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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
ACMSD ENST00000356140 56.86 61.27 59.28 0.58 0.53 0.51 1.59 1.39 1.68
ACN9 ENST00000432641 64.77 91.56 81.52 0.54 0.23 0.35 1.17 0.32 0.48
ACO1 ENST00000309951 37.30 50.41 42.09 0.95 0.66 0.71 1.72 1.95 1.99
ACO2 ENST00000216254 14.95 20.14 15.30 1.57 1.43 1.82 0.75 0.75 0.66
ACOT1 ENST00000311148 74.74 70.75 75.74 0.38 0.48 0.38 0.78 1.08 0.64
ACOT11 ENST00000371316 58.96 59.32 59.39 0.56 0.51 0.49 1.49 1.41 1.71
ACOT12 ENST00000307624 55.13 57.96 56.30 0.62 0.56 0.49 1.69 1.46 1.75
ACOT13 ENST00000230048 78.93 96.03 90.55 0.32 0.23 0.15 0.64 0.20 0.21
ACOT2 ENST00000238651 83.05 73.91 81.85 0.29 0.53 0.37 0.55 1.02 0.46
ACOT4 ENST00000326303 78.22 84.72 84.85 0.34 0.27 0.34 0.67 0.42 0.40
ACOT6 ENST00000381139 35.92 84.34 60.68 0.94 0.28 0.44 1.88 0.44 1.61
ACOT7 ENST00000377855 16.22 20.39 16.10 1.48 1.43 1.70 0.80 0.76 0.66
ACOT8 ENST00000217455 65.57 54.49 60.56 0.57 0.59 0.44 1.09 1.66 1.58
ACOT9 ENST00000379303 51.45 67.97 60.12 0.59 0.52 0.47 1.86 1.17 1.61
ACOX1 ENST00000293217 21.78 21.69 19.80 1.54 1.46 1.49 1.05 0.81 0.85
ACOX2 ENST00000302819 68.20 48.90 58.63 0.56 0.63 0.52 1.01 2.04 1.65
ACOX3 ENST00000356406 77.50 59.48 70.85 0.34 0.51 0.43 0.67 1.40 0.86
ACOXL ENST00000439055 54.41 61.54 58.05 0.65 0.54 0.47 1.71 1.41 1.66
ACP1 ENST00000272067 55.21 89.59 75.31 0.61 0.27 0.37 1.68 0.37 0.65
ACP2 ENST00000256997 33.68 35.02 32.53 0.96 0.75 0.89 1.70 1.58 1.61
ACP5 ENST00000592828 53.26 39.56 45.05 0.63 0.68 0.70 1.75 1.65 2.02
ACP6 ENST00000369238 60.78 77.22 71.52 0.57 0.43 0.44 1.34 0.78 0.84
ACPL2 ENST00000286353 37.70 40.64 37.41 0.94 0.63 0.85 1.74 1.77 2.00
ACPP ENST00000351273 53.29 76.44 66.52 0.63 0.43 0.51 1.74 0.85 1.21
ACPT ENST00000270593 77.99 79.11 81.94 0.33 0.39 0.37 0.67 0.69 0.47

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