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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
ERVMER34-1 ENST00000443173 94.82 98.58 98.84 0.10 0.20 0.10 0.11 0.15 0.05
SPRR2B ENST00000341611 87.89 98.57 95.92 0.23 0.20 0.07 0.36 0.15 0.10
PRR23B ENST00000329447 96.91 98.57 99.42 0.09 0.20 0.11 0.11 0.15 0.05
FUT6 ENST00000318336 88.50 98.56 96.37 0.20 0.20 0.07 0.34 0.15 0.09
CALML5 ENST00000380332 98.53 98.56 99.76 0.10 0.20 0.12 0.11 0.15 0.04
TAS2R19 ENST00000390673 98.88 98.55 99.83 0.10 0.20 0.12 0.11 0.15 0.04
TAS2R13 ENST00000390677 95.36 98.55 99.02 0.11 0.20 0.11 0.11 0.15 0.04
TAS2R31 ENST00000390675 98.27 98.54 99.87 0.09 0.20 0.12 0.10 0.15 0.04
ZNF83 ENST00000597597 98.36 98.54 99.57 0.10 0.20 0.12 0.10 0.15 0.05
ZNF645 ENST00000323684 97.05 98.53 99.21 0.10 0.20 0.11 0.11 0.15 0.04
MGC10955 ENST00000401851 91.65 98.53 97.06 0.14 0.21 0.08 0.20 0.15 0.07
AC127496.1 ENST00000321930 91.64 98.52 97.92 0.14 0.21 0.09 0.20 0.15 0.04
ZNF835 ENST00000537055 97.03 98.52 99.46 0.10 0.21 0.11 0.11 0.15 0.05
MAGEB5 ENST00000602297 87.89 98.51 95.66 0.23 0.21 0.07 0.36 0.15 0.11
MAGEA12 ENST00000393900 97.43 98.51 99.31 0.10 0.21 0.11 0.11 0.15 0.04
MAGEA3 ENST00000393902 95.97 98.50 98.93 0.11 0.21 0.10 0.11 0.15 0.04
IFNA17 ENST00000413767 96.77 98.50 99.36 0.11 0.21 0.11 0.11 0.15 0.04
C10orf85 ENST00000369071 91.60 98.49 97.24 0.15 0.21 0.08 0.20 0.15 0.06
C8orf49 ENST00000525043 95.12 98.49 98.93 0.10 0.21 0.10 0.12 0.15 0.04
NAT8 ENST00000272425 88.12 98.48 96.14 0.20 0.21 0.07 0.35 0.15 0.10
TAS2R42 ENST00000334266 96.92 98.48 99.13 0.09 0.21 0.11 0.11 0.14 0.04
AC097381.1 ENST00000429019 91.53 98.47 97.60 0.15 0.21 0.09 0.20 0.14 0.06
AC011484.1 ENST00000377652 95.66 98.47 98.73 0.11 0.21 0.10 0.11 0.14 0.05
LINC00346 ENST00000538077 95.50 98.46 99.04 0.11 0.21 0.11 0.11 0.14 0.04
ANP32D ENST00000266594 96.26 98.46 99.24 0.12 0.21 0.11 0.11 0.14 0.04

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