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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
DCX ENST00000338081 6.46 30.78 16.43 3.05 1.06 1.71 0.37 1.37 0.69
EGR2 ENST00000242480 6.47 29.67 15.90 3.05 1.10 1.76 0.37 1.39 0.66
PPP1CA ENST00000312989 6.47 11.45 6.23 3.05 2.10 3.15 0.37 0.56 0.32
MTF1 ENST00000373036 6.48 13.78 7.49 3.04 2.06 2.77 0.37 0.60 0.33
ACTN4 ENST00000252699 6.48 1.05 1.66 3.04 4.06 4.26 0.37 0.28 0.23
MGAT3 ENST00000341184 6.49 32.77 17.49 3.04 0.84 1.62 0.37 1.44 0.75
C16orf72 ENST00000327827 6.49 11.49 6.29 3.04 2.11 3.14 0.37 0.57 0.32
RIC8B ENST00000392839 6.50 6.33 3.76 3.04 2.69 3.79 0.37 0.37 0.24
SOCS3 ENST00000330871 6.50 34.75 18.58 3.04 0.77 1.59 0.37 1.54 0.81
ATRX ENST00000373344 6.51 0.80 1.62 3.02 4.10 4.29 0.37 0.27 0.23
ZBTB17 ENST00000375743 6.51 12.49 6.90 3.02 2.07 2.90 0.37 0.59 0.33
UBR7 ENST00000013070 6.52 21.58 11.68 3.02 1.44 2.23 0.37 0.81 0.47
PBRM1 ENST00000394830 6.52 2.22 2.11 3.02 3.67 4.10 0.37 0.30 0.23
LPAR1 ENST00000374431 6.53 36.98 19.81 3.04 0.76 1.49 0.37 1.69 0.85
TBCEL ENST00000422003 6.53 13.02 7.13 3.04 2.07 2.87 0.37 0.59 0.33
EMX1 ENST00000258106 6.54 19.06 10.36 3.02 1.52 2.19 0.37 0.76 0.43
UBC ENST00000536769 6.54 31.25 16.74 3.01 1.00 1.68 0.37 1.37 0.70
NUCKS1 ENST00000367142 6.55 12.86 7.05 3.01 2.07 2.88 0.37 0.59 0.33
PTPLB ENST00000383657 6.55 40.34 21.59 3.00 0.61 1.28 0.37 1.74 0.92
IPO7 ENST00000379719 6.56 1.28 1.78 3.00 3.97 4.24 0.37 0.27 0.23
DEF6 ENST00000316637 6.56 9.19 5.15 3.00 2.48 3.59 0.37 0.46 0.25
GLYR1 ENST00000321919 6.57 5.80 3.60 3.00 2.86 3.84 0.37 0.35 0.23
GTF2B ENST00000370500 6.58 51.85 27.34 2.99 0.59 0.97 0.37 1.87 1.25
EDNRA ENST00000324300 6.58 9.41 5.25 2.99 2.49 3.56 0.37 0.49 0.26
RFX4 ENST00000357881 6.59 2.85 2.41 2.99 3.51 4.03 0.37 0.28 0.23

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