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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
C7orf65 ENST00000408988 95.43 91.92 96.44 0.11 0.23 0.07 0.11 0.32 0.09
CST9L ENST00000376979 95.43 97.33 98.57 0.11 0.23 0.10 0.11 0.19 0.05
IFNA7 ENST00000239347 95.44 99.36 98.85 0.11 0.16 0.10 0.11 0.12 0.05
RP11-422N16.3 ENST00000499579 95.44 84.41 92.67 0.11 0.29 0.14 0.11 0.44 0.15
C1orf110 ENST00000367910 95.45 81.73 91.47 0.11 0.33 0.15 0.11 0.52 0.18
NLRP2 ENST00000543010 95.45 78.52 90.08 0.11 0.42 0.18 0.11 0.74 0.22
C9orf163 ENST00000354376 95.46 99.35 98.68 0.11 0.16 0.10 0.11 0.12 0.05
NOXO1 ENST00000397280 95.47 83.56 92.18 0.11 0.27 0.14 0.11 0.47 0.16
RP1L1 ENST00000382483 95.47 97.13 98.51 0.11 0.24 0.10 0.11 0.18 0.05
AL590708.2 ENST00000443493 95.48 88.14 94.53 0.11 0.24 0.10 0.11 0.38 0.12
H2AFB1 ENST00000354461 95.48 98.30 98.97 0.11 0.21 0.10 0.11 0.14 0.04
FXYD5 ENST00000342879 95.49 59.83 81.00 0.11 0.52 0.39 0.11 1.37 0.50
SIGLEC6 ENST00000425629 95.49 37.72 68.60 0.11 0.78 0.47 0.11 1.70 1.05
SPATA31A6 ENST00000332857 95.50 95.07 97.84 0.11 0.23 0.09 0.11 0.21 0.04
LINC00346 ENST00000538077 95.50 98.46 99.04 0.11 0.21 0.11 0.11 0.14 0.04
OXCT2 ENST00000327582 95.51 96.98 98.48 0.11 0.24 0.10 0.11 0.19 0.05
TFF1 ENST00000291527 95.51 94.39 97.56 0.11 0.23 0.09 0.11 0.24 0.06
HOPX ENST00000554144 95.52 94.93 97.78 0.11 0.23 0.09 0.11 0.23 0.04
MISP ENST00000215582 95.52 69.15 85.65 0.11 0.56 0.32 0.11 1.12 0.34
OR1N1 ENST00000304880 95.53 99.22 99.22 0.11 0.15 0.11 0.11 0.13 0.04
KLK1 ENST00000301420 95.53 75.66 88.74 0.11 0.44 0.20 0.11 0.90 0.28
SERPINA3 ENST00000467132 95.54 94.45 97.59 0.11 0.23 0.09 0.11 0.24 0.06
IFNA13 ENST00000449498 95.54 98.79 99.11 0.11 0.16 0.11 0.11 0.14 0.04
C22orf29 ENST00000405640 95.55 99.32 99.25 0.11 0.16 0.11 0.11 0.12 0.04
LRRC56 ENST00000270115 95.55 69.66 85.89 0.11 0.53 0.33 0.11 1.12 0.33

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