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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
OR5A2 ENST00000302040 88.95 97.84 96.17 0.19 0.21 0.07 0.32 0.17 0.10
OCLM ENST00000574641 88.06 98.29 96.18 0.20 0.21 0.07 0.35 0.15 0.10
RP11-625H11.1 ENST00000558940 95.81 91.10 96.18 0.11 0.25 0.07 0.11 0.35 0.10
FAM163B ENST00000496132 94.03 93.64 96.19 0.10 0.28 0.07 0.13 0.28 0.10
PSG9 ENST00000270077 95.13 91.80 96.19 0.10 0.23 0.07 0.12 0.32 0.10
HEPN1 ENST00000408930 87.35 99.51 96.20 0.23 0.16 0.07 0.38 0.13 0.10
KRTAP15-1 ENST00000334067 87.61 99.99 96.20 0.23 0.18 0.07 0.37 0.09 0.10
RP11-272B17.2 ENST00000548613 89.90 96.94 96.21 0.18 0.24 0.07 0.28 0.19 0.10
NBPF20 ENST00000369202 89.59 97.39 96.21 0.16 0.22 0.07 0.30 0.19 0.10
SMIM22 ENST00000589327 93.58 95.79 96.22 0.13 0.22 0.07 0.14 0.20 0.09
AC003101.1 ENST00000412403 94.43 92.54 96.22 0.10 0.29 0.07 0.11 0.31 0.09
FRG2 ENST00000378763 97.97 89.01 96.23 0.11 0.27 0.07 0.11 0.35 0.09
TGIF2LX ENST00000561129 88.97 97.92 96.23 0.19 0.20 0.07 0.32 0.17 0.09
TSPY8 ENST00000330628 93.23 93.51 96.24 0.15 0.28 0.07 0.15 0.28 0.09
TBC1D28 ENST00000345096 97.24 89.78 96.25 0.10 0.27 0.07 0.11 0.37 0.09
CST11 ENST00000377009 96.47 90.57 96.25 0.10 0.25 0.07 0.11 0.37 0.09
HIST1H4K ENST00000357549 89.85 97.09 96.26 0.16 0.24 0.07 0.28 0.19 0.09
GOLGA8H ENST00000566740 91.88 97.36 96.26 0.14 0.22 0.07 0.20 0.19 0.09
RBMXL3 ENST00000424776 88.54 98.31 96.27 0.20 0.21 0.07 0.34 0.14 0.09
ZNF80 ENST00000482457 88.74 99.35 96.27 0.19 0.16 0.07 0.33 0.12 0.09
OR5H6 ENST00000383696 94.81 92.26 96.28 0.10 0.25 0.07 0.11 0.30 0.09
AC106876.2 ENST00000409905 99.77 87.30 96.28 0.12 0.22 0.07 0.13 0.41 0.09
SPANXN3 ENST00000370503 99.77 87.33 96.29 0.12 0.22 0.07 0.13 0.41 0.09
CRCT1 ENST00000368790 90.11 96.80 96.29 0.16 0.23 0.07 0.25 0.19 0.09
OR2M5 ENST00000366476 88.81 98.18 96.30 0.19 0.20 0.07 0.33 0.16 0.09

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