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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
ZNF649 ENST00000354957 72.88 41.33 56.95 0.32 0.62 0.49 0.78 1.81 1.72
ZNF648 ENST00000339948 86.29 86.68 89.61 0.25 0.24 0.18 0.42 0.40 0.23
ZNF646 ENST00000300850 42.32 27.96 33.31 0.76 1.19 0.89 1.75 1.19 1.70
ZNF645 ENST00000323684 97.05 98.53 99.21 0.10 0.20 0.11 0.11 0.15 0.04
ZNF644 ENST00000370440 8.19 8.91 5.81 2.56 2.44 3.31 0.43 0.47 0.28
ZNF641 ENST00000544117 20.29 36.89 26.77 1.54 0.76 0.97 1.02 1.70 1.27
ZNF639 ENST00000326361 21.05 46.95 32.22 1.53 0.71 0.91 1.02 1.95 1.60
ZNF638 ENST00000409544 32.34 3.88 15.95 0.99 3.29 1.77 1.71 0.31 0.66
ZNF630 ENST00000409324 83.27 61.38 75.20 0.28 0.54 0.37 0.54 1.40 0.67
ZNF629 ENST00000262525 1.01 3.96 0.86 4.38 3.28 4.52 0.18 0.32 0.20
ZNF628 ENST00000598519 54.49 16.40 33.61 0.63 1.81 0.90 1.72 0.69 1.72
ZNF627 ENST00000361113 94.71 59.57 80.48 0.10 0.52 0.39 0.11 1.41 0.50
ZNF626 ENST00000601440 62.31 50.48 56.12 0.67 0.65 0.49 1.27 1.95 1.77
ZNF625 ENST00000439556 88.91 36.49 63.98 0.19 0.81 0.52 0.32 1.64 1.38
ZNF624 ENST00000311331 29.13 24.17 24.70 1.10 1.33 1.05 1.54 0.98 1.09
ZNF623 ENST00000501748 72.78 63.29 70.34 0.32 0.47 0.43 0.79 1.31 0.90
ZNF622 ENST00000308683 33.86 28.80 29.51 0.92 1.14 0.84 1.73 1.30 1.38
ZNF621 ENST00000339296 69.70 58.76 65.81 0.53 0.54 0.51 0.96 1.43 1.25
ZNF620 ENST00000314529 86.74 60.07 76.50 0.24 0.52 0.38 0.40 1.38 0.61
ZNF619 ENST00000447116 83.44 54.43 71.44 0.30 0.62 0.46 0.51 1.66 0.86
ZNF618 ENST00000288466 12.39 9.31 8.23 1.67 2.48 2.58 0.61 0.48 0.37
ZNF616 ENST00000600228 97.60 90.31 96.75 0.10 0.25 0.08 0.11 0.38 0.08
ZNF615 ENST00000594083 80.63 53.63 69.25 0.32 0.63 0.44 0.58 1.71 0.97
ZNF614 ENST00000270649 76.93 56.14 68.53 0.33 0.52 0.47 0.73 1.55 1.06
ZNF613 ENST00000293471 74.79 37.78 55.98 0.38 0.80 0.49 0.78 1.70 1.76

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