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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
ABCA2 ENST00000341511 7.81 3.25 2.94 2.69 3.45 4.00 0.40 0.28 0.23
ABCA13 ENST00000435803 82.68 56.56 72.31 0.30 0.52 0.44 0.57 1.55 0.82
ABCA12 ENST00000272895 29.03 23.27 24.18 1.10 1.43 1.11 1.55 0.93 1.05
ABCA10 ENST00000269081 85.99 53.21 72.29 0.25 0.66 0.43 0.44 1.75 0.81
ABCA1 ENST00000374736 20.35 23.07 19.75 1.52 1.46 1.52 1.03 0.91 0.85
ABAT ENST00000396600 33.99 29.28 29.82 0.92 1.14 0.86 1.75 1.35 1.43
AATK ENST00000326724 75.30 17.27 44.95 0.37 1.61 0.68 0.75 0.75 2.04
AATF ENST00000225402 48.03 55.32 50.75 0.54 0.57 0.66 1.80 1.61 1.84
AASS ENST00000393376 34.46 43.02 36.95 0.97 0.61 0.80 1.80 1.89 1.95
AASDHPPT ENST00000278618 40.63 37.42 37.32 0.86 0.75 0.84 1.75 1.66 2.02
AASDH ENST00000205214 48.80 44.91 45.57 0.52 0.68 0.68 1.83 1.99 1.97
AARSD1 ENST00000427569 53.09 62.14 57.57 0.63 0.53 0.51 1.78 1.35 1.66
AARS2 ENST00000244571 47.63 46.42 45.73 0.54 0.73 0.67 1.80 2.04 1.98
AARS ENST00000261772 28.30 33.56 29.07 1.18 0.85 0.84 1.49 1.53 1.32
AARD ENST00000378279 87.96 61.84 78.14 0.22 0.57 0.39 0.35 1.36 0.55
AAR2 ENST00000373932 33.72 73.37 52.87 0.94 0.54 0.61 1.70 1.03 1.87
AANAT ENST00000250615 81.75 69.58 78.96 0.32 0.52 0.39 0.59 1.10 0.52
AAMP ENST00000248450 17.71 19.56 16.45 1.47 1.43 1.72 0.89 0.74 0.69
AAMDC ENST00000526415 50.98 88.07 72.18 0.62 0.24 0.43 1.85 0.38 0.82
AAK1 ENST00000409085 20.68 2.21 8.79 1.56 3.67 2.49 1.00 0.30 0.38
AAGAB ENST00000261880 72.74 57.42 66.79 0.32 0.54 0.53 0.78 1.49 1.20
AAED1 ENST00000375234 72.05 90.41 84.58 0.34 0.25 0.34 0.80 0.37 0.40
AADAT ENST00000337664 12.32 25.73 16.86 1.68 1.24 1.70 0.61 1.05 0.70
AADACL4 ENST00000376221 97.04 84.82 93.71 0.10 0.27 0.10 0.11 0.42 0.14
AADACL3 ENST00000359318 86.12 85.42 88.91 0.25 0.25 0.19 0.42 0.45 0.28

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