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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
AC129492.6 ENST00000399413 95.18 97.97 98.70 0.10 0.20 0.10 0.12 0.17 0.05
AC131971.1 ENST00000332881 90.86 98.17 97.42 0.16 0.20 0.08 0.21 0.16 0.07
AC132186.1 ENST00000544589 92.43 98.99 97.49 0.15 0.17 0.08 0.18 0.15 0.07
AC132216.1 ENST00000330381 92.28 87.27 92.74 0.15 0.22 0.14 0.19 0.41 0.15
AC135178.1 ENST00000535173 90.60 98.01 97.24 0.16 0.20 0.08 0.24 0.16 0.07
AC137932.1 ENST00000602042 91.43 94.80 96.07 0.15 0.23 0.07 0.20 0.24 0.11
AC138647.1 ENST00000427937 91.49 95.90 96.69 0.15 0.22 0.08 0.20 0.20 0.08
AC139426.2 ENST00000435655 91.99 98.73 98.02 0.15 0.16 0.09 0.20 0.15 0.05
AC140481.2 ENST00000409982 96.81 85.40 93.86 0.09 0.25 0.09 0.11 0.44 0.12
AC145676.2 ENST00000514988 90.65 98.04 97.28 0.16 0.20 0.08 0.24 0.16 0.07
AC174470.1 ENST00000457257 93.45 58.10 79.17 0.13 0.53 0.38 0.15 1.46 0.54
AC226150.4 ENST00000545350 91.85 98.63 97.51 0.14 0.20 0.08 0.20 0.15 0.07
ACAA1 ENST00000333167 53.85 64.24 59.25 0.63 0.49 0.49 1.75 1.20 1.68
ACAA2 ENST00000285093 68.12 72.32 72.97 0.57 0.51 0.40 1.02 1.03 0.81
ACACA ENST00000353139 2.28 6.58 2.15 4.14 2.63 4.07 0.28 0.37 0.23
ACACB ENST00000338432 52.16 44.43 47.03 0.59 0.62 0.70 1.83 1.97 1.89
ACAD10 ENST00000455480 65.84 60.78 64.66 0.61 0.56 0.51 1.06 1.39 1.32
ACAD11 ENST00000264990 47.95 47.82 46.54 0.54 0.59 0.66 1.80 1.99 1.90
ACAD8 ENST00000281182 37.81 66.43 51.21 0.92 0.56 0.63 1.73 1.20 1.92
ACAD9 ENST00000308982 55.46 46.21 49.78 0.61 0.73 0.65 1.65 2.04 1.87
ACADL ENST00000233710 40.24 63.36 50.90 0.86 0.48 0.66 1.73 1.30 1.85
ACADM ENST00000420607 40.21 63.87 51.14 0.86 0.49 0.65 1.74 1.21 1.90
ACADS ENST00000242592 46.02 54.47 49.16 0.58 0.59 0.73 1.79 1.66 1.84
ACADSB ENST00000358776 55.98 63.89 60.42 0.58 0.48 0.44 1.63 1.22 1.58
ACADVL ENST00000543245 54.07 59.59 56.64 0.63 0.52 0.52 1.73 1.41 1.72

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