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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
SRSF3 ENST00000373715 0.19 12.57 3.72 4.52 2.10 3.80 0.16 0.58 0.23
GNAO1 ENST00000262494 0.18 9.71 2.54 4.52 2.45 4.01 0.16 0.50 0.23
ARF1 ENST00000541182 0.18 20.54 7.71 4.52 1.43 2.68 0.16 0.78 0.33
UBE2D2 ENST00000398733 0.17 10.85 2.92 4.53 2.13 4.00 0.16 0.50 0.23
MEIS1 ENST00000272369 0.17 2.93 0.39 4.53 3.49 4.77 0.16 0.29 0.18
YY1 ENST00000262238 0.16 5.49 1.05 4.54 3.04 4.44 0.16 0.33 0.21
ARIH1 ENST00000379887 0.15 2.01 0.19 4.54 3.72 4.88 0.16 0.28 0.18
RBM39 ENST00000253363 0.15 6.05 1.22 4.52 2.81 4.42 0.16 0.35 0.21
UBE2I ENST00000355803 0.14 10.75 2.86 4.53 2.13 4.01 0.16 0.51 0.23
PRPS1 ENST00000372435 0.14 16.63 5.66 4.53 1.72 3.37 0.16 0.71 0.27
PUF60 ENST00000526683 0.13 8.52 2.06 4.54 2.52 4.11 0.16 0.46 0.23
PBX1 ENST00000420696 0.13 9.31 2.40 4.54 2.48 4.04 0.16 0.48 0.23
CALM1 ENST00000356978 0.12 14.06 4.36 4.55 2.07 3.73 0.15 0.59 0.24
ETF1 ENST00000360541 0.12 8.80 2.14 4.55 2.47 4.08 0.15 0.48 0.23
SPOP ENST00000393331 0.11 2.61 0.28 4.55 3.54 4.87 0.15 0.29 0.18
RAC1 ENST00000356142 0.11 24.90 10.07 4.56 1.32 2.26 0.15 1.06 0.42
SRSF1 ENST00000258962 0.10 8.77 2.14 4.56 2.47 4.08 0.15 0.48 0.23
TUBB ENST00000327892 0.10 11.63 3.30 4.57 2.09 3.90 0.15 0.57 0.24
UBE2H ENST00000355621 0.09 15.43 5.01 4.57 1.89 3.68 0.15 0.67 0.25
PHF5A ENST00000216252 0.09 21.84 8.32 4.58 1.47 2.54 0.15 0.81 0.37
PPP1CB ENST00000395366 0.08 2.75 0.30 4.58 3.53 4.84 0.15 0.29 0.18
RBBP4 ENST00000373493 0.08 9.03 2.23 4.59 2.43 4.06 0.15 0.47 0.23
NUDT21 ENST00000300291 0.07 7.52 1.68 4.59 2.52 4.26 0.15 0.40 0.23
RAN ENST00000543796 0.07 10.15 2.62 4.57 2.32 4.00 0.15 0.49 0.23
MAPRE2 ENST00000300249 0.06 18.74 6.76 4.58 1.52 3.00 0.15 0.74 0.32

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