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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
CTD-2144E22.5 ENST00000319817 90.65 98.05 98.13 0.16 0.20 0.09 0.24 0.16 0.05
FABP5 ENST00000297258 90.66 61.71 79.62 0.16 0.57 0.38 0.24 1.38 0.53
EBF4 ENST00000380648 90.66 34.23 63.91 0.16 0.84 0.51 0.24 1.56 1.38
CTD-2547L24.3 ENST00000554096 90.67 92.81 94.65 0.16 0.29 0.09 0.24 0.30 0.11
AL031666.2 ENST00000599904 90.67 84.75 91.22 0.16 0.27 0.15 0.24 0.42 0.18
KM-PA-2 ENST00000377412 90.68 76.93 87.16 0.16 0.43 0.28 0.24 0.79 0.30
FAM27E2 ENST00000377529 90.68 98.06 97.31 0.16 0.20 0.08 0.24 0.16 0.07
PRR18 ENST00000322583 90.69 80.93 89.13 0.16 0.35 0.19 0.24 0.57 0.26
SPACA5 ENST00000304355 90.69 87.69 92.08 0.16 0.24 0.14 0.24 0.36 0.16
C21orf37 ENST00000440664 90.70 90.99 93.52 0.16 0.25 0.13 0.24 0.35 0.15
ZNF705D ENST00000400085 90.70 98.06 97.77 0.16 0.20 0.09 0.24 0.16 0.04
ANKRD63 ENST00000434396 90.71 58.86 78.23 0.16 0.54 0.37 0.24 1.41 0.55
AC112721.1 ENST00000409162 90.71 98.07 97.05 0.16 0.20 0.08 0.23 0.16 0.07
NRGN ENST00000284292 90.72 78.27 87.80 0.16 0.43 0.24 0.23 0.74 0.32
TPGS1 ENST00000359315 90.72 82.80 90.03 0.16 0.32 0.18 0.23 0.50 0.22
RP11-159G9.5 ENST00000473136 90.73 6.87 47.84 0.16 2.62 0.63 0.23 0.37 1.89
GPR42 ENST00000454971 90.73 86.32 91.57 0.16 0.25 0.15 0.23 0.43 0.18
RPS4Y1 ENST00000250784 90.74 51.27 75.32 0.16 0.65 0.37 0.23 1.90 0.65
CYP4F31P ENST00000416266 90.74 76.61 87.08 0.16 0.42 0.28 0.23 0.83 0.30
AC105020.1 ENST00000435356 90.75 98.10 96.93 0.16 0.20 0.08 0.23 0.16 0.07
PET100 ENST00000594797 90.75 91.06 93.88 0.16 0.25 0.09 0.23 0.36 0.11
TRNP1 ENST00000522111 90.76 89.20 94.38 0.16 0.27 0.10 0.23 0.36 0.12
DNAH17-AS1 ENST00000598378 90.76 94.43 95.56 0.16 0.23 0.08 0.23 0.24 0.11
TBC1D3B ENST00000454519 90.77 79.61 88.52 0.16 0.38 0.22 0.22 0.66 0.28
AP001652.1 ENST00000454512 90.78 78.82 88.17 0.16 0.42 0.23 0.22 0.71 0.30

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