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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
TGIF2LX ENST00000561129 88.97 97.92 96.23 0.19 0.20 0.07 0.32 0.17 0.09
PPP1R15A ENST00000200453 88.98 68.95 82.32 0.19 0.54 0.33 0.32 1.16 0.44
CALML6 ENST00000307786 88.98 84.40 89.79 0.19 0.29 0.18 0.32 0.44 0.23
MARCKS ENST00000368635 88.99 63.42 79.48 0.19 0.48 0.38 0.32 1.28 0.52
ZNF486 ENST00000335117 88.99 93.35 93.94 0.19 0.28 0.09 0.32 0.28 0.11
PF4 ENST00000296029 89.00 88.82 91.74 0.19 0.25 0.14 0.32 0.35 0.18
C1orf141 ENST00000371007 89.00 67.24 81.47 0.19 0.54 0.35 0.32 1.22 0.48
CBWD5 ENST00000377395 89.01 92.73 93.63 0.19 0.29 0.13 0.32 0.30 0.15
DNAAF3 ENST00000527223 89.01 58.91 77.12 0.19 0.53 0.37 0.32 1.42 0.59
CCDC154 ENST00000389176 89.02 59.12 77.23 0.19 0.49 0.35 0.32 1.44 0.59
IFI6 ENST00000339145 89.02 84.57 89.88 0.19 0.29 0.18 0.32 0.42 0.23
A1BG ENST00000263100 89.03 64.30 79.99 0.19 0.49 0.35 0.32 1.20 0.52
TEX13A ENST00000413579 89.03 79.49 87.41 0.19 0.38 0.28 0.32 0.66 0.31
CCDC57 ENST00000392343 89.04 54.72 74.79 0.19 0.58 0.39 0.32 1.64 0.66
ZNF724P ENST00000418100 89.04 69.43 82.66 0.19 0.54 0.32 0.32 1.13 0.43
ASMTL ENST00000381317 89.05 53.15 73.88 0.19 0.66 0.42 0.32 1.76 0.71
KRTAP9-4 ENST00000334109 89.06 99.98 97.03 0.19 0.18 0.08 0.32 0.09 0.07
TACC3 ENST00000313288 89.06 36.76 64.18 0.19 0.76 0.51 0.32 1.65 1.36
OR2L3 ENST00000359959 89.07 99.12 96.94 0.19 0.15 0.08 0.32 0.14 0.07
HIST1H1T ENST00000338379 89.07 98.93 96.33 0.19 0.17 0.07 0.32 0.15 0.09
MAGEB17 ENST00000400004 89.08 99.95 97.22 0.19 0.18 0.08 0.32 0.09 0.06
RP11-467N20.5 ENST00000558241 89.08 97.19 95.87 0.19 0.24 0.07 0.32 0.19 0.11
RSPH10B ENST00000405415 89.09 44.39 68.76 0.19 0.61 0.46 0.32 1.97 1.06
SLC16A8 ENST00000320521 89.09 70.84 83.33 0.19 0.49 0.32 0.32 1.07 0.40
C11orf35 ENST00000329451 89.10 86.69 90.92 0.19 0.24 0.15 0.32 0.40 0.20

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