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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
ACOT6 ENST00000381139 35.92 84.34 60.68 0.94 0.28 0.44 1.88 0.44 1.61
ACOT4 ENST00000326303 78.22 84.72 84.85 0.34 0.27 0.34 0.67 0.42 0.40
ACOT2 ENST00000238651 83.05 73.91 81.85 0.29 0.53 0.37 0.55 1.02 0.46
ACOT13 ENST00000230048 78.93 96.03 90.55 0.32 0.23 0.15 0.64 0.20 0.21
ACOT12 ENST00000307624 55.13 57.96 56.30 0.62 0.56 0.49 1.69 1.46 1.75
ACOT11 ENST00000371316 58.96 59.32 59.39 0.56 0.51 0.49 1.49 1.41 1.71
ACOT1 ENST00000311148 74.74 70.75 75.74 0.38 0.48 0.38 0.78 1.08 0.64
ACO2 ENST00000216254 14.95 20.14 15.30 1.57 1.43 1.82 0.75 0.75 0.66
ACO1 ENST00000309951 37.30 50.41 42.09 0.95 0.66 0.71 1.72 1.95 1.99
ACN9 ENST00000432641 64.77 91.56 81.52 0.54 0.23 0.35 1.17 0.32 0.48
ACMSD ENST00000356140 56.86 61.27 59.28 0.58 0.53 0.51 1.59 1.39 1.68
ACLY ENST00000352035 14.63 17.90 13.96 1.56 1.54 2.06 0.73 0.73 0.59
ACKR4 ENST00000249887 46.89 87.08 69.06 0.56 0.22 0.44 1.80 0.40 1.03
ACKR3 ENST00000272928 23.81 36.82 28.51 1.37 0.76 0.78 1.12 1.66 1.31
ACKR2 ENST00000422265 61.73 78.24 72.67 0.71 0.43 0.43 1.29 0.74 0.81
ACIN1 ENST00000262710 12.19 6.36 6.65 1.68 2.67 3.01 0.60 0.37 0.32
ACHE ENST00000302913 13.02 6.20 6.99 1.71 2.73 2.90 0.64 0.35 0.33
ACER3 ENST00000532485 9.69 14.40 9.49 2.15 2.05 2.30 0.49 0.61 0.40
ACER2 ENST00000340967 45.92 35.72 39.20 0.58 0.78 0.78 1.78 1.58 2.06
ACER1 ENST00000301452 58.79 55.95 57.27 0.56 0.49 0.52 1.48 1.56 1.70
ACE2 ENST00000427411 32.48 8.73 18.61 0.97 2.48 1.58 1.71 0.48 0.81
ACE ENST00000290866 60.68 59.20 60.46 0.57 0.49 0.44 1.33 1.44 1.58
ACD ENST00000393919 76.20 68.98 75.56 0.34 0.54 0.37 0.76 1.15 0.64
ACCSL ENST00000378832 78.10 71.29 77.90 0.34 0.53 0.38 0.67 1.07 0.54
ACCS ENST00000263776 55.76 44.63 49.11 0.58 0.66 0.72 1.64 1.97 1.83

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