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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
CLDN18 ENST00000183605 52.70 70.72 62.64 0.67 0.48 0.48 1.77 1.09 1.40
ROPN1 ENST00000184183 60.00 69.91 66.66 0.62 0.53 0.53 1.40 1.15 1.20
NDUFB4 ENST00000184266 67.49 77.82 75.64 0.57 0.42 0.38 1.06 0.79 0.63
HEATR6 ENST00000184956 47.93 48.10 46.73 0.54 0.63 0.66 1.80 1.99 1.87
ERLEC1 ENST00000185150 33.40 35.69 32.74 0.92 0.78 0.86 1.70 1.57 1.65
CLIC5 ENST00000185206 54.91 67.05 61.70 0.63 0.54 0.46 1.70 1.24 1.46
TMEM131 ENST00000186436 43.20 7.25 23.33 0.82 2.58 1.19 1.80 0.37 0.98
TMEM38A ENST00000187762 41.84 66.06 53.34 0.80 0.56 0.62 1.74 1.21 1.86
ACTR6 ENST00000188312 13.58 59.02 34.52 1.66 0.51 0.90 0.67 1.43 1.77
FAP ENST00000188790 37.31 57.24 45.96 0.95 0.56 0.70 1.72 1.49 1.97
DMRT3 ENST00000190165 75.98 66.59 74.13 0.34 0.54 0.39 0.76 1.22 0.69
GAL3ST2 ENST00000192314 87.00 93.15 92.79 0.23 0.28 0.14 0.39 0.30 0.15
UHRF1BP1 ENST00000192788 36.54 33.04 32.96 0.95 0.85 0.86 1.78 1.49 1.67
OSTM1 ENST00000193322 5.49 33.76 17.48 3.33 0.85 1.62 0.33 1.56 0.75
IMPG2 ENST00000193391 50.51 36.92 41.96 0.58 0.76 0.68 1.80 1.70 2.01
SLC13A1 ENST00000194130 43.40 68.24 55.48 0.81 0.52 0.51 1.79 1.21 1.73
PCDHB4 ENST00000194152 66.05 74.43 72.99 0.59 0.53 0.40 1.05 1.00 0.80
PCDHB2 ENST00000194155 65.77 62.35 65.65 0.58 0.53 0.51 1.06 1.33 1.29
HSPB11 ENST00000194214 29.51 73.45 50.50 1.08 0.53 0.67 1.55 1.03 1.86
STRADB ENST00000194530 17.52 35.45 24.56 1.47 0.77 1.06 0.88 1.56 1.09
C4orf6 ENST00000195455 97.79 97.44 99.29 0.11 0.22 0.11 0.11 0.19 0.04
PLOD1 ENST00000196061 45.49 48.91 45.89 0.57 0.63 0.70 1.75 2.04 1.98
OXCT1 ENST00000196371 9.91 28.09 16.83 2.09 1.19 1.70 0.50 1.20 0.70
ZNF416 ENST00000196489 95.42 56.71 79.36 0.11 0.53 0.39 0.11 1.56 0.54
ZNF8 ENST00000196548 47.68 37.49 40.76 0.53 0.78 0.81 1.80 1.67 2.04

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