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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
HES7 ENST00000541682 33.45 26.95 28.39 0.92 1.23 0.78 1.70 1.12 1.29
RPL32 ENST00000429711 33.45 34.09 31.98 0.92 0.84 0.90 1.70 1.53 1.59
SNAPIN ENST00000368685 33.46 77.20 54.89 0.92 0.43 0.51 1.70 0.78 1.75
KY ENST00000423778 33.46 47.52 38.76 0.92 0.62 0.82 1.70 2.02 2.02
FBXO10 ENST00000432825 33.47 34.37 32.12 0.92 0.82 0.89 1.70 1.56 1.60
TSHZ1 ENST00000322038 33.47 8.17 18.83 0.91 2.57 1.56 1.70 0.44 0.83
ZFYVE26 ENST00000347230 33.48 30.84 30.37 0.91 1.08 0.81 1.70 1.36 1.45
DIO3 ENST00000510508 33.48 35.57 32.72 0.91 0.77 0.86 1.70 1.58 1.65
GPSM3 ENST00000375040 33.49 43.34 36.52 0.91 0.59 0.85 1.70 1.94 1.90
ALOX5AP ENST00000380490 33.50 50.77 40.38 0.91 0.63 0.80 1.70 1.94 2.01
IDH1 ENST00000415913 33.50 71.97 51.92 0.91 0.51 0.62 1.71 1.06 1.94
DMBX1 ENST00000360032 33.51 16.16 22.99 0.91 1.82 1.20 1.71 0.69 0.98
FAM163A ENST00000341785 33.51 65.00 48.13 0.91 0.49 0.66 1.71 1.24 1.87
DPP9 ENST00000262960 33.52 10.79 20.22 0.91 2.11 1.48 1.71 0.51 0.88
B3GALT4 ENST00000451237 33.52 38.01 33.93 0.92 0.77 0.90 1.71 1.71 1.73
ATP5O ENST00000290299 33.53 40.18 35.03 0.92 0.61 0.87 1.71 1.72 1.74
MKL2 ENST00000318282 33.53 4.30 16.78 0.92 3.25 1.70 1.71 0.32 0.70
STK3 ENST00000523601 33.54 48.19 39.22 0.92 0.63 0.78 1.70 1.99 2.05
DUSP16 ENST00000228862 33.54 26.70 28.27 0.92 1.19 0.80 1.70 1.11 1.29
LAMA4 ENST00000230538 33.55 37.82 33.85 0.92 0.80 0.89 1.71 1.70 1.73
SERTAD2 ENST00000313349 33.55 20.08 24.84 0.94 1.44 1.02 1.71 0.74 1.10
TCEAL1 ENST00000372625 33.56 58.27 44.41 0.94 0.54 0.61 1.71 1.43 2.04
MCM8 ENST00000378896 33.56 51.45 40.64 0.95 0.63 0.81 1.70 1.89 2.05
TATDN3 ENST00000532324 33.57 64.97 48.16 0.95 0.49 0.66 1.70 1.24 1.87
SLC27A4 ENST00000300456 33.57 37.46 33.70 0.95 0.77 0.90 1.70 1.66 1.73

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