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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
RIMKLA ENST00000431473 29.96 55.85 41.11 1.08 0.51 0.76 1.59 1.58 2.04
LMBRD1 ENST00000370577 30.06 49.73 38.14 1.05 0.66 0.86 1.60 2.03 2.04
CDR2 ENST00000268383 30.81 55.06 41.12 0.96 0.58 0.76 1.63 1.63 2.04
UMPS ENST00000232607 30.96 50.92 39.32 0.97 0.63 0.80 1.66 1.94 2.04
C11orf68 ENST00000438576 32.26 49.48 39.26 0.96 0.66 0.78 1.70 2.03 2.04
S1PR3 ENST00000375846 32.46 59.52 44.53 0.96 0.51 0.62 1.70 1.41 2.04
SFRP4 ENST00000436072 32.58 52.96 40.99 0.96 0.63 0.76 1.70 1.78 2.04
CPXM1 ENST00000380605 32.60 49.21 39.29 0.96 0.66 0.80 1.70 2.04 2.04
TAGLN2 ENST00000368097 32.68 52.14 40.60 0.95 0.62 0.81 1.70 1.85 2.04
WDR62 ENST00000401500 32.97 47.10 38.33 0.94 0.67 0.85 1.71 2.01 2.04
SPC25 ENST00000282074 33.02 48.04 38.83 0.94 0.63 0.82 1.71 2.00 2.04
ACSS2 ENST00000253382 33.07 48.94 39.36 0.92 0.65 0.80 1.71 2.04 2.04
UBOX5 ENST00000217173 33.10 46.65 38.13 0.92 0.75 0.86 1.71 1.98 2.04
PLEKHA8 ENST00000449726 33.28 51.76 40.68 0.91 0.61 0.81 1.71 1.89 2.04
OSGEP ENST00000206542 33.37 59.07 44.86 0.92 0.49 0.68 1.70 1.44 2.04
LIX1 ENST00000274382 33.69 46.69 38.46 0.96 0.73 0.84 1.70 1.97 2.04
GLP2R ENST00000262441 33.87 47.91 39.26 0.92 0.59 0.80 1.73 1.99 2.04
KIAA0930 ENST00000251993 33.92 45.90 38.21 0.92 0.75 0.85 1.75 2.02 2.04
KRT8 ENST00000552150 34.01 58.39 44.82 0.91 0.54 0.66 1.76 1.41 2.04
LINGO3 ENST00000585527 34.05 45.78 38.22 0.92 0.75 0.85 1.75 2.02 2.04
KCTD15 ENST00000430256 34.09 47.78 39.30 0.95 0.59 0.80 1.77 1.99 2.04
CCDC71 ENST00000321895 34.11 47.75 39.31 0.95 0.59 0.80 1.76 1.99 2.04
ME2 ENST00000321341 34.57 57.78 44.80 0.99 0.57 0.66 1.79 1.47 2.04
ARG1 ENST00000356962 34.61 51.11 41.08 0.97 0.66 0.76 1.79 1.92 2.04
IFT122 ENST00000296266 34.65 45.08 38.15 0.97 0.67 0.86 1.78 1.97 2.04

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