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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
SMARCE1 ENST00000348513 0.28 5.40 1.06 4.46 3.06 4.43 0.17 0.33 0.21
CSK ENST00000220003 2.22 3.78 1.17 4.17 3.32 4.43 0.28 0.31 0.21
SPTBN1 ENST00000356805 5.57 0.51 1.20 3.23 4.16 4.43 0.33 0.27 0.21
MAU2 ENST00000392313 3.87 1.77 1.05 3.77 3.81 4.43 0.30 0.26 0.21
SHOC2 ENST00000369452 3.53 2.48 1.17 3.83 3.57 4.43 0.30 0.29 0.20
DNMT1 ENST00000359526 4.46 1.61 1.19 3.71 3.87 4.44 0.29 0.26 0.21
YY1 ENST00000262238 0.16 5.49 1.05 4.54 3.04 4.44 0.16 0.33 0.21
DCAF5 ENST00000341516 5.29 0.70 1.16 3.40 4.08 4.44 0.32 0.28 0.20
KPNA4 ENST00000334256 2.74 3.32 1.19 4.01 3.42 4.44 0.29 0.27 0.21
PAFAH1B1 ENST00000397195 4.19 1.44 1.04 3.70 3.93 4.44 0.30 0.26 0.21
RRM1 ENST00000300738 5.05 0.32 0.98 3.52 4.14 4.44 0.30 0.28 0.21
STAG2 ENST00000218089 4.70 0.90 1.04 3.63 4.07 4.44 0.31 0.29 0.21
DLG3 ENST00000374360 4.55 0.82 0.98 3.68 4.09 4.45 0.29 0.28 0.21
OTUD5 ENST00000156084 1.22 4.37 1.03 4.40 3.27 4.45 0.17 0.32 0.21
NAA25 ENST00000261745 3.91 1.42 0.95 3.79 3.94 4.45 0.30 0.27 0.21
DHX30 ENST00000445061 3.47 1.93 1.00 3.83 3.74 4.45 0.30 0.25 0.21
MEIS2 ENST00000561208 0.38 5.06 0.97 4.40 3.21 4.45 0.16 0.32 0.21
BTK ENST00000308731 4.40 1.15 1.03 3.72 3.99 4.45 0.30 0.28 0.21
USP47 ENST00000339865 3.19 2.11 0.94 3.88 3.68 4.45 0.30 0.28 0.21
RORB ENST00000376896 3.92 1.49 1.00 3.81 3.90 4.45 0.30 0.26 0.21
PPP3CA ENST00000394854 2.08 3.30 0.97 4.22 3.43 4.46 0.24 0.27 0.21
RLF ENST00000372771 5.46 0.04 1.02 3.31 4.09 4.46 0.33 0.28 0.21
CPSF6 ENST00000435070 1.63 3.75 0.99 4.29 3.33 4.46 0.21 0.31 0.21
SNRNP200 ENST00000323853 4.59 0.68 0.93 3.67 4.10 4.46 0.30 0.28 0.21
MDM4 ENST00000367182 4.09 1.42 1.02 3.73 3.95 4.46 0.31 0.27 0.21

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