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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
FAM131B ENST00000443739 20.41 9.12 12.34 1.53 2.47 2.25 1.03 0.47 0.50
SSTR2 ENST00000357585 20.41 34.31 25.43 1.53 0.84 1.02 1.03 1.57 1.18
RFX6 ENST00000332958 20.42 22.88 19.67 1.53 1.47 1.53 1.03 0.90 0.85
C1orf95 ENST00000366788 20.42 81.01 49.67 1.53 0.35 0.66 1.03 0.55 1.84
CTC-349C3.1 ENST00000432382 20.43 87.45 53.33 1.53 0.23 0.62 1.03 0.40 1.86
MYH14 ENST00000601313 20.43 11.96 13.88 1.53 2.07 2.10 1.03 0.59 0.59
TMED7 ENST00000456936 20.44 32.44 24.48 1.53 0.86 1.08 1.03 1.48 1.08
DLX5 ENST00000222598 20.44 37.20 27.00 1.53 0.77 1.00 1.03 1.66 1.28
BRD3 ENST00000303407 20.45 13.39 14.68 1.53 2.05 1.96 1.03 0.59 0.61
CACNA2D2 ENST00000479441 20.45 7.69 11.69 1.53 2.52 2.21 1.03 0.42 0.47
EIF1AD ENST00000312234 20.46 69.20 43.21 1.53 0.56 0.65 1.03 1.13 1.99
RAB11FIP4 ENST00000325874 20.46 11.00 13.34 1.53 2.09 2.05 1.03 0.52 0.55
MEOX2 ENST00000262041 20.47 17.09 16.60 1.53 1.62 1.72 1.03 0.74 0.70
TTC39C ENST00000317571 20.47 30.14 23.41 1.53 1.09 1.19 1.03 1.40 1.00
HAT1 ENST00000264108 20.48 18.26 17.23 1.53 1.48 1.64 1.03 0.74 0.74
ZNF516 ENST00000443185 20.48 4.17 9.85 1.53 3.26 2.30 1.03 0.32 0.40
CCT3 ENST00000295688 20.49 1.07 8.15 1.53 4.05 2.59 1.02 0.28 0.37
TLX1 ENST00000370196 20.49 28.69 22.75 1.54 1.16 1.18 1.02 1.29 0.98
CUX2 ENST00000261726 20.50 1.98 8.58 1.54 3.73 2.53 1.02 0.28 0.36
DLD ENST00000205402 20.51 28.26 22.58 1.54 1.19 1.18 1.01 1.22 0.96
RASD2 ENST00000216127 20.51 40.67 28.72 1.54 0.63 0.80 1.01 1.77 1.34
CAMK1G ENST00000009105 20.52 36.11 26.40 1.54 0.81 1.01 1.01 1.59 1.25
WARS ENST00000355338 20.52 24.15 20.41 1.54 1.34 1.51 1.01 0.99 0.88
ACYP1 ENST00000238618 20.53 79.43 48.88 1.54 0.38 0.71 1.01 0.67 1.85
POLB ENST00000265421 20.53 43.15 30.01 1.54 0.62 0.82 1.01 1.90 1.45

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