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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
FOXD4L3 ENST00000342833 86.52 81.74 87.33 0.25 0.33 0.28 0.41 0.52 0.31
TLDC1 ENST00000343629 86.52 93.59 92.81 0.25 0.28 0.14 0.41 0.28 0.15
GGACT ENST00000376250 86.53 94.79 93.39 0.25 0.23 0.11 0.41 0.24 0.15
IL5RA ENST00000446632 86.53 59.65 76.14 0.25 0.52 0.37 0.41 1.40 0.62
OR5D16 ENST00000378396 86.54 98.27 95.25 0.25 0.21 0.08 0.41 0.15 0.10
VPREB1 ENST00000403807 86.55 93.05 92.54 0.25 0.28 0.14 0.41 0.30 0.15
C4orf26 ENST00000435974 86.55 87.16 89.93 0.25 0.20 0.18 0.41 0.41 0.23
SLC16A11 ENST00000308009 86.56 74.17 83.76 0.24 0.53 0.34 0.41 1.03 0.41
C6orf141 ENST00000529246 86.56 98.67 95.49 0.24 0.20 0.08 0.41 0.15 0.11
ZC3HAV1 ENST00000242351 86.57 30.54 58.64 0.24 1.09 0.52 0.41 1.38 1.65
TNFRSF13B ENST00000261652 86.57 97.01 94.51 0.24 0.24 0.10 0.41 0.19 0.12
ZAR1L ENST00000533490 86.58 36.06 62.08 0.24 0.81 0.48 0.41 1.59 1.45
CXCL2 ENST00000508487 86.58 96.47 94.26 0.24 0.22 0.10 0.41 0.19 0.12
BOK ENST00000318407 86.59 56.93 74.66 0.24 0.56 0.40 0.41 1.53 0.68
HBQ1 ENST00000199708 86.59 94.78 93.42 0.24 0.23 0.11 0.41 0.24 0.15
ISX ENST00000308700 86.60 86.14 89.49 0.24 0.27 0.18 0.41 0.42 0.23
ACTL10 ENST00000330271 86.60 75.42 84.33 0.24 0.46 0.33 0.41 0.90 0.41
CCDC78 ENST00000293889 86.61 87.97 90.33 0.24 0.25 0.15 0.41 0.37 0.21
LSP1 ENST00000381775 86.61 48.18 69.60 0.24 0.63 0.44 0.41 1.97 0.95
FGFBP3 ENST00000311575 86.62 94.18 93.18 0.24 0.25 0.14 0.41 0.25 0.15
FIGLA ENST00000332372 86.62 73.85 83.63 0.24 0.53 0.33 0.41 1.03 0.40
SOX15 ENST00000250055 86.63 50.37 70.85 0.24 0.66 0.43 0.41 1.95 0.86
AMY2A ENST00000414303 86.63 84.08 88.49 0.24 0.27 0.22 0.41 0.45 0.29
CST8 ENST00000246012 86.64 82.93 87.92 0.24 0.30 0.24 0.41 0.49 0.32
COX19 ENST00000344111 86.64 86.88 89.86 0.24 0.22 0.18 0.41 0.41 0.23

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