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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
SPRR3 ENST00000331860 98.28 98.33 99.56 0.09 0.21 0.12 0.10 0.14 0.05
DEFB132 ENST00000382376 99.44 96.88 99.57 0.11 0.23 0.12 0.12 0.19 0.05
ZNF83 ENST00000597597 98.36 98.54 99.57 0.10 0.20 0.12 0.10 0.15 0.05
ZNF491 ENST00000323169 96.62 99.65 99.58 0.11 0.17 0.12 0.11 0.12 0.05
LINC00696 ENST00000541313 98.76 97.58 99.58 0.10 0.22 0.12 0.11 0.20 0.05
COLCA1 ENST00000532918 98.49 97.87 99.59 0.10 0.21 0.12 0.11 0.17 0.05
TAS2R43 ENST00000531678 97.08 99.91 99.59 0.10 0.17 0.12 0.11 0.10 0.05
OR7C1 ENST00000248073 98.45 97.99 99.60 0.10 0.20 0.12 0.11 0.17 0.05
C3orf27 ENST00000356020 98.98 97.56 99.60 0.11 0.22 0.12 0.12 0.19 0.05
RPA4 ENST00000373040 97.52 98.86 99.61 0.10 0.16 0.12 0.11 0.14 0.05
PSAPL1 ENST00000319098 97.21 99.28 99.61 0.10 0.15 0.12 0.11 0.12 0.05
PBOV1 ENST00000527246 97.37 99.14 99.62 0.10 0.15 0.12 0.11 0.14 0.05
OR2M2 ENST00000359682 98.95 97.67 99.62 0.10 0.21 0.12 0.11 0.19 0.04
C5orf20 ENST00000503143 96.73 99.93 99.63 0.11 0.17 0.12 0.11 0.10 0.04
ADAM20 ENST00000256389 96.83 99.85 99.63 0.09 0.17 0.12 0.11 0.11 0.04
OR14C36 ENST00000317861 97.88 98.68 99.64 0.11 0.18 0.12 0.11 0.15 0.04
STH ENST00000537309 99.10 97.61 99.64 0.11 0.22 0.12 0.12 0.20 0.04
SCGB1D1 ENST00000306238 99.59 97.17 99.65 0.12 0.24 0.12 0.13 0.19 0.04
OR14I1 ENST00000342623 98.65 98.02 99.65 0.10 0.20 0.12 0.11 0.16 0.04
MAGEA1 ENST00000356661 98.14 98.44 99.66 0.11 0.21 0.12 0.11 0.14 0.04
MAGEB4 ENST00000378982 99.03 97.73 99.66 0.11 0.21 0.12 0.12 0.17 0.04
KRTAP21-2 ENST00000333892 97.83 98.82 99.67 0.11 0.16 0.12 0.11 0.14 0.04
SPZ1 ENST00000296739 99.21 97.62 99.67 0.11 0.22 0.12 0.12 0.20 0.04
OR14A16 ENST00000357627 98.48 99.12 99.68 0.10 0.15 0.12 0.11 0.14 0.04
C3orf56 ENST00000398112 98.74 98.08 99.68 0.10 0.20 0.12 0.11 0.16 0.04

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