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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
ZBTB25 ENST00000608382 29.48 61.73 44.01 1.06 0.57 0.62 1.55 1.38 2.03
SCOC ENST00000608372 67.15 66.57 68.89 0.61 0.56 0.46 1.04 1.21 1.04
SLC5A3 ENST00000608209 7.58 14.10 8.21 2.73 2.06 2.58 0.40 0.59 0.37
TMEM80 ENST00000608174 82.98 96.71 92.60 0.30 0.23 0.14 0.55 0.19 0.15
GTF2H5 ENST00000607778 43.03 86.96 66.73 0.82 0.22 0.54 1.77 0.40 1.20
CNKSR3 ENST00000607772 38.46 26.62 30.80 0.92 1.20 0.78 1.72 1.12 1.49
DCP1A ENST00000607628 38.62 16.79 25.83 0.92 1.67 1.01 1.74 0.71 1.23
CHURC1 ENST00000607599 56.38 90.95 76.77 0.58 0.25 0.34 1.63 0.35 0.61
SRRM5 ENST00000607544 94.93 97.72 99.03 0.10 0.21 0.11 0.12 0.17 0.04
UQCC2 ENST00000607484 51.35 56.24 53.22 0.59 0.52 0.61 1.84 1.56 1.88
RP11-156E8.1 ENST00000607453 92.28 98.87 98.22 0.15 0.17 0.09 0.19 0.14 0.05
PRIM2 ENST00000607273 56.09 47.70 50.95 0.58 0.61 0.66 1.61 1.97 1.85
HEBP2 ENST00000607197 60.85 80.76 73.58 0.59 0.37 0.40 1.36 0.57 0.74
HIST1H2BJ ENST00000607124 66.83 92.40 82.96 0.59 0.25 0.32 1.05 0.30 0.40
NUDT3 ENST00000607016 21.85 33.84 25.97 1.53 0.85 0.99 1.04 1.56 1.25
TOR1AIP1 ENST00000606911 45.74 51.45 47.35 0.58 0.63 0.66 1.77 1.89 1.86
APLNR ENST00000606794 45.95 26.87 34.63 0.58 1.23 0.90 1.78 1.12 1.76
CTD-2116N17.1 ENST00000606793 14.59 25.17 17.78 1.56 1.32 1.66 0.73 1.02 0.78
TRABD2B ENST00000606738 60.82 20.27 38.84 0.59 1.43 0.82 1.34 0.75 2.04
XXcos-LUCA11.5 ENST00000606589 30.26 90.73 61.11 1.02 0.25 0.43 1.61 0.35 1.52
TBC1D7 ENST00000606214 46.07 83.56 66.49 0.58 0.27 0.51 1.80 0.47 1.21
SIRT5 ENST00000606117 73.33 64.78 71.59 0.34 0.49 0.44 0.80 1.24 0.83
FRK ENST00000606080 45.21 59.97 51.76 0.63 0.53 0.62 1.75 1.37 1.93
AC007040.11 ENST00000606025 15.40 64.73 38.36 1.56 0.48 0.85 0.76 1.24 2.04
RER1 ENST00000605895 10.27 28.45 17.20 2.02 1.15 1.64 0.54 1.24 0.73

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