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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
MYOF ENST00000359263 44.62 49.81 45.90 0.65 0.66 0.70 1.79 2.02 1.98
FAM20A ENST00000592554 44.84 45.95 43.76 0.63 0.76 0.61 1.75 2.02 2.02
AGBL2 ENST00000525123 46.20 48.44 46.04 0.54 0.63 0.68 1.80 2.02 1.97
PRDX2 ENST00000301522 46.63 49.55 46.82 0.56 0.66 0.67 1.81 2.02 1.88
DHX32 ENST00000284690 46.82 45.88 44.99 0.56 0.75 0.68 1.81 2.02 2.04
BNIP2 ENST00000267859 47.14 45.98 45.26 0.56 0.76 0.70 1.82 2.02 2.00
MARS2 ENST00000282276 47.31 45.94 45.32 0.56 0.76 0.70 1.82 2.02 2.01
UFL1 ENST00000369278 47.52 46.00 45.47 0.56 0.77 0.70 1.79 2.02 1.98
NUCB1 ENST00000405315 48.23 45.93 45.77 0.56 0.76 0.68 1.79 2.02 1.98
UNC45B ENST00000268876 48.30 49.84 47.92 0.56 0.66 0.66 1.82 2.02 1.89
HSD11B2 ENST00000326152 48.40 48.42 47.15 0.56 0.63 0.67 1.81 2.02 1.89
ASZ1 ENST00000284629 48.47 49.80 47.95 0.53 0.66 0.67 1.82 2.02 1.88
NT5DC1 ENST00000319550 48.82 48.83 47.62 0.52 0.63 0.65 1.82 2.02 1.88
MRPS7 ENST00000245539 49.06 49.96 48.38 0.54 0.66 0.67 1.78 2.02 1.88
HIBADH ENST00000265395 49.18 45.91 46.23 0.57 0.76 0.67 1.80 2.02 1.94
JAM3 ENST00000299106 50.58 45.82 46.94 0.59 0.73 0.70 1.81 2.02 1.87
GTF3C5 ENST00000372108 51.01 48.81 48.80 0.61 0.63 0.70 1.85 2.02 1.86
CCDC138 ENST00000295124 51.28 49.69 49.35 0.59 0.66 0.70 1.85 2.02 1.84
DUSP5 ENST00000369583 53.14 49.83 50.52 0.63 0.66 0.67 1.76 2.02 1.86
FOCAD ENST00000380249 53.48 45.92 48.60 0.62 0.76 0.67 1.77 2.02 1.85
CCKAR ENST00000295589 54.72 48.45 50.62 0.63 0.63 0.66 1.73 2.02 1.85
ABCC3 ENST00000285238 54.89 49.29 51.15 0.63 0.65 0.65 1.71 2.02 1.90
COL24A1 ENST00000370571 55.19 49.56 51.52 0.61 0.66 0.62 1.69 2.02 1.92
VIL1 ENST00000248444 56.19 47.55 50.92 0.58 0.61 0.66 1.62 2.02 1.85
CHML ENST00000366553 56.29 49.97 52.40 0.58 0.66 0.61 1.63 2.02 1.90

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