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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
FNDC9 ENST00000312349 62.37 73.95 70.46 0.67 0.53 0.43 1.27 1.02 0.91
HOXD4 ENST00000306324 62.38 60.42 62.23 0.67 0.53 0.48 1.27 1.41 1.43
OR10Z1 ENST00000361284 62.38 66.37 65.98 0.67 0.54 0.51 1.27 1.20 1.23
PCDHGB2 ENST00000522605 62.39 66.40 66.03 0.67 0.54 0.51 1.28 1.20 1.22
UGT2A2 ENST00000457664 62.39 78.48 73.17 0.67 0.42 0.43 1.28 0.74 0.79
DSC1 ENST00000257198 62.40 51.92 57.04 0.68 0.61 0.51 1.28 1.85 1.70
C20orf85 ENST00000371168 62.40 88.80 78.84 0.68 0.25 0.39 1.28 0.35 0.52
FERD3L ENST00000275461 62.41 65.64 65.59 0.68 0.53 0.51 1.28 1.22 1.29
SCN10A ENST00000449082 62.41 60.10 61.99 0.68 0.52 0.49 1.28 1.39 1.45
S100A14 ENST00000368702 62.42 89.03 79.01 0.68 0.27 0.39 1.28 0.35 0.54
TRMT1 ENST00000592062 62.42 51.48 56.79 0.68 0.63 0.52 1.28 1.88 1.70
ABRA ENST00000311955 62.43 63.96 64.50 0.68 0.48 0.51 1.28 1.21 1.34
OR56B3P ENST00000316517 62.43 92.53 80.79 0.68 0.29 0.39 1.28 0.31 0.52
ECT2L ENST00000423192 62.44 78.28 73.10 0.68 0.43 0.42 1.28 0.74 0.80
AGER ENST00000375076 62.45 75.26 71.33 0.68 0.49 0.43 1.28 0.90 0.87
PECR ENST00000265322 62.45 74.09 70.57 0.68 0.53 0.43 1.28 1.03 0.90
CLRN1 ENST00000328863 62.46 90.03 79.51 0.68 0.25 0.38 1.28 0.37 0.52
P2RY2 ENST00000311131 62.46 48.82 55.23 0.68 0.63 0.51 1.28 2.02 1.74
EHHADH ENST00000231887 62.47 53.38 57.96 0.68 0.66 0.47 1.28 1.70 1.67
SORBS3 ENST00000240123 62.47 42.50 51.61 0.67 0.59 0.62 1.28 1.87 1.93
P2RY4 ENST00000374519 62.48 53.44 58.03 0.66 0.65 0.47 1.28 1.70 1.66
TNIP2 ENST00000315423 62.48 37.59 48.92 0.66 0.80 0.71 1.28 1.68 1.84
S100A11 ENST00000271638 62.49 89.85 79.43 0.65 0.27 0.39 1.28 0.37 0.52
ALG14 ENST00000370205 62.49 64.42 64.86 0.65 0.48 0.51 1.28 1.22 1.34
SMYD1 ENST00000419482 62.50 56.32 59.73 0.65 0.52 0.49 1.28 1.55 1.66

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