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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
PGK1 ENST00000373316 35.65 22.31 27.14 0.96 1.52 0.99 1.90 0.82 1.25
KIFC1 ENST00000428849 35.66 30.82 31.47 0.96 1.08 0.86 1.90 1.37 1.56
PEX12 ENST00000225873 35.66 90.71 64.49 0.96 0.25 0.51 1.90 0.35 1.32
STK16 ENST00000409638 35.67 50.64 41.36 0.96 0.63 0.73 1.90 1.95 2.02
ARHGEF25 ENST00000333972 35.67 45.50 38.91 0.95 0.71 0.80 1.90 1.98 2.06
CLEC16A ENST00000409790 35.68 18.21 24.99 0.95 1.49 1.04 1.90 0.74 1.14
GMCL1 ENST00000282570 35.72 38.30 35.24 0.95 0.75 0.86 1.90 1.72 1.76
GPR124 ENST00000412232 35.73 30.19 31.16 0.95 1.09 0.85 1.90 1.41 1.54
NOP2 ENST00000382421 35.77 4.29 17.94 0.95 3.26 1.70 1.90 0.32 0.77
PRKAB1 ENST00000229328 35.77 45.83 39.18 0.95 0.73 0.78 1.90 2.02 2.06
WWTR1 ENST00000465804 35.78 15.52 23.74 0.95 1.87 1.14 1.90 0.67 1.02
MAMDC2 ENST00000377182 35.78 41.39 36.75 0.95 0.62 0.82 1.90 1.80 1.94
FUNDC2 ENST00000369498 35.79 54.60 43.56 0.95 0.59 0.62 1.90 1.66 2.01
NRG2 ENST00000361474 35.80 7.05 19.43 0.95 2.57 1.54 1.90 0.37 0.84
FUNDC1 ENST00000378045 35.44 52.88 42.43 0.97 0.65 0.68 1.89 1.80 2.01
PDLIM5 ENST00000514743 35.45 28.38 30.11 0.97 1.16 0.82 1.89 1.22 1.46
UBE2C ENST00000356455 35.45 49.23 40.55 0.97 0.66 0.80 1.89 2.02 2.04
G6PC2 ENST00000375363 35.46 89.04 63.41 0.97 0.27 0.49 1.89 0.35 1.37
TMEM120B ENST00000449592 35.49 25.44 28.63 0.96 1.25 0.80 1.89 1.05 1.34
NOC3L ENST00000371361 35.50 46.52 39.37 0.96 0.73 0.80 1.89 2.02 2.04
OPRK1 ENST00000265572 35.50 72.90 53.62 0.96 0.49 0.63 1.89 1.03 1.82
MEGF9 ENST00000373930 35.51 11.00 21.37 0.96 2.09 1.34 1.89 0.52 0.91
PARL ENST00000317096 35.53 40.25 35.99 0.97 0.61 0.87 1.89 1.73 1.78
MATN2 ENST00000520016 35.54 46.06 39.17 0.97 0.76 0.78 1.89 2.03 2.06
SPARC ENST00000231061 35.55 18.68 25.19 0.97 1.52 1.05 1.89 0.75 1.17

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