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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
CFHR5 ENST00000256785 96.89 91.04 96.74 0.09 0.25 0.08 0.11 0.36 0.08
RP11-481A20.11 ENST00000527396 90.43 96.10 96.74 0.15 0.21 0.08 0.25 0.20 0.08
ZNF776 ENST00000317178 96.49 91.38 96.73 0.10 0.23 0.08 0.11 0.33 0.08
C10orf105 ENST00000441508 93.16 94.46 96.73 0.15 0.23 0.08 0.16 0.24 0.08
AP001885.1 ENST00000444002 93.36 99.53 96.72 0.15 0.16 0.08 0.15 0.13 0.08
PRLH ENST00000165524 94.80 93.04 96.72 0.10 0.28 0.08 0.11 0.30 0.08
C12orf74 ENST00000397833 94.78 93.06 96.71 0.10 0.28 0.08 0.11 0.30 0.08
LY6D ENST00000301263 94.71 93.15 96.70 0.10 0.28 0.08 0.11 0.30 0.08
SPINT3 ENST00000217428 93.78 95.65 96.70 0.11 0.23 0.08 0.13 0.20 0.08
AC138647.1 ENST00000427937 91.49 95.90 96.69 0.15 0.22 0.08 0.20 0.20 0.08
WFDC9 ENST00000326000 98.90 88.96 96.69 0.10 0.25 0.08 0.11 0.35 0.08
RP11-219B4.5 ENST00000546501 91.23 96.12 96.68 0.15 0.21 0.08 0.21 0.20 0.08
DAZ2 ENST00000382440 94.06 93.78 96.68 0.10 0.27 0.08 0.13 0.26 0.08
PRAMEF18 ENST00000376126 95.07 92.72 96.67 0.10 0.29 0.08 0.12 0.30 0.08
ZNF766 ENST00000439461 97.74 90.02 96.67 0.10 0.25 0.08 0.10 0.37 0.08
QRFP ENST00000343079 89.38 98.07 96.66 0.16 0.20 0.08 0.32 0.16 0.08
DEFB105B ENST00000335510 94.18 93.56 96.66 0.10 0.28 0.08 0.13 0.28 0.08
AE000662.92 ENST00000557595 93.50 94.07 96.65 0.13 0.25 0.08 0.14 0.26 0.08
AC016586.1 ENST00000535853 89.87 97.66 96.65 0.16 0.21 0.08 0.28 0.19 0.08
KRTAP4-3 ENST00000391356 89.57 99.63 96.64 0.16 0.16 0.08 0.30 0.12 0.08
TPRXL ENST00000424053 89.87 97.65 96.64 0.16 0.21 0.08 0.28 0.19 0.08
FOXD4L6 ENST00000377473 93.47 99.58 96.63 0.13 0.16 0.08 0.15 0.12 0.08
KLRC2 ENST00000381902 97.98 89.73 96.63 0.11 0.27 0.08 0.11 0.37 0.08
RP11-480I12.4 ENST00000330493 87.96 98.11 96.62 0.22 0.20 0.08 0.35 0.16 0.08
ZNF671 ENST00000317398 97.08 90.57 96.62 0.10 0.25 0.08 0.11 0.37 0.08

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