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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
PNN ENST00000216832 30.87 21.61 24.29 0.99 1.44 1.09 1.66 0.81 1.06
SGCE ENST00000445866 30.87 29.41 28.32 0.97 1.10 0.78 1.66 1.38 1.28
NGEF ENST00000264051 30.88 17.87 22.55 0.97 1.52 1.15 1.66 0.72 0.97
SPIRE1 ENST00000409402 30.88 19.75 23.41 0.97 1.43 1.19 1.66 0.74 1.01
GRM2 ENST00000395052 30.89 24.59 25.87 0.97 1.30 1.01 1.65 1.05 1.23
NMRK1 ENST00000361092 30.89 77.70 53.72 0.97 0.42 0.62 1.66 0.79 1.80
PDE6C ENST00000371447 30.90 47.72 37.55 0.97 0.61 0.84 1.66 1.99 2.01
DEGS1 ENST00000323699 30.90 41.10 34.28 0.97 0.59 0.87 1.66 1.82 1.75
SMEK2 ENST00000345102 30.91 17.10 22.14 0.97 1.62 1.16 1.66 0.75 0.97
GDPD5 ENST00000336898 30.91 31.26 29.24 0.97 1.00 0.84 1.66 1.38 1.34
TADA1 ENST00000367874 30.92 31.41 29.32 0.97 0.96 0.82 1.66 1.41 1.34
TRAIP ENST00000331456 30.92 39.47 33.38 0.97 0.70 0.87 1.66 1.63 1.72
CELSR2 ENST00000271332 30.93 9.59 18.21 0.97 2.49 1.66 1.66 0.50 0.79
TMED8 ENST00000216468 30.93 38.52 32.91 0.97 0.73 0.86 1.66 1.68 1.67
CIZ1 ENST00000393608 30.94 19.02 23.09 0.97 1.51 1.20 1.66 0.76 1.00
RAG2 ENST00000311485 30.94 45.16 36.18 0.97 0.70 0.87 1.66 1.98 1.82
ZFP28 ENST00000301318 30.95 28.77 28.04 0.97 1.15 0.82 1.66 1.29 1.28
ESCO1 ENST00000269214 30.95 4.33 15.45 0.97 3.27 1.81 1.66 0.32 0.67
UMPS ENST00000232607 30.96 50.92 39.32 0.97 0.63 0.80 1.66 1.94 2.04
ATP2B3 ENST00000263519 30.96 7.78 17.25 0.96 2.54 1.64 1.66 0.43 0.74
TDRD3 ENST00000535286 30.97 28.30 27.79 0.96 1.16 0.90 1.66 1.22 1.27
MICAL3 ENST00000441493 30.97 8.48 17.60 0.96 2.52 1.63 1.67 0.46 0.77
ZSCAN21 ENST00000292450 30.98 77.46 53.64 0.96 0.42 0.63 1.67 0.76 1.80
ORC5 ENST00000297431 30.98 46.30 36.87 0.96 0.73 0.81 1.67 2.05 1.94
SOX18 ENST00000340356 30.99 58.60 43.15 0.96 0.54 0.65 1.68 1.42 2.00

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