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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
DCAKD ENST00000452796 56.56 55.22 55.57 0.58 0.57 0.53 1.63 1.62 1.73
TAS2R38 ENST00000547270 56.57 61.53 59.25 0.58 0.54 0.49 1.63 1.41 1.68
MAN2B1 ENST00000456935 56.57 53.79 54.77 0.58 0.63 0.54 1.63 1.70 1.74
ABCC2 ENST00000370449 56.58 63.74 60.70 0.58 0.49 0.44 1.63 1.22 1.61
TAL2 ENST00000334077 56.58 78.29 69.63 0.58 0.43 0.44 1.63 0.74 0.95
CD2BP2 ENST00000305596 56.59 61.21 59.07 0.58 0.53 0.49 1.63 1.40 1.67
ATP1A4 ENST00000368081 56.59 51.29 53.32 0.58 0.65 0.62 1.63 1.90 1.86
EXOSC5 ENST00000221233 56.60 63.24 60.38 0.58 0.47 0.44 1.63 1.31 1.58
CRYL1 ENST00000298248 56.60 58.07 57.22 0.58 0.53 0.52 1.63 1.46 1.69
MGAM ENST00000549489 56.61 44.45 49.44 0.58 0.63 0.70 1.63 1.98 1.83
ELTD1 ENST00000370742 56.61 49.64 52.37 0.58 0.66 0.61 1.63 2.02 1.90
EPX ENST00000225371 56.62 68.28 63.67 0.58 0.52 0.49 1.63 1.20 1.39
MRPL12 ENST00000333676 56.62 66.77 62.61 0.58 0.56 0.48 1.62 1.22 1.39
MCL1 ENST00000369026 56.63 11.29 32.12 0.58 2.13 0.90 1.62 0.55 1.60
RAB19 ENST00000537763 56.63 94.00 78.56 0.58 0.25 0.38 1.62 0.26 0.55
PTPLA ENST00000361271 56.64 87.71 75.11 0.58 0.24 0.39 1.62 0.37 0.67
ATIC ENST00000236959 56.64 69.25 64.22 0.58 0.57 0.51 1.62 1.14 1.35
MYBPHL ENST00000357155 56.65 41.03 47.64 0.58 0.59 0.65 1.62 1.81 1.88
PCDHA13 ENST00000289272 56.66 65.87 62.02 0.57 0.54 0.49 1.62 1.23 1.44
COX18 ENST00000295890 56.66 81.45 71.58 0.57 0.33 0.44 1.62 0.55 0.83
HMOX1 ENST00000216117 56.67 53.58 54.71 0.57 0.62 0.57 1.61 1.70 1.73
PDE4C ENST00000355502 56.67 44.40 49.44 0.57 0.61 0.70 1.61 1.97 1.84
HMCES ENST00000383463 56.68 60.76 58.81 0.57 0.56 0.51 1.61 1.40 1.65
ZNF286A ENST00000464847 56.68 52.50 54.12 0.57 0.66 0.59 1.61 1.83 1.75
KRT33B ENST00000251646 56.69 86.83 74.68 0.57 0.23 0.40 1.61 0.40 0.67

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