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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
NEU1 ENST00000375631 42.49 50.40 45.13 0.76 0.66 0.70 1.75 1.95 2.00
POC1B ENST00000313546 42.49 48.46 43.84 0.76 0.63 0.61 1.75 2.02 2.02
RHO ENST00000296271 42.50 58.68 49.51 0.76 0.54 0.67 1.76 1.43 1.84
C1QTNF5 ENST00000445041 42.50 24.93 31.91 0.76 1.32 0.91 1.76 1.07 1.57
NUAK2 ENST00000367157 42.51 41.29 40.19 0.76 0.61 0.82 1.76 1.82 1.99
TAF4B ENST00000269142 42.51 19.83 29.35 0.76 1.42 0.82 1.76 0.74 1.35
CABLES1 ENST00000256925 42.52 34.31 36.51 0.76 0.84 0.85 1.76 1.57 1.90
SDS ENST00000257549 42.52 61.68 51.16 0.76 0.56 0.65 1.76 1.39 1.90
LMAN2L ENST00000377079 42.53 70.18 56.08 0.76 0.53 0.49 1.76 1.12 1.75
PRDM8 ENST00000339711 42.53 20.84 29.91 0.76 1.42 0.86 1.77 0.83 1.44
HOXA1 ENST00000343060 42.54 34.56 36.72 0.76 0.80 0.82 1.77 1.55 1.94
WDR36 ENST00000506538 42.54 21.67 30.28 0.76 1.47 0.84 1.77 0.81 1.44
C8orf34 ENST00000518698 42.55 62.30 51.57 0.76 0.53 0.62 1.77 1.33 1.93
NSDHL ENST00000370274 42.55 11.08 24.85 0.76 2.09 1.02 1.77 0.53 1.10
KIAA1524 ENST00000295746 42.56 45.14 42.07 0.76 0.70 0.71 1.77 1.96 1.99
NUDT12 ENST00000230792 42.56 72.87 57.73 0.76 0.49 0.49 1.78 1.05 1.68
CD44 ENST00000428726 42.57 35.07 37.06 0.76 0.76 0.80 1.78 1.58 1.95
USP30 ENST00000257548 42.58 34.18 36.47 0.76 0.84 0.84 1.78 1.55 1.89
TMEM169 ENST00000454545 42.58 47.37 43.32 0.76 0.66 0.63 1.78 2.01 2.01
ERCC2 ENST00000391945 42.59 62.57 51.73 0.76 0.52 0.62 1.78 1.31 1.93
MLXIPL ENST00000313375 42.59 23.36 31.18 0.76 1.42 0.85 1.78 0.93 1.55
CHRDL1 ENST00000372042 42.60 25.94 32.46 0.76 1.21 0.90 1.77 1.10 1.63
RP11-57H12.6 ENST00000604534 42.60 45.41 42.23 0.76 0.68 0.70 1.77 2.01 2.01
SFXN5 ENST00000272433 42.61 42.26 40.62 0.76 0.61 0.81 1.77 1.88 2.05
PXN ENST00000267257 42.61 26.18 32.60 0.76 1.19 0.87 1.77 1.08 1.63

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