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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
ABI3BP ENST00000284322 39.84 27.50 31.87 0.89 1.25 0.91 1.75 1.16 1.58
ABL1 ENST00000372348 7.00 4.40 3.14 2.92 3.26 3.92 0.37 0.32 0.24
ABL2 ENST00000502732 16.01 29.52 20.90 1.53 1.10 1.44 0.79 1.39 0.87
ABLIM1 ENST00000277895 11.88 14.72 10.93 1.63 1.97 2.23 0.59 0.62 0.44
ABLIM2 ENST00000447017 71.84 23.82 46.50 0.34 1.38 0.66 0.82 0.93 1.91
ABLIM3 ENST00000506113 32.48 29.82 29.29 0.97 1.13 0.84 1.71 1.40 1.34
ABR ENST00000302538 9.98 14.31 9.61 2.06 2.05 2.28 0.52 0.61 0.40
ABRA ENST00000311955 62.43 63.96 64.50 0.68 0.48 0.51 1.28 1.21 1.34
ABRACL ENST00000367660 32.87 74.04 52.77 0.94 0.53 0.61 1.70 1.03 1.89
ABT1 ENST00000274849 62.50 57.74 60.67 0.65 0.57 0.44 1.28 1.47 1.61
ABTB1 ENST00000232744 58.13 39.96 47.90 0.56 0.63 0.66 1.54 1.68 1.89
ABTB2 ENST00000435224 14.21 23.69 16.81 1.61 1.39 1.70 0.72 0.93 0.70
AC002472.13 ENST00000342608 93.83 84.41 91.80 0.11 0.29 0.14 0.13 0.44 0.18
AC003101.1 ENST00000412403 94.43 92.54 96.22 0.10 0.29 0.07 0.11 0.31 0.09
AC003102.1 ENST00000399246 90.13 97.78 96.90 0.16 0.21 0.08 0.25 0.17 0.07
AC004076.9 ENST00000596831 88.31 78.10 86.39 0.20 0.43 0.32 0.35 0.74 0.33
AC004381.6 ENST00000261377 40.66 41.63 39.51 0.86 0.62 0.80 1.75 1.80 2.03
AC004466.1 ENST00000599515 83.07 97.08 92.81 0.29 0.24 0.14 0.55 0.19 0.15
AC004899.1 ENST00000596947 89.32 98.97 96.99 0.18 0.17 0.08 0.32 0.15 0.07
AC005003.1 ENST00000504184 93.70 80.79 89.94 0.13 0.35 0.18 0.13 0.57 0.23
AC005008.2 ENST00000431501 90.86 91.76 94.29 0.16 0.24 0.10 0.21 0.32 0.12
AC005358.1 ENST00000609971 28.79 10.42 17.47 1.13 2.23 1.62 1.53 0.50 0.75
AC005477.1 ENST00000542853 93.42 99.56 98.50 0.13 0.16 0.10 0.15 0.12 0.05
AC005481.5 ENST00000409610 90.15 83.58 90.05 0.16 0.27 0.18 0.25 0.47 0.22
AC005609.1 ENST00000502505 68.71 88.45 81.97 0.56 0.23 0.37 0.95 0.37 0.47

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