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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
MAGI1 ENST00000402939 18.86 14.47 14.40 1.57 2.04 2.01 0.93 0.61 0.59
DPAGT1 ENST00000409993 18.86 58.53 36.92 1.57 0.54 0.80 0.93 1.40 1.94
DNAJC6 ENST00000371069 18.87 5.81 9.87 1.57 2.85 2.30 0.93 0.35 0.41
MYH2 ENST00000245503 18.87 35.34 25.17 1.57 0.77 1.05 0.93 1.57 1.17
SCYL2 ENST00000360820 18.88 19.80 17.18 1.57 1.42 1.64 0.94 0.74 0.73
DYRK2 ENST00000344096 18.88 3.99 8.81 1.57 3.27 2.49 0.94 0.32 0.38
MLF2 ENST00000203630 18.89 21.67 18.24 1.57 1.46 1.64 0.94 0.81 0.79
BEST4 ENST00000372207 18.89 45.67 30.50 1.57 0.75 0.80 0.94 2.01 1.46
SPTBN2 ENST00000533211 18.90 16.47 15.50 1.57 1.78 1.81 0.94 0.69 0.67
TOMM40 ENST00000426677 18.90 6.36 10.19 1.57 2.67 2.21 0.94 0.37 0.42
VDR ENST00000550325 18.91 46.22 30.84 1.57 0.73 0.78 0.94 2.04 1.49
PPM1L ENST00000498165 18.91 28.41 21.79 1.57 1.16 1.24 0.94 1.24 0.94
ADAP1 ENST00000265846 18.92 20.90 17.80 1.57 1.43 1.66 0.94 0.84 0.78
PCBP4 ENST00000461554 18.92 38.30 26.77 1.57 0.75 0.97 0.94 1.72 1.27
ZSWIM6 ENST00000252744 18.93 0.37 7.00 1.58 4.13 2.88 0.94 0.28 0.33
NLRP3 ENST00000336119 18.93 26.65 20.93 1.58 1.19 1.43 0.94 1.12 0.87
ALYREF ENST00000505490 18.94 15.97 15.21 1.58 1.86 1.83 0.95 0.68 0.64
B3GALT2 ENST00000367434 18.95 17.60 16.08 1.58 1.57 1.70 0.95 0.73 0.66
INSR ENST00000302850 18.95 22.75 18.85 1.58 1.46 1.56 0.95 0.88 0.83
HVCN1 ENST00000356742 18.96 26.77 20.96 1.58 1.21 1.43 0.95 1.12 0.88
SH3GL2 ENST00000380607 18.96 41.15 28.24 1.58 0.59 0.81 0.95 1.83 1.29
GATM ENST00000396659 18.97 27.08 21.15 1.58 1.23 1.40 0.95 1.12 0.90
USP24 ENST00000294383 18.97 2.66 8.18 1.58 3.54 2.59 0.95 0.29 0.37
ADD1 ENST00000264758 18.98 11.79 12.93 1.58 2.09 2.10 0.95 0.57 0.53
MIOS ENST00000340080 18.98 37.65 26.41 1.58 0.78 1.01 0.95 1.70 1.26

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