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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
NDUFB3 ENST00000237889 62.24 96.47 82.74 0.68 0.22 0.32 1.27 0.19 0.42
COX5B ENST00000258424 62.25 26.42 42.60 0.68 1.16 0.67 1.28 1.09 2.02
NSUN7 ENST00000381782 62.25 39.66 49.93 0.68 0.68 0.61 1.28 1.66 1.89
ALDH1L1 ENST00000273450 62.26 41.06 50.74 0.68 0.59 0.66 1.27 1.81 1.84
TICAM1 ENST00000248244 62.26 97.81 83.34 0.68 0.21 0.32 1.27 0.18 0.40
GJB3 ENST00000373366 62.27 73.16 69.92 0.68 0.53 0.46 1.27 1.02 0.92
NINJ1 ENST00000375446 62.27 65.38 65.31 0.68 0.52 0.53 1.27 1.25 1.32
OR2K2 ENST00000302681 62.28 80.74 74.40 0.68 0.37 0.40 1.27 0.57 0.70
FICD ENST00000552695 62.29 51.93 56.95 0.67 0.61 0.49 1.27 1.85 1.72
PROP1 ENST00000308304 62.29 47.90 54.68 0.67 0.59 0.56 1.27 1.98 1.73
SERPINF1 ENST00000254722 62.30 68.11 66.94 0.67 0.52 0.53 1.27 1.20 1.19
RPL36A ENST00000427805 62.30 50.35 56.01 0.67 0.66 0.49 1.27 1.97 1.77
ELAC2 ENST00000338034 62.31 56.72 59.95 0.67 0.53 0.49 1.27 1.56 1.63
ZNF626 ENST00000601440 62.31 50.48 56.12 0.67 0.65 0.49 1.27 1.95 1.77
PCOLCE ENST00000223061 62.32 47.05 54.22 0.67 0.68 0.59 1.27 1.99 1.75
MBD4 ENST00000249910 62.32 66.94 66.32 0.67 0.53 0.53 1.27 1.25 1.20
HLA-DRB1 ENST00000360004 62.33 65.38 65.40 0.68 0.52 0.53 1.27 1.25 1.32
DAP ENST00000230895 62.33 83.24 75.79 0.68 0.28 0.38 1.27 0.47 0.63
MATN3 ENST00000407540 62.34 69.55 67.84 0.68 0.53 0.51 1.27 1.11 1.11
ASB4 ENST00000325885 62.34 74.88 70.99 0.68 0.53 0.43 1.26 0.95 0.85
PPP1R1A ENST00000257905 62.35 55.49 59.09 0.67 0.57 0.49 1.26 1.61 1.68
CCDC69 ENST00000355417 62.35 68.29 67.06 0.67 0.52 0.52 1.26 1.20 1.16
AK8 ENST00000298545 62.36 66.12 65.85 0.67 0.53 0.51 1.26 1.20 1.25
KCNE2 ENST00000290310 62.36 95.79 82.48 0.67 0.22 0.33 1.27 0.20 0.44
MYZAP ENST00000267853 62.37 67.51 66.63 0.67 0.54 0.52 1.27 1.20 1.20

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