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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
NPAS2 ENST00000335681 8.79 2.45 3.05 2.42 3.59 3.95 0.45 0.29 0.24
ARRB2 ENST00000412477 8.79 22.58 13.31 2.42 1.47 2.05 0.45 0.85 0.54
DNAJC7 ENST00000457167 8.80 12.06 7.77 2.42 2.06 2.66 0.45 0.57 0.33
FGFR1 ENST00000425967 8.80 7.48 5.47 2.42 2.54 3.43 0.45 0.40 0.26
ZNF521 ENST00000361524 8.81 1.04 2.52 2.42 4.06 4.01 0.45 0.28 0.24
PDE4B ENST00000329654 8.81 18.91 11.52 2.42 1.52 2.20 0.45 0.76 0.45
MYH10 ENST00000360416 8.82 2.91 3.31 2.40 3.49 3.90 0.45 0.29 0.24
ADAMTS6 ENST00000381055 8.82 5.89 4.70 2.40 2.82 3.68 0.45 0.35 0.25
GLUD1 ENST00000277865 8.83 31.48 18.12 2.40 0.96 1.67 0.45 1.43 0.78
DNAJB5 ENST00000453597 8.83 34.11 19.48 2.40 0.84 1.53 0.45 1.53 0.84
MED31 ENST00000225728 8.84 69.70 37.52 2.40 0.53 0.84 0.45 1.12 2.01
DNAJC8 ENST00000263697 8.84 30.62 17.60 2.40 1.06 1.64 0.45 1.39 0.77
HNF4A ENST00000316099 8.85 25.18 14.78 2.39 1.32 1.96 0.45 1.02 0.62
PPARG ENST00000287820 8.85 28.69 16.61 2.38 1.16 1.72 0.45 1.29 0.70
PPIG ENST00000260970 8.86 13.66 8.59 2.38 2.05 2.53 0.45 0.59 0.36
HBP1 ENST00000222574 8.86 27.71 16.09 2.38 1.27 1.70 0.45 1.18 0.66
RPS27 ENST00000368567 8.87 32.54 18.72 2.38 0.86 1.57 0.45 1.49 0.81
FAM120A ENST00000277165 8.87 2.36 3.04 2.38 3.63 3.95 0.45 0.29 0.24
MAST3 ENST00000262811 8.88 7.32 5.42 2.38 2.54 3.47 0.45 0.37 0.26
THAP1 ENST00000254250 8.88 23.49 13.87 2.38 1.42 2.10 0.45 0.92 0.59
YTHDF2 ENST00000373812 8.89 2.65 3.19 2.38 3.54 3.89 0.45 0.29 0.24
CDK7 ENST00000256443 8.89 52.32 28.73 2.37 0.62 0.80 0.45 1.82 1.34
NR3C2 ENST00000358102 8.90 15.82 9.92 2.37 1.89 2.29 0.45 0.68 0.41
KMT2C ENST00000262189 8.90 1.63 2.73 2.35 3.86 4.01 0.45 0.26 0.23
NOS1AP ENST00000361897 8.91 20.09 12.07 2.35 1.43 2.29 0.45 0.74 0.48

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