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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
DDR2 ENST00000367922 11.11 15.20 10.75 1.82 1.89 2.19 0.59 0.67 0.43
CLCN7 ENST00000382745 11.12 18.14 12.20 1.82 1.53 2.29 0.59 0.74 0.50
HDAC9 ENST00000441542 11.12 7.53 6.71 1.82 2.52 3.00 0.59 0.40 0.32
TRMT1L ENST00000367506 11.13 16.35 11.41 1.81 1.80 2.19 0.59 0.69 0.45
ARHGEF9 ENST00000253401 11.13 3.05 4.35 1.81 3.46 3.74 0.59 0.28 0.24
ADCY5 ENST00000462833 11.14 9.17 7.52 1.81 2.48 2.77 0.59 0.46 0.33
PPARD ENST00000311565 11.14 5.69 5.68 1.81 2.94 3.34 0.59 0.34 0.27
MIER3 ENST00000381213 11.15 7.32 6.59 1.81 2.56 3.00 0.59 0.37 0.32
ARHGAP5 ENST00000345122 11.15 9.92 7.89 1.81 2.33 2.61 0.59 0.50 0.35
EGLN1 ENST00000366641 11.16 12.10 9.01 1.81 2.06 2.44 0.59 0.57 0.38
MED27 ENST00000292035 11.16 56.46 32.02 1.81 0.52 0.90 0.59 1.54 1.59
LRRC41 ENST00000343304 11.17 4.74 5.21 1.81 3.27 3.57 0.59 0.32 0.26
NOTCH2 ENST00000256646 11.17 1.52 3.72 1.81 3.90 3.80 0.59 0.26 0.23
RBM27 ENST00000265271 11.18 6.26 5.97 1.80 2.72 3.26 0.59 0.36 0.30
WIBG ENST00000408946 11.18 53.80 30.76 1.80 0.63 0.78 0.59 1.70 1.49
SULT4A1 ENST00000330884 11.19 13.69 9.99 1.80 2.06 2.25 0.59 0.59 0.42
MAP1LC3A ENST00000374837 11.19 71.03 39.45 1.80 0.49 0.77 0.59 1.07 2.05
LRRC4B ENST00000599957 11.20 5.32 5.57 1.80 3.10 3.40 0.59 0.32 0.27
ZFYVE1 ENST00000556143 11.20 20.91 13.71 1.80 1.43 2.05 0.59 0.83 0.58
TRIM9 ENST00000298355 11.21 4.01 4.87 1.80 3.26 3.67 0.59 0.32 0.25
MMP24 ENST00000246186 11.21 17.40 11.88 1.80 1.59 2.25 0.59 0.74 0.46
KDM2B ENST00000377071 11.22 4.49 5.11 1.78 3.27 3.62 0.59 0.32 0.25
LUC7L2 ENST00000541515 11.22 32.74 20.03 1.78 0.84 1.49 0.59 1.44 0.85
C2orf66 ENST00000342506 11.23 91.17 50.22 1.78 0.24 0.65 0.59 0.35 1.90
SMOC1 ENST00000361956 11.23 29.72 18.43 1.78 1.11 1.62 0.59 1.39 0.81

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