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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
GPKOW ENST00000156109 64.54 5.05 32.95 0.56 3.21 0.86 1.18 0.32 1.67
AQR ENST00000156471 6.88 5.96 3.77 2.92 2.82 3.78 0.36 0.35 0.24
ST6GALNAC1 ENST00000156626 89.25 61.72 78.73 0.18 0.57 0.38 0.32 1.38 0.54
MBD3 ENST00000156825 28.19 9.57 16.72 1.16 2.49 1.68 1.47 0.50 0.70
LMCD1 ENST00000157600 40.49 40.49 38.77 0.86 0.62 0.82 1.73 1.77 2.03
PSMC4 ENST00000157812 1.79 24.43 10.71 4.27 1.32 2.19 0.22 1.00 0.43
FNDC8 ENST00000158009 60.34 71.26 67.65 0.61 0.53 0.51 1.38 1.07 1.13
CAMKK1 ENST00000158166 22.91 30.42 24.75 1.43 1.09 1.04 1.06 1.39 1.10
ACAP1 ENST00000158762 19.83 21.48 18.65 1.54 1.42 1.58 0.99 0.79 0.81
DERL2 ENST00000158771 5.96 14.74 7.71 3.07 1.96 2.68 0.34 0.62 0.33
NOX3 ENST00000159060 62.92 58.20 61.23 0.58 0.54 0.43 1.27 1.44 1.49
ANO8 ENST00000159087 34.03 14.41 22.41 0.91 2.05 1.15 1.76 0.61 0.97
KDM4B ENST00000159111 20.21 2.79 8.87 1.53 3.52 2.47 1.00 0.28 0.38
ICAM3 ENST00000160262 96.88 96.42 98.71 0.09 0.22 0.10 0.11 0.19 0.05
CTTNBP2 ENST00000160373 38.39 31.35 33.01 0.90 0.97 0.85 1.73 1.40 1.66
ACTL6B ENST00000160382 2.50 34.20 16.15 4.08 0.84 1.71 0.27 1.55 0.66
KIF22 ENST00000160827 39.81 45.49 40.81 0.89 0.71 0.80 1.75 1.98 2.04
PRSS22 ENST00000161006 49.20 52.68 49.91 0.57 0.67 0.62 1.80 1.80 1.89
CEACAM1 ENST00000161559 98.68 39.17 71.42 0.10 0.70 0.46 0.11 1.61 0.87
YTHDC2 ENST00000161863 28.14 1.70 12.48 1.16 3.85 2.21 1.47 0.25 0.50
MEF2B ENST00000162023 58.71 55.56 57.03 0.57 0.54 0.51 1.50 1.60 1.70
TMEM161A ENST00000162044 58.02 44.04 50.02 0.56 0.61 0.61 1.53 1.97 1.92
FOXJ2 ENST00000162391 30.62 9.66 18.08 0.96 2.45 1.68 1.63 0.50 0.78
TNFRSF1A ENST00000162749 17.72 7.78 10.28 1.47 2.54 2.20 0.89 0.43 0.42
GOLGA5 ENST00000163416 44.94 26.39 33.81 0.63 1.18 0.89 1.74 1.09 1.73

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