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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
AGMAT ENST00000375826 56.17 82.09 71.70 0.58 0.34 0.46 1.62 0.50 0.82
RAB37 ENST00000392614 56.18 76.16 68.15 0.58 0.43 0.49 1.62 0.87 1.08
VIL1 ENST00000248444 56.19 47.55 50.92 0.58 0.61 0.66 1.62 2.02 1.85
S1PR5 ENST00000439028 56.19 42.20 48.06 0.59 0.61 0.67 1.62 1.87 1.88
PON3 ENST00000265627 56.20 70.47 64.70 0.59 0.52 0.49 1.61 1.08 1.33
PRL ENST00000306482 56.20 75.82 67.91 0.59 0.43 0.51 1.61 0.89 1.10
C12orf57 ENST00000229281 56.21 91.86 77.19 0.59 0.23 0.35 1.61 0.32 0.59
F2RL1 ENST00000296677 56.21 68.67 63.66 0.59 0.53 0.49 1.61 1.17 1.39
KIAA1217 ENST00000376454 56.22 20.46 36.44 0.58 1.43 0.84 1.61 0.77 1.88
EAPP ENST00000250454 56.22 79.24 69.96 0.58 0.39 0.47 1.61 0.68 0.92
NCMAP ENST00000374392 56.23 88.12 75.11 0.58 0.24 0.39 1.62 0.38 0.67
CAPNS1 ENST00000246533 56.23 61.57 59.07 0.58 0.54 0.49 1.62 1.41 1.68
CARS ENST00000380525 56.24 24.72 38.74 0.58 1.32 0.82 1.62 1.05 2.02
LYPD1 ENST00000397463 56.24 87.16 74.63 0.58 0.20 0.40 1.63 0.41 0.68
AURKC ENST00000302804 56.25 37.47 45.59 0.58 0.77 0.68 1.62 1.67 1.97
MEP1B ENST00000269202 56.25 69.47 64.12 0.58 0.54 0.52 1.62 1.12 1.37
TAAR8 ENST00000275200 56.26 79.98 70.43 0.58 0.37 0.43 1.62 0.61 0.91
EMILIN1 ENST00000380320 56.26 23.49 38.16 0.58 1.42 0.85 1.62 0.92 2.05
MCAM ENST00000264036 56.27 30.68 41.70 0.58 1.05 0.72 1.63 1.38 2.01
GPR15 ENST00000284311 56.27 85.66 73.78 0.58 0.27 0.42 1.63 0.44 0.71
FBXO16 ENST00000380254 56.28 66.61 62.27 0.58 0.54 0.48 1.63 1.22 1.43
PTGES3L ENST00000409446 56.28 59.04 57.63 0.58 0.51 0.51 1.63 1.43 1.67
CHML ENST00000366553 56.29 49.97 52.40 0.58 0.66 0.61 1.63 2.02 1.90
PARD3B ENST00000358768 56.29 38.78 46.22 0.58 0.70 0.67 1.63 1.66 1.94
GYLTL1B ENST00000531526 56.30 57.55 56.73 0.58 0.57 0.52 1.63 1.48 1.71

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