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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
LINC00346 ENST00000538077 95.50 98.46 99.04 0.11 0.21 0.11 0.11 0.14 0.04
CTAGE4 ENST00000486333 92.30 98.90 98.23 0.15 0.17 0.09 0.19 0.14 0.05
AC011484.1 ENST00000377652 95.66 98.47 98.73 0.11 0.21 0.10 0.11 0.14 0.05
RP11-347C12.1 ENST00000520915 92.31 98.91 98.24 0.15 0.17 0.09 0.19 0.14 0.05
AC097381.1 ENST00000429019 91.53 98.47 97.60 0.15 0.21 0.09 0.20 0.14 0.06
MBD3L2 ENST00000381393 94.39 98.91 98.80 0.10 0.17 0.10 0.11 0.14 0.05
TAS2R42 ENST00000334266 96.92 98.48 99.13 0.09 0.21 0.11 0.11 0.14 0.04
AL359878.1 ENST00000381466 99.71 98.92 99.96 0.12 0.17 0.13 0.13 0.15 0.04
NAT8 ENST00000272425 88.12 98.48 96.14 0.20 0.21 0.07 0.35 0.15 0.10
H1FNT ENST00000335017 94.88 98.92 98.78 0.10 0.17 0.10 0.11 0.15 0.05
C8orf49 ENST00000525043 95.12 98.49 98.93 0.10 0.21 0.10 0.12 0.15 0.04
SSBP3-AS1 ENST00000361350 92.36 98.93 98.24 0.15 0.17 0.09 0.18 0.15 0.05
C10orf85 ENST00000369071 91.60 98.49 97.24 0.15 0.21 0.08 0.20 0.15 0.06
HIST1H1T ENST00000338379 89.07 98.93 96.33 0.19 0.17 0.07 0.32 0.15 0.09
IFNA17 ENST00000413767 96.77 98.50 99.36 0.11 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
EPB41L4A-AS2 ENST00000600409 92.37 98.94 98.27 0.15 0.17 0.09 0.18 0.15 0.05
MAGEA12 ENST00000393900 97.43 98.51 99.31 0.10 0.21 0.11 0.11 0.15 0.04
MTRNR2L7 ENST00000544824 92.37 98.94 98.28 0.15 0.17 0.09 0.18 0.15 0.05
MAGEB5 ENST00000602297 87.89 98.51 95.66 0.23 0.21 0.07 0.36 0.15 0.11
TAS2R60 ENST00000332690 80.18 98.95 92.34 0.32 0.17 0.14 0.59 0.15 0.15
ZNF835 ENST00000537055 97.03 98.52 99.46 0.10 0.21 0.11 0.11 0.15 0.05
AC026703.1 ENST00000326958 96.88 98.95 99.13 0.09 0.17 0.11 0.11 0.15 0.04
AC127496.1 ENST00000321930 91.64 98.52 97.92 0.14 0.21 0.09 0.20 0.15 0.04
ZNF781 ENST00000358582 94.96 98.96 99.01 0.10 0.17 0.11 0.12 0.15 0.04

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