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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
OR2T11 ENST00000330803 75.54 95.88 88.77 0.35 0.22 0.19 0.75 0.20 0.28
ZNF581 ENST00000587252 75.55 70.28 75.94 0.35 0.52 0.38 0.75 1.10 0.62
OR2T6 ENST00000355728 75.55 92.65 87.29 0.35 0.29 0.28 0.75 0.31 0.31
LAX1 ENST00000442561 75.56 64.84 72.95 0.35 0.48 0.40 0.75 1.24 0.81
MKRN3 ENST00000314520 75.56 31.51 52.86 0.35 0.96 0.61 0.75 1.42 1.88
SPRR4 ENST00000328051 75.57 87.35 84.81 0.35 0.22 0.34 0.75 0.41 0.40
DPPA5 ENST00000370370 75.57 84.49 83.39 0.35 0.29 0.33 0.75 0.44 0.40
TARBP1 ENST00000040877 75.58 43.33 59.86 0.34 0.59 0.49 0.75 1.94 1.63
FCRLA ENST00000367959 75.58 75.88 79.05 0.34 0.43 0.39 0.75 0.88 0.53
DPEP1 ENST00000393092 75.59 70.93 76.36 0.34 0.49 0.35 0.75 1.06 0.61
GHRL ENST00000335542 75.60 97.21 89.53 0.34 0.24 0.18 0.75 0.19 0.23
DLGAP5 ENST00000247191 75.60 49.32 63.67 0.34 0.65 0.49 0.75 2.02 1.39
OR5AC2 ENST00000358642 75.61 84.05 83.20 0.34 0.27 0.29 0.75 0.45 0.40
KRTAP29-1 ENST00000391353 75.61 89.23 85.74 0.34 0.27 0.33 0.75 0.36 0.33
OR10H2 ENST00000305899 75.62 86.53 84.39 0.34 0.24 0.33 0.75 0.42 0.40
DKK4 ENST00000220812 75.62 72.75 77.38 0.34 0.48 0.35 0.75 1.04 0.58
HAPLN3 ENST00000359595 75.63 68.56 75.02 0.34 0.53 0.39 0.75 1.19 0.66
LGALS3 ENST00000254301 75.63 76.74 79.44 0.34 0.40 0.39 0.75 0.83 0.52
CRISP2 ENST00000339139 75.64 86.42 84.35 0.34 0.24 0.33 0.75 0.42 0.40
MIA2 ENST00000280082 75.64 35.54 55.18 0.35 0.77 0.51 0.75 1.58 1.75
SERPINB8 ENST00000397985 75.65 77.60 79.96 0.35 0.42 0.35 0.75 0.79 0.52
OTOP3 ENST00000328801 75.65 64.54 72.84 0.35 0.47 0.42 0.75 1.22 0.80
CAMK2N2 ENST00000296238 75.66 77.51 79.88 0.35 0.42 0.37 0.75 0.78 0.52
CACNG6 ENST00000252729 75.66 86.75 84.55 0.35 0.24 0.34 0.75 0.40 0.40
CENPQ ENST00000335783 75.67 67.55 74.54 0.35 0.53 0.40 0.75 1.20 0.69

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