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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
AC011484.1 ENST00000377652 95.66 98.47 98.73 0.11 0.21 0.10 0.11 0.14 0.05
AC011897.1 ENST00000581929 81.51 84.00 86.00 0.33 0.27 0.33 0.60 0.46 0.33
AC011997.1 ENST00000409845 24.60 95.19 60.36 1.35 0.23 0.46 1.13 0.21 1.58
AC012123.1 ENST00000426194 81.32 74.38 81.19 0.33 0.53 0.38 0.60 1.00 0.49
AC012215.1 ENST00000437887 89.67 97.54 96.36 0.16 0.22 0.07 0.29 0.19 0.09
AC012493.2 ENST00000595083 93.98 99.80 98.64 0.10 0.17 0.10 0.13 0.11 0.05
AC013449.1 ENST00000599234 80.82 99.64 92.91 0.32 0.17 0.14 0.60 0.12 0.15
AC015987.2 ENST00000416501 92.93 91.33 95.02 0.16 0.23 0.09 0.16 0.34 0.10
AC015989.2 ENST00000593319 93.51 99.61 97.88 0.13 0.16 0.09 0.14 0.12 0.04
AC016251.1 ENST00000378936 92.88 81.04 89.96 0.15 0.35 0.18 0.16 0.55 0.23
AC016586.1 ENST00000535853 89.87 97.66 96.65 0.16 0.21 0.08 0.28 0.19 0.08
AC016722.1 ENST00000409912 95.62 96.67 98.41 0.11 0.23 0.10 0.11 0.20 0.05
AC016757.3 ENST00000409070 93.51 96.61 95.91 0.13 0.23 0.07 0.14 0.20 0.10
AC018470.1 ENST00000595354 91.63 55.74 77.07 0.15 0.52 0.37 0.20 1.59 0.61
AC018755.1 ENST00000301439 90.28 78.98 87.87 0.16 0.40 0.24 0.26 0.69 0.32
AC018816.3 ENST00000449914 89.36 91.05 92.94 0.16 0.25 0.14 0.32 0.36 0.15
AC018867.2 ENST00000595956 89.68 88.43 94.01 0.16 0.23 0.09 0.29 0.37 0.11
AC019294.1 ENST00000543887 91.01 98.23 97.54 0.16 0.21 0.08 0.21 0.15 0.07
AC020907.1 ENST00000313865 83.20 99.59 94.00 0.28 0.16 0.09 0.54 0.12 0.11
AC020922.1 ENST00000539076 99.04 97.99 99.71 0.11 0.20 0.12 0.12 0.17 0.04
AC021218.2 ENST00000377722 93.35 83.83 91.56 0.15 0.28 0.15 0.15 0.47 0.18
AC021860.1 ENST00000436901 91.36 98.39 98.17 0.15 0.21 0.09 0.20 0.14 0.05
AC022400.2 ENST00000595757 90.16 93.32 94.50 0.16 0.28 0.10 0.25 0.29 0.12
AC022431.2 ENST00000438651 90.25 79.27 88.03 0.16 0.38 0.24 0.26 0.67 0.31
AC022498.1 ENST00000392468 90.79 98.13 97.40 0.16 0.20 0.08 0.22 0.16 0.07

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