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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
CPAMD8 ENST00000443236 76.83 35.78 55.99 0.34 0.78 0.49 0.73 1.58 1.77
TCN2 ENST00000215838 76.84 48.23 63.78 0.34 0.63 0.49 0.72 1.99 1.38
CPPED1 ENST00000381774 76.85 78.92 81.23 0.34 0.40 0.38 0.72 0.70 0.49
VASN ENST00000304735 76.85 25.27 50.05 0.34 1.29 0.61 0.72 1.02 1.92
KRT77 ENST00000341809 76.86 68.41 75.62 0.34 0.52 0.38 0.72 1.21 0.63
TMEM200B ENST00000420504 76.86 73.48 78.42 0.34 0.53 0.38 0.73 1.03 0.54
CCL22 ENST00000219235 76.87 90.61 86.92 0.34 0.25 0.29 0.72 0.37 0.31
SLCO1B1 ENST00000256958 76.87 73.78 78.60 0.34 0.53 0.38 0.72 1.02 0.54
RNASE1 ENST00000397967 76.88 93.00 88.08 0.34 0.28 0.23 0.72 0.30 0.30
AC087645.1 ENST00000600484 76.88 54.05 67.30 0.34 0.65 0.52 0.73 1.69 1.15
PRSS3 ENST00000361005 76.89 94.69 88.93 0.33 0.23 0.19 0.73 0.24 0.28
ZNF672 ENST00000306562 76.89 27.06 51.05 0.33 1.23 0.66 0.73 1.11 1.89
TRH ENST00000302649 76.90 62.83 72.54 0.33 0.51 0.46 0.73 1.29 0.83
OR10C1 ENST00000444197 76.90 33.93 55.00 0.33 0.84 0.52 0.73 1.56 1.74
SORCS2 ENST00000507866 76.91 19.52 46.99 0.33 1.43 0.70 0.73 0.74 1.87
CELA2A ENST00000359621 76.91 89.99 86.64 0.33 0.25 0.30 0.73 0.37 0.33
ZNF226 ENST00000590089 76.92 64.81 73.65 0.33 0.48 0.40 0.73 1.24 0.74
EID3 ENST00000527879 76.92 34.35 55.22 0.33 0.82 0.51 0.73 1.56 1.75
ZNF614 ENST00000270649 76.93 56.14 68.53 0.33 0.52 0.47 0.73 1.55 1.06
LIPE ENST00000244289 76.93 47.47 63.29 0.33 0.63 0.49 0.73 2.02 1.36
NOC2L ENST00000327044 76.94 72.84 78.12 0.33 0.49 0.39 0.73 1.05 0.55
GPHA2 ENST00000279168 76.94 95.53 89.34 0.33 0.23 0.18 0.73 0.21 0.25
CRTAM ENST00000227348 76.95 64.57 73.56 0.33 0.48 0.40 0.73 1.22 0.75
SELL ENST00000236147 76.95 56.87 68.95 0.33 0.56 0.46 0.73 1.53 1.04
THUMPD2 ENST00000505747 76.96 66.99 74.88 0.33 0.53 0.39 0.73 1.24 0.64

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