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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
PTPRB ENST00000334414 30.61 12.81 19.76 0.97 2.09 1.51 1.63 0.59 0.85
LCA5 ENST00000392959 30.61 34.17 30.65 0.97 0.84 0.80 1.63 1.55 1.47
DAB2IP ENST00000259371 30.62 6.21 16.22 0.97 2.73 1.71 1.63 0.36 0.65
FOXJ2 ENST00000162391 30.62 9.66 18.08 0.96 2.45 1.68 1.63 0.50 0.78
CRTC1 ENST00000338797 30.63 21.03 23.86 0.96 1.44 1.09 1.63 0.82 1.04
ZBED4 ENST00000216268 30.63 18.60 22.77 0.96 1.48 1.19 1.63 0.75 0.98
SELRC1 ENST00000371538 30.64 56.08 41.59 0.96 0.51 0.73 1.63 1.56 2.00
CHMP2B ENST00000263780 30.64 66.27 47.22 0.96 0.54 0.67 1.63 1.20 1.89
RBM45 ENST00000286070 30.65 56.44 41.76 0.96 0.52 0.72 1.63 1.54 2.01
SLC4A1 ENST00000262418 30.65 15.92 21.41 0.96 1.89 1.33 1.63 0.68 0.91
AP2A2 ENST00000448903 30.66 1.53 13.74 0.96 3.89 2.06 1.63 0.26 0.57
CAV1 ENST00000341049 30.66 74.77 51.89 0.96 0.54 0.62 1.63 0.96 1.94
TRAK1 ENST00000327628 30.67 27.67 27.32 0.96 1.27 0.97 1.63 1.18 1.24
HIVEP3 ENST00000372583 30.68 13.48 20.18 0.96 2.05 1.48 1.63 0.61 0.87
LRRK1 ENST00000388948 30.68 23.28 25.01 0.96 1.43 1.04 1.63 0.93 1.15
LIX1L ENST00000369308 30.69 54.06 40.56 0.96 0.65 0.80 1.63 1.69 2.04
RNMT ENST00000383314 30.69 37.31 32.21 0.96 0.76 0.91 1.63 1.66 1.60
NEDD1 ENST00000557644 30.70 19.55 23.21 0.96 1.43 1.19 1.63 0.74 1.02
TNFSF13 ENST00000338784 30.70 22.32 24.59 0.96 1.52 1.06 1.63 0.82 1.10
COL4A3 ENST00000396578 30.71 25.37 26.20 0.96 1.27 0.99 1.63 1.03 1.25
HADH ENST00000603302 30.71 53.41 40.33 0.96 0.65 0.80 1.63 1.70 2.00
CDK5RAP3 ENST00000338399 30.72 58.27 42.81 0.96 0.54 0.70 1.63 1.44 2.01
TP73 ENST00000378295 30.72 9.30 17.93 0.96 2.48 1.68 1.63 0.47 0.76
ARHGEF10L ENST00000361221 30.73 21.83 24.31 0.96 1.47 1.09 1.63 0.81 1.07
GALNT18 ENST00000227756 30.73 34.18 30.71 0.96 0.84 0.78 1.63 1.55 1.48

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