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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
OPN1SW ENST00000249389 55.92 41.81 47.62 0.57 0.61 0.65 1.64 1.80 1.88
HEXA ENST00000268097 55.92 54.41 54.76 0.57 0.62 0.56 1.64 1.66 1.74
SLC35B2 ENST00000393812 55.93 36.88 45.05 0.57 0.76 0.70 1.64 1.70 2.02
OXSM ENST00000280701 55.93 66.62 62.05 0.58 0.54 0.48 1.64 1.22 1.44
TCTE3 ENST00000366774 55.94 91.97 77.10 0.58 0.23 0.37 1.64 0.33 0.61
ANXA10 ENST00000359299 55.94 66.78 62.15 0.58 0.56 0.48 1.64 1.23 1.44
CCDC88C ENST00000389857 55.95 21.95 37.25 0.58 1.47 0.82 1.64 0.80 1.99
LAMA1 ENST00000389658 55.95 30.13 41.26 0.58 1.09 0.75 1.64 1.41 2.01
TTC30B ENST00000408939 55.96 65.85 61.62 0.58 0.54 0.46 1.63 1.23 1.48
BRCA1 ENST00000471181 55.96 49.20 51.72 0.58 0.66 0.62 1.63 2.03 1.94
WDR16 ENST00000352665 55.97 68.98 63.70 0.58 0.54 0.49 1.63 1.15 1.39
NDUFS4 ENST00000296684 55.97 65.84 61.65 0.58 0.54 0.46 1.63 1.22 1.47
FGD3 ENST00000375482 55.98 37.06 45.18 0.58 0.78 0.70 1.63 1.68 2.00
ACADSB ENST00000358776 55.98 63.89 60.42 0.58 0.48 0.44 1.63 1.22 1.58
TMEM159 ENST00000233047 55.99 84.06 72.73 0.58 0.27 0.43 1.63 0.45 0.81
ETV4 ENST00000319349 55.99 46.70 50.39 0.58 0.73 0.67 1.63 1.97 1.90
TRPM1 ENST00000542188 56.00 56.69 56.05 0.58 0.53 0.49 1.63 1.55 1.76
THEMIS ENST00000543064 56.00 46.99 50.52 0.58 0.70 0.67 1.63 1.96 1.85
USPL1 ENST00000255304 56.01 22.08 37.33 0.58 1.49 0.84 1.63 0.82 2.01
BIN3 ENST00000276416 56.01 82.58 71.89 0.58 0.34 0.43 1.63 0.51 0.82
GALNT6 ENST00000543196 56.02 49.41 51.87 0.58 0.65 0.62 1.63 2.01 1.93
FAM83G ENST00000388995 56.02 35.85 44.42 0.58 0.80 0.61 1.63 1.58 2.04
SPHK2 ENST00000245222 56.03 53.67 54.39 0.58 0.63 0.58 1.62 1.69 1.75
RAB11FIP5 ENST00000258098 56.04 38.49 45.96 0.58 0.73 0.70 1.62 1.68 1.97
FGF4 ENST00000168712 56.04 60.46 58.30 0.58 0.52 0.48 1.62 1.41 1.65

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