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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
KIAA1467 ENST00000197268 42.80 26.22 32.70 0.78 1.19 0.86 1.77 1.08 1.63
PILRA ENST00000198536 98.66 86.43 95.27 0.10 0.24 0.08 0.11 0.42 0.10
RRN3 ENST00000198767 53.69 33.97 42.04 0.63 0.84 0.70 1.77 1.55 1.98
MOGAT2 ENST00000198801 65.43 41.13 52.58 0.56 0.59 0.61 1.12 1.82 1.89
AQP2 ENST00000199280 42.39 82.02 63.33 0.76 0.34 0.48 1.75 0.50 1.36
DIMT1 ENST00000199320 23.53 53.46 36.61 1.38 0.65 0.85 1.08 1.72 1.93
EIF2AK1 ENST00000199389 50.31 37.05 41.90 0.57 0.78 0.68 1.81 1.68 2.01
NME8 ENST00000199447 69.80 72.98 74.26 0.52 0.51 0.39 0.95 1.03 0.69
EPDR1 ENST00000199448 64.61 60.15 63.56 0.56 0.52 0.49 1.19 1.39 1.39
MRPL28 ENST00000199706 79.75 81.37 83.91 0.33 0.33 0.35 0.58 0.54 0.43
HBQ1 ENST00000199708 86.59 94.78 93.42 0.24 0.23 0.11 0.41 0.24 0.15
CEACAM6 ENST00000199764 95.64 70.71 86.37 0.11 0.49 0.33 0.11 1.09 0.33
RBM22 ENST00000199814 1.30 2.73 0.60 4.38 3.54 4.68 0.17 0.29 0.18
HSD17B2 ENST00000199936 85.63 86.22 89.04 0.28 0.27 0.19 0.46 0.42 0.26
ZW10 ENST00000200135 32.35 26.82 27.75 0.99 1.23 0.90 1.71 1.12 1.27
ITGB4 ENST00000200181 44.46 33.48 37.26 0.65 0.84 0.82 1.77 1.53 2.00
PPP1R15A ENST00000200453 88.98 68.95 82.32 0.19 0.54 0.33 0.32 1.16 0.44
TRIP6 ENST00000200457 64.59 38.22 50.44 0.56 0.76 0.67 1.18 1.70 1.88
ADAM11 ENST00000200557 10.65 27.25 16.80 1.99 1.25 1.70 0.57 1.15 0.70
SLC22A4 ENST00000200652 23.82 55.72 38.05 1.35 0.52 0.85 1.12 1.60 2.02
CETP ENST00000200676 76.54 79.61 81.40 0.34 0.38 0.37 0.73 0.66 0.48
MT3 ENST00000200691 41.72 79.37 61.17 0.80 0.38 0.43 1.73 0.67 1.50
TFAP2C ENST00000201031 4.77 16.67 8.08 3.61 1.72 2.59 0.30 0.71 0.37
SULT2B1 ENST00000201586 64.46 28.88 45.38 0.56 1.15 0.70 1.20 1.30 2.00
EPS8L1 ENST00000201647 79.76 57.18 70.80 0.33 0.56 0.43 0.58 1.49 0.86

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