.15
ARPC4-TTLL3 ENST00000397256 32.20 58.82 43.90 0.96 0.54 0.62 1.73 1.41 2.02
PCDH11X ENST00000373094 32.20 28.14 28.35 0.96 1.18 0.78 1.73 1.20 1.29
CCT4 ENST00000394440 32.21 6.73 17.33 0.96 2.67 1.63 1.73 0.37 0.75
TAP2 ENST00000374899 32.21 40.90 34.77 0.96 0.61 0.90 1.73 1.78 1.76
GTF2H4 ENST00000259895 32.22 44.37 36.38 0.96 0.62 0.84 1.72 1.95 1.87
GPR171 ENST00000309180 32.22 72.18 51.32 0.96 0.52 0.63 1.72 1.04 1.91
PPEF1 ENST00000361511 32.23 12.40 20.39 0.96 2.06 1.49 1.71 0.59 0.88
DRAM1 ENST00000258534 32.23 37.50 33.01 0.96 0.78 0.85 1.72 1.67 1.66
ORMDL3 ENST00000394169 32.24 30.61 29.60 0.96 1.06 0.84 1.71 1.39 1.39
GTF2E2 ENST00000355904 32.25 31.43 30.00 0.96 0.96 0.84 1.71 1.42 1.46
UHMK1 ENST00000489294 32.25 19.22 23.80 0.96 1.47 1.11 1.70 0.76 1.03
EEF1B2 ENST00000392222 32.26 39.07 33.82 0.96 0.70 0.89 1.70 1.63 1.73
C11orf68 ENST00000438576 32.26 49.48 39.26 0.96 0.66 0.78 1.70 2.03 2.04
FAM53C ENST00000239906 32.27 32.05 30.35 0.96 0.92 0.81 1.70 1.47 1.45
ERCC1 ENST00000013807 32.27 69.75 50.00 0.97 0.53 0.62 1.70 1.13 1.90
ENOX2 ENST00000338144 32.28 45.20 36.95 0.97 0.70 0.80 1.70 1.98 1.95
TRMT13 ENST00000370141 32.28 50.86 39.91 0.97 0.63 0.80 1.70 1.92 2.02

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