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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
CDC34 ENST00000215574 18.60 13.06 13.44 1.53 2.07 2.05 0.91 0.59 0.56
VANGL2 ENST00000368061 18.60 18.36 16.31 1.53 1.48 1.71 0.91 0.75 0.67
BLNK ENST00000224337 18.61 15.53 14.84 1.53 1.87 1.95 0.91 0.67 0.63
F8 ENST00000360256 18.61 0.81 7.07 1.53 4.10 2.86 0.91 0.28 0.33
G6PD ENST00000393562 18.62 15.59 14.90 1.53 1.87 1.92 0.91 0.68 0.63
SETD1A ENST00000262519 18.63 2.46 7.92 1.53 3.58 2.61 0.90 0.29 0.35
FAM126B ENST00000418596 18.63 22.46 18.49 1.53 1.52 1.62 0.90 0.83 0.81
SMIM4 ENST00000477703 18.64 79.65 48.01 1.52 0.37 0.67 0.90 0.65 1.88
B4GALT2 ENST00000309519 18.64 29.87 22.46 1.52 1.13 1.16 0.90 1.40 0.97
FNBP1 ENST00000446176 18.65 11.55 12.66 1.52 2.10 2.19 0.90 0.57 0.52
NSFL1C ENST00000476071 18.65 30.29 22.63 1.52 1.08 1.16 0.90 1.40 0.96
EIF6 ENST00000374450 18.66 34.49 24.64 1.52 0.80 1.06 0.90 1.56 1.10
DLG2 ENST00000376104 18.66 12.20 13.01 1.52 2.07 2.09 0.90 0.59 0.52
BMP2 ENST00000378827 18.67 7.33 10.60 1.53 2.56 2.16 0.90 0.37 0.44
FOS ENST00000303562 18.67 35.06 24.91 1.53 0.76 1.02 0.90 1.58 1.11
EIF2D ENST00000271764 18.68 43.77 29.40 1.53 0.61 0.84 0.90 1.96 1.36
COX7B ENST00000481445 18.68 43.64 29.31 1.53 0.62 0.82 0.90 1.97 1.34
ZNF184 ENST00000211936 18.69 27.74 21.31 1.53 1.25 1.39 0.90 1.19 0.91
PLXNA2 ENST00000367033 18.69 21.41 17.98 1.53 1.43 1.70 0.91 0.80 0.78
XPNPEP1 ENST00000502935 18.70 18.98 16.68 1.53 1.52 1.70 0.91 0.76 0.70
SLC10A7 ENST00000335472 18.70 51.71 33.37 1.53 0.61 0.87 0.91 1.88 1.72
LARP4B ENST00000316157 18.71 3.74 8.55 1.52 3.33 2.51 0.91 0.31 0.37
MPC1 ENST00000360961 18.71 66.44 40.75 1.52 0.56 0.81 0.91 1.20 2.05
CCT5 ENST00000280326 18.72 4.79 9.20 1.52 3.28 2.32 0.91 0.32 0.38
ZC3H7A ENST00000396516 18.72 1.67 7.56 1.53 3.83 2.75 0.91 0.26 0.33

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