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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
IL31 ENST00000377035 99.86 85.94 95.66 0.12 0.28 0.07 0.13 0.43 0.11
MAGEB5 ENST00000602297 87.89 98.51 95.66 0.23 0.21 0.07 0.36 0.15 0.11
PRAMEF19 ENST00000540591 89.50 96.28 95.67 0.16 0.22 0.07 0.30 0.19 0.11
OR2M7 ENST00000317965 86.90 98.70 95.67 0.24 0.18 0.07 0.39 0.15 0.11
KRTAP22-1 ENST00000334680 87.90 97.83 95.68 0.23 0.21 0.07 0.36 0.17 0.11
ZNF705B ENST00000443676 91.79 91.68 95.68 0.14 0.24 0.07 0.20 0.32 0.11
ZNF443 ENST00000301547 96.64 89.24 95.69 0.11 0.27 0.07 0.11 0.36 0.11
C5orf27 ENST00000357880 90.61 94.89 95.69 0.16 0.23 0.07 0.24 0.23 0.11
SSX7 ENST00000298181 96.21 89.65 95.70 0.12 0.27 0.07 0.11 0.36 0.11
ZNF860 ENST00000360311 86.91 99.73 95.70 0.24 0.17 0.07 0.39 0.11 0.11
OR7D2 ENST00000344248 86.95 98.70 95.71 0.24 0.18 0.07 0.39 0.15 0.11
DEFB1 ENST00000297439 96.68 89.19 95.71 0.11 0.27 0.07 0.11 0.36 0.11
SLC35G5 ENST00000382435 88.20 97.64 95.72 0.20 0.21 0.07 0.34 0.19 0.11
POLR2J2 ENST00000591000 89.98 95.73 95.72 0.18 0.23 0.07 0.27 0.20 0.11
CDRT15 ENST00000420162 94.75 91.15 95.73 0.10 0.24 0.07 0.11 0.35 0.11
KHDC1 ENST00000370384 96.67 89.22 95.73 0.11 0.27 0.07 0.11 0.36 0.11
CLC ENST00000221804 96.72 89.21 95.74 0.11 0.27 0.07 0.11 0.36 0.11
C11orf24 ENST00000304271 98.21 87.71 95.74 0.11 0.24 0.07 0.11 0.37 0.11
CCL3L3 ENST00000378354 92.09 92.51 95.75 0.15 0.29 0.07 0.20 0.30 0.11
RP11-322E11.6 ENST00000589258 92.10 93.40 95.75 0.15 0.28 0.07 0.19 0.28 0.11
ZNF479 ENST00000331162 96.61 89.34 95.76 0.11 0.27 0.07 0.11 0.37 0.11
C1QTNF8 ENST00000328449 88.65 97.31 95.76 0.19 0.23 0.07 0.34 0.19 0.11
RP11-1102P16.1 ENST00000523987 93.31 92.43 95.77 0.15 0.27 0.07 0.15 0.30 0.11
ZNF658 ENST00000602553 94.60 91.41 95.78 0.10 0.23 0.07 0.12 0.33 0.11
DEFB115 ENST00000400552 89.22 96.78 95.78 0.18 0.23 0.07 0.32 0.19 0.11

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