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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
WDR44 ENST00000254029 11.24 5.67 5.69 1.78 2.96 3.33 0.59 0.34 0.28
ANKH ENST00000284268 11.24 24.13 15.51 1.77 1.35 1.80 0.59 0.98 0.67
CA7 ENST00000338437 11.25 34.32 20.92 1.76 0.82 1.44 0.59 1.57 0.87
DAGLA ENST00000257215 11.25 3.80 4.79 1.76 3.31 3.67 0.59 0.31 0.24
KLF12 ENST00000377669 11.26 11.39 8.68 1.76 2.11 2.53 0.59 0.56 0.36
NEK8 ENST00000268766 11.26 43.97 25.70 1.76 0.61 1.05 0.59 1.96 1.22
MSI2 ENST00000284073 11.27 8.10 7.02 1.76 2.52 2.90 0.59 0.44 0.33
SYT11 ENST00000368324 11.28 18.38 12.40 1.76 1.48 2.23 0.59 0.75 0.50
SUPT4H1 ENST00000225504 11.28 72.03 40.00 1.76 0.52 0.81 0.59 1.03 1.99
PHF10 ENST00000339209 11.29 34.63 21.11 1.76 0.80 1.42 0.59 1.54 0.90
DNAJA2 ENST00000317089 11.29 6.28 6.05 1.76 2.71 3.29 0.59 0.36 0.30
LIN28B ENST00000345080 11.30 29.83 18.50 1.76 1.13 1.62 0.59 1.40 0.81
IKZF5 ENST00000368886 11.30 22.14 14.45 1.76 1.52 2.00 0.59 0.83 0.58
ACTN1 ENST00000394419 11.31 6.94 6.46 1.76 2.58 3.07 0.59 0.37 0.32
OLFM3 ENST00000370103 11.31 35.38 21.51 1.76 0.77 1.30 0.59 1.56 0.91
KCNS2 ENST00000287042 11.32 40.54 23.98 1.76 0.63 1.09 0.59 1.77 1.05
SLC35F4 ENST00000339762 11.32 34.56 21.07 1.76 0.80 1.42 0.59 1.54 0.89
MPPED2 ENST00000358117 11.33 5.77 5.82 1.76 2.87 3.30 0.59 0.34 0.28
TARBP2 ENST00000266987 11.33 26.01 16.51 1.76 1.20 1.71 0.59 1.10 0.69
SEPT7 ENST00000399034 11.34 5.36 5.62 1.76 3.09 3.39 0.59 0.32 0.27
ATXN7L3B ENST00000519948 11.34 87.28 48.18 1.76 0.22 0.66 0.59 0.41 1.87
KIF1B ENST00000263934 11.35 3.98 4.94 1.76 3.27 3.69 0.59 0.32 0.25
ANKRD34A ENST00000323397 11.35 8.62 7.37 1.76 2.49 2.78 0.59 0.47 0.34
ANAPC7 ENST00000455511 11.36 16.99 11.80 1.76 1.63 2.21 0.59 0.73 0.46
SPAG9 ENST00000262013 11.36 2.90 4.41 1.76 3.49 3.73 0.59 0.29 0.25

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